Fri Dec 13 16:18:52 UTC 2024 I: starting to build lammps/unstable/amd64 on jenkins on '2024-12-13 16:18' Fri Dec 13 16:18:52 UTC 2024 I: The jenkins build log is/was available at https://jenkins.debian.net/userContent/reproducible/debian/build_service/amd64_36/40557/console.log Fri Dec 13 16:18:52 UTC 2024 I: Downloading source for unstable/lammps=20240207+dfsg-2 --2024-12-13 16:18:52-- http://deb.debian.org/debian/pool/main/l/lammps/lammps_20240207%2bdfsg-2.dsc Connecting to 46.16.76.132:3128... connected. Proxy request sent, awaiting response... 200 OK Length: 3158 (3.1K) [text/prs.lines.tag] Saving to: ‘lammps_20240207+dfsg-2.dsc’ 0K ... 100% 345M=0s 2024-12-13 16:18:52 (345 MB/s) - ‘lammps_20240207+dfsg-2.dsc’ saved [3158/3158] Fri Dec 13 16:18:52 UTC 2024 I: lammps_20240207+dfsg-2.dsc -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA512 Format: 3.0 (quilt) Source: lammps Binary: lammps, liblammps-dev, liblammps0t64, python3-lammps, lammps-doc, lammps-data, lammps-examples Architecture: any all Version: 20240207+dfsg-2 Maintainer: Debian Science Maintainers Uploaders: Anton Gladky Homepage: https://lammps.sandia.gov/ Standards-Version: 4.7.0 Vcs-Browser: https://salsa.debian.org/science-team/lammps Vcs-Git: https://salsa.debian.org/science-team/lammps.git Testsuite: autopkgtest Testsuite-Triggers: python3 Build-Depends: dpkg-dev (>= 1.22.5), cmake, debhelper-compat (= 13), dh-python, pybuild-plugin-pyproject, python3-setuptools, gfortran | fortran-compiler, libavcodec-dev, libeigen3-dev, libfftw3-dev, libhdf5-mpi-dev, libjpeg-dev, libkim-api-dev, libnetcdf-dev, libpnetcdf-dev [amd64 arm64 mips64el ppc64el riscv64 s390x ia64 ppc64 sparc64], libsymspg-dev, libvtk9-dev, libvtk9-qt-dev, mpi-default-bin, mpi-default-dev, ocl-icd-opencl-dev | opencl-dev, python3-all-dev, python3-sphinx, voro++-dev Build-Depends-Indep: libjs-sphinxdoc, libjs-jquery, libjs-mathjax, libjs-underscore, texlive-latex-recommended, texlive-fonts-recommended, texlive-latex-extra, tex-gyre, doxygen, sphinx-rtd-theme-common, latexmk, htmldoc, python3-sphinx-tabs, python3-sphinxcontrib.jquery, python3-sphinxcontrib.spelling, python3-breathe, python3-venv, git Package-List: lammps deb science optional arch=any lammps-data deb doc optional arch=all lammps-doc deb doc optional arch=all lammps-examples deb doc optional arch=all liblammps-dev deb science optional arch=any liblammps0t64 deb science optional arch=any python3-lammps deb python optional arch=any Checksums-Sha1: d976c02ea7e609f7b5df447890393bc39e3dc046 153400656 lammps_20240207+dfsg.orig.tar.xz fd378d56d807d84243c2562ec61c1dd604b83aac 17176 lammps_20240207+dfsg-2.debian.tar.xz Checksums-Sha256: dfc5347ab37e918c73edb6f67f0669683197d8218c74acab4e3a0496d39bedf4 153400656 lammps_20240207+dfsg.orig.tar.xz 0509610d39bab52c4d788bbf2d93822e843efd5173ffe06d05903bc5749771f8 17176 lammps_20240207+dfsg-2.debian.tar.xz Files: e8f446c3282aa89ff9ab7b67fa710586 153400656 lammps_20240207+dfsg.orig.tar.xz 988dac548d7d5895de66a52ac5e21409 17176 lammps_20240207+dfsg-2.debian.tar.xz -----BEGIN PGP SIGNATURE----- iQIzBAEBCgAdFiEEu71F6oGKuG/2fnKF0+Fzg8+n/wYFAmdb0MUACgkQ0+Fzg8+n /wYK7A//XrjIQIKNU+PJgB/T1Xw5U0jYOm6MvvxNSsnzANcID04vibIi1/d9BCq5 jheBgJi+w8iq5dtxcmdZahv6wiWRie4RdJVKraXUeGLQ3hulIpmTfxh8vHIHhhCV pENgT8MrOzE0d5o7tik5iUSoGPwxlT0NqfC7WRPfeLCJo4feRrxtJ9/y8tyzYLhz 1Q6isj9KwQ2h9hCFvannCSGgw8FCZfY+iOQxbgnJLAZpHcL+91wOTrVSUA0Sp1eN Y9qRgX8PwHaecEt298mPMr8+Q6liEuYtNP58Vwgxqcy+CUiZvRVeECgbeePOwfV6 DgzS3Hqx+kMq65gU6dy3KrOcHO6O0SspDzPKuW52aU5WhXdo0kMn/BsXMTvZz3Sb xjEY6UAnfhOscr76gsPj4b4AS9DFkfJWXaHMi6c9DOVSWHZDG5ieYQW1rPN2o2aI BkUPMH4u6Qo8o6ztVJLerOWywFhiPlxQSOxqk7n2hywHYRhWOCjMVRt8kFHs1Y2G R4BOurtG4D9IpBC3KMWC4M9W0GZ/lY2PYhMIpa/Nys3EX0j5FCTNen/k1zV7ZNh3 W5TJA2BqdrqA+R6cMbsV7Z2FTxn/LSGEeLJ/lCEEpGi545CxSIYJiv/0mrqy2uYL tOWPzTpflGwNzVrJbfrW/5kvB+dOc5LIqfvFUCMf47e6OqQSWzA= =PnrS -----END PGP SIGNATURE----- Fri Dec 13 16:18:52 UTC 2024 I: Checking whether the package is not for us Fri Dec 13 16:18:52 UTC 2024 I: Starting 1st build on remote node infom02-amd64.debian.net. Fri Dec 13 16:18:52 UTC 2024 I: Preparing to do remote build '1' on infom02-amd64.debian.net. Fri Dec 13 16:34:52 UTC 2024 I: Deleting $TMPDIR on infom02-amd64.debian.net. I: pbuilder: network access will be disabled during build I: Current time: Thu Jan 15 10:41:56 -12 2026 I: pbuilder-time-stamp: 1768516916 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [lammps_20240207+dfsg-2.dsc] I: copying [./lammps_20240207+dfsg.orig.tar.xz] I: copying [./lammps_20240207+dfsg-2.debian.tar.xz] I: Extracting source gpgv: Signature made Fri Dec 13 06:14:29 2024 gpgv: using RSA key BBBD45EA818AB86FF67E7285D3E17383CFA7FF06 gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./lammps_20240207+dfsg-2.dsc: no acceptable signature found dpkg-source: info: extracting lammps in lammps-20240207+dfsg dpkg-source: info: unpacking lammps_20240207+dfsg.orig.tar.xz dpkg-source: info: unpacking lammps_20240207+dfsg-2.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 20_set_potentials_path.patch dpkg-source: info: applying 30_build_docs.patch dpkg-source: info: applying do-not-install-potentials.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1128056/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='amd64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=12 ' DISTRIBUTION='unstable' HOME='/root' HOST_ARCH='amd64' IFS=' ' INVOCATION_ID='508117b27e204bbf94a64e268de0b149' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1128056' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.UZ1wfsBI/pbuilderrc_SkCn --distribution unstable --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.UZ1wfsBI/b1 --logfile b1/build.log lammps_20240207+dfsg-2.dsc' SUDO_GID='109' SUDO_UID='104' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' I: uname -a Linux infom02-amd64 6.11.5+bpo-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.11.5-1~bpo12+1 (2024-11-11) x86_64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Nov 22 2024 /bin -> usr/bin I: user script /srv/workspace/pbuilder/1128056/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: amd64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: dpkg-dev (>= 1.22.5), cmake, debhelper-compat (= 13), dh-python, pybuild-plugin-pyproject, python3-setuptools, gfortran | fortran-compiler, libavcodec-dev, libeigen3-dev, libfftw3-dev, libhdf5-mpi-dev, libjpeg-dev, libkim-api-dev, libnetcdf-dev, libpnetcdf-dev, libsymspg-dev, libvtk9-dev, libvtk9-qt-dev, mpi-default-bin, mpi-default-dev, ocl-icd-opencl-dev | opencl-dev, python3-all-dev, python3-sphinx, voro++-dev, libjs-sphinxdoc, libjs-jquery, libjs-mathjax, libjs-underscore, texlive-latex-recommended, texlive-fonts-recommended, texlive-latex-extra, tex-gyre, doxygen, sphinx-rtd-theme-common, latexmk, htmldoc, python3-sphinx-tabs, python3-sphinxcontrib.jquery, python3-sphinxcontrib.spelling, python3-breathe, python3-venv, git dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 19965 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on pybuild-plugin-pyproject; however: Package pybuild-plugin-pyproject is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on gfortran | fortran-compiler; however: Package gfortran is not installed. Package fortran-compiler is not installed. pbuilder-satisfydepends-dummy depends on libavcodec-dev; however: Package libavcodec-dev is not installed. pbuilder-satisfydepends-dummy depends on libeigen3-dev; however: Package libeigen3-dev is not installed. pbuilder-satisfydepends-dummy depends on libfftw3-dev; however: Package libfftw3-dev is not installed. pbuilder-satisfydepends-dummy depends on libhdf5-mpi-dev; however: Package libhdf5-mpi-dev is not installed. pbuilder-satisfydepends-dummy depends on libjpeg-dev; however: Package libjpeg-dev is not installed. pbuilder-satisfydepends-dummy depends on libkim-api-dev; however: Package libkim-api-dev is not installed. pbuilder-satisfydepends-dummy depends on libnetcdf-dev; however: Package libnetcdf-dev is not installed. pbuilder-satisfydepends-dummy depends on libpnetcdf-dev; however: Package libpnetcdf-dev is not installed. pbuilder-satisfydepends-dummy depends on libsymspg-dev; however: Package libsymspg-dev is not installed. pbuilder-satisfydepends-dummy depends on libvtk9-dev; however: Package libvtk9-dev is not installed. pbuilder-satisfydepends-dummy depends on libvtk9-qt-dev; however: Package libvtk9-qt-dev is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-bin; however: Package mpi-default-bin is not installed. pbuilder-satisfydepends-dummy depends on mpi-default-dev; however: Package mpi-default-dev is not installed. pbuilder-satisfydepends-dummy depends on ocl-icd-opencl-dev | opencl-dev; however: Package ocl-icd-opencl-dev is not installed. Package opencl-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx; however: Package python3-sphinx is not installed. pbuilder-satisfydepends-dummy depends on voro++-dev; however: Package voro++-dev is not installed. pbuilder-satisfydepends-dummy depends on libjs-sphinxdoc; however: Package libjs-sphinxdoc is not installed. pbuilder-satisfydepends-dummy depends on libjs-jquery; however: Package libjs-jquery is not installed. pbuilder-satisfydepends-dummy depends on libjs-mathjax; however: Package libjs-mathjax is not installed. pbuilder-satisfydepends-dummy depends on libjs-underscore; however: Package libjs-underscore is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-recommended; however: Package texlive-latex-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-fonts-recommended; however: Package texlive-fonts-recommended is not installed. pbuilder-satisfydepends-dummy depends on texlive-latex-extra; however: Package texlive-latex-extra is not installed. pbuilder-satisfydepends-dummy depends on tex-gyre; however: Package tex-gyre is not installed. pbuilder-satisfydepends-dummy depends on doxygen; however: Package doxygen is not installed. pbuilder-satisfydepends-dummy depends on sphinx-rtd-theme-common; however: Package sphinx-rtd-theme-common is not installed. pbuilder-satisfydepends-dummy depends on latexmk; however: Package latexmk is not installed. pbuilder-satisfydepends-dummy depends on htmldoc; however: Package htmldoc is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinx-tabs; however: Package python3-sphinx-tabs is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinxcontrib.jquery; however: Package python3-sphinxcontrib.jquery is not installed. pbuilder-satisfydepends-dummy depends on python3-sphinxcontrib.spelling; however: Package python3-sphinxcontrib.spelling is not installed. pbuilder-satisfydepends-dummy depends on python3-breathe; however: Package python3-breathe is not installed. pbuilder-satisfydepends-dummy depends on python3-venv; however: Package python3-venv is not installed. pbuilder-satisfydepends-dummy depends on git; however: Package git is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: adwaita-icon-theme{a} at-spi2-common{a} autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdextrautils{a} ca-certificates{a} ca-certificates-java{a} cfortran{a} cmake{a} cmake-data{a} comerr-dev{a} dbus{a} dbus-bin{a} dbus-daemon{a} dbus-session-bus-common{a} dbus-system-bus-common{a} dbus-user-session{a} dconf-gsettings-backend{a} dconf-service{a} debhelper{a} default-jdk{a} default-jdk-headless{a} default-jre{a} default-jre-headless{a} default-libmysqlclient-dev{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dictionaries-common{a} dirmngr{a} docutils-common{a} doxygen{a} dwz{a} emacsen-common{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-dejavu-mono{a} fonts-font-awesome{a} fonts-lato{a} fonts-lmodern{a} fonts-mathjax{a} gdal-data{a} gdal-plugins{a} gettext{a} gettext-base{a} gfortran{a} gfortran-14{a} gfortran-14-x86-64-linux-gnu{a} gfortran-x86-64-linux-gnu{a} git{a} git-man{a} gnupg{a} gnupg-l10n{a} gpg{a} gpg-agent{a} gpgconf{a} gpgsm{a} graphviz{a} groff-base{a} gtk-update-icon-cache{a} hdf5-helpers{a} hicolor-icon-theme{a} htmldoc{a} htmldoc-common{a} hunspell-en-us{a} ibverbs-providers{a} icu-devtools{a} intltool-debian{a} iso-codes{a} java-common{a} krb5-multidev{a} latexmk{a} libabsl20230802{a} libaec-dev{a} libaec0{a} libamd-comgr2{a} libamdhip64-5{a} libann0{a} libaom3{a} libapache-pom-java{a} libapparmor1{a} libarchive-zip-perl{a} libarchive13t64{a} libarmadillo-dev{a} libarmadillo14{a} libarpack2-dev{a} libarpack2t64{a} libasound2-data{a} libasound2t64{a} libaspell15{a} libassuan9{a} libatk-bridge2.0-0t64{a} libatk1.0-0t64{a} libatspi2.0-0t64{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libavcodec-dev{a} libavcodec61{a} libavformat-dev{a} libavformat61{a} libavif16{a} libavutil-dev{a} libavutil59{a} libblas-dev{a} libblas3{a} libblosc-dev{a} libblosc1{a} libbluray2{a} libboost-dev{a} libboost1.83-dev{a} libbrotli-dev{a} libbrotli1{a} libbz2-dev{a} libcairo-gobject2{a} libcairo2{a} libcap2-bin{a} libcbor0.10{a} libcdt5{a} libcfitsio-dev{a} libcfitsio10t64{a} libcgraph6{a} libchromaprint1{a} libcjson1{a} libclang-cpp19{a} libclang1-19{a} libcloudproviders0{a} libcodec2-1.2{a} libcolord2{a} libcom-err2{a} libcommons-logging-java{a} libcommons-parent-java{a} libcups2t64{a} libcurl3t64-gnutls{a} libcurl4-openssl-dev{a} libcurl4t64{a} libdatrie1{a} libdav1d7{a} libdbus-1-3{a} libdconf1{a} libde265-0{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdouble-conversion-dev{a} libdouble-conversion3{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-radeon1{a} libdrm2{a} libdvdnav4{a} libdvdread8t64{a} libdw1t64{a} libedit2{a} libegl-dev{a} libegl-mesa0{a} libegl1{a} libeigen3-dev{a} 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libpango-1.0-0{a} libpangocairo-1.0-0{a} libpangoft2-1.0-0{a} libpaper-utils{a} libpaper1{a} libpathplan4{a} libpciaccess0{a} libpcre2-16-0{a} libpcre2-32-0{a} libpcre2-dev{a} libpcre2-posix3{a} libpcsclite1{a} libpdfbox-java{a} libpgm-5.3-0t64{a} libpipeline1{a} libpixman-1-0{a} libpkgconf3{a} libpmix-dev{a} libpmix2t64{a} libpnetcdf-dev{a} libpnetcdf6{a} libpng-dev{a} libpng16-16t64{a} libpoppler-dev{a} libpoppler-private-dev{a} libpoppler140{a} libpotrace0{a} libpq-dev{a} libpq5{a} libproc2-0{a} libproj-dev{a} libproj25{a} libpsl-dev{a} libpsl5t64{a} libpsm-infinipath1{a} libpsm2-2{a} libptexenc1{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.12-dev{a} libpython3.12-minimal{a} libpython3.12-stdlib{a} libpython3.12t64{a} libpython3.13{a} libpython3.13-dev{a} libpython3.13-minimal{a} libpython3.13-stdlib{a} libqhull-dev{a} libqhull-r8.0{a} libqhull8.0{a} libqhullcpp8.0{a} libqt5concurrent5t64{a} libqt5core5t64{a} libqt5dbus5t64{a} libqt5designer5{a} libqt5designercomponents5{a} libqt5gui5t64{a} libqt5help5{a} libqt5network5t64{a} libqt5opengl5-dev{a} libqt5opengl5t64{a} libqt5positioning5{a} libqt5printsupport5t64{a} libqt5qml5{a} libqt5qmlmodels5{a} libqt5qmlworkerscript5{a} libqt5quick5{a} libqt5quickparticles5{a} libqt5quickshapes5{a} libqt5quicktest5{a} libqt5quickwidgets5{a} libqt5sensors5{a} libqt5sql5-sqlite{a} libqt5sql5t64{a} libqt5test5t64{a} libqt5webchannel5{a} libqt5webkit5{a} libqt5webkit5-dev{a} libqt5widgets5t64{a} libqt5xml5t64{a} librabbitmq4{a} libraqm0{a} librav1e0.7{a} librdmacm1t64{a} libreadline8t64{a} librhash1{a} librist4{a} librsvg2-2{a} librtmp-dev{a} librtmp1{a} librttopo-dev{a} librttopo1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsharpyuv-dev{a} libsharpyuv0{a} libshine3{a} libsm-dev{a} libsm6{a} libsnappy1v5{a} libsodium23{a} libsoxr0{a} libspatialite-dev{a} libspatialite8t64{a} libspeex1{a} libsqlite3-dev{a} libsrt1.5-gnutls{a} libssh-4{a} libssh2-1-dev{a} libssh2-1t64{a} libssl-dev{a} libsuperlu-dev{a} libsuperlu7{a} libsvtav1enc2{a} libswresample-dev{a} libswresample5{a} libswscale-dev{a} libswscale8{a} libsymspg-dev{a} libsymspg2{a} libsynctex2{a} libsystemd-shared{a} libsz2{a} libtasn1-6-dev{a} libtbb-dev{a} libtbb12{a} libtbbbind-2-5{a} libtbbmalloc2{a} libtcl8.6{a} libteckit0{a} libtexlua53-5{a} libtext-iconv-perl{a} libthai-data{a} libthai0{a} libtheora-dev{a} libtheora0{a} libtiff-dev{a} libtiff6{a} libtiffxx6{a} libtirpc-common{a} libtirpc-dev{a} libtirpc3t64{a} libtk8.6{a} libtool{a} libtwolame0{a} libuchardet0{a} libucx0{a} libudfread0{a} libunbound8{a} libunwind8{a} liburiparser-dev{a} liburiparser1{a} libutfcpp-dev{a} libuv1t64{a} libva-drm2{a} libva-x11-2{a} libva2{a} libvdpau1{a} libvorbis0a{a} libvorbisenc2{a} libvorbisfile3{a} libvoro++1{a} libvpl2{a} libvpx9{a} libvtk9-dev{a} libvtk9-java{a} libvtk9-qt-dev{a} libvtk9.3{a} libvtk9.3-qt{a} libvulkan-dev{a} libvulkan1{a} libwacom-common{a} libwacom9{a} libwayland-client0{a} libwayland-cursor0{a} libwayland-egl1{a} libwayland-server0{a} libwebp-dev{a} libwebp7{a} libwebpdecoder3{a} libwebpdemux2{a} libwebpmux3{a} libwoff1{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx11-xcb1{a} libx264-164{a} libx265-209{a} libxau-dev{a} libxau6{a} libxaw7{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-icccm4{a} libxcb-image0{a} libxcb-keysyms1{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render-util0{a} libxcb-render0{a} libxcb-shape0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-util1{a} libxcb-xfixes0{a} libxcb-xinerama0{a} libxcb-xinput0{a} libxcb-xkb1{a} libxcb1{a} libxcb1-dev{a} libxcomposite1{a} libxcursor1{a} libxdamage1{a} libxdmcp-dev{a} libxdmcp6{a} libxerces-c-dev{a} libxerces-c3.2t64{a} libxext-dev{a} libxext6{a} libxfixes3{a} libxft-dev{a} libxft2{a} libxi6{a} libxinerama1{a} libxkbcommon-x11-0{a} libxkbcommon0{a} libxml2{a} libxml2-dev{a} libxmu6{a} libxnvctrl0{a} libxpm4{a} libxrandr2{a} libxrender-dev{a} libxrender1{a} libxshmfence1{a} libxslt1.1{a} libxss-dev{a} libxss1{a} libxt-dev{a} libxt6t64{a} libxtst6{a} libxvidcore4{a} libxxf86vm1{a} libyuv0{a} libz3-4{a} libzmq5{a} libzstd-dev{a} libzvbi-common{a} libzvbi0t64{a} libzzip-0-13t64{a} m4{a} man-db{a} mariadb-common{a} media-types{a} mesa-libgallium{a} mpi-default-bin{a} mpi-default-dev{a} mysql-common{a} netbase{a} nettle-dev{a} ocl-icd-libopencl1{a} ocl-icd-opencl-dev{a} opencl-c-headers{a} opencl-clhpp-headers{a} openjdk-21-jdk{a} openjdk-21-jdk-headless{a} openjdk-21-jre{a} openjdk-21-jre-headless{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} openssl{a} pinentry-curses{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} preview-latex-style{a} procps{a} proj-data{a} pybuild-plugin-pyproject{a} python-babel-localedata{a} python3{a} python3-alabaster{a} python3-all{a} python3-all-dev{a} python3-autocommand{a} python3-babel{a} python3-breathe{a} python3-build{a} python3-certifi{a} python3-chardet{a} python3-charset-normalizer{a} python3-defusedxml{a} python3-dev{a} python3-docutils{a} python3-enchant{a} python3-idna{a} python3-imagesize{a} python3-importlib-metadata{a} python3-inflect{a} python3-installer{a} python3-jaraco.context{a} python3-jaraco.functools{a} python3-jaraco.text{a} python3-jinja2{a} python3-markupsafe{a} python3-minimal{a} python3-more-itertools{a} python3-mpi4py{a} python3-packaging{a} python3-pip-whl{a} python3-pkg-resources{a} python3-pygments{a} python3-pyproject-hooks{a} python3-requests{a} python3-roman{a} python3-setuptools{a} python3-setuptools-whl{a} python3-snowballstemmer{a} python3-sphinx{a} python3-sphinx-tabs{a} python3-sphinxcontrib.jquery{a} python3-sphinxcontrib.spelling{a} python3-toml{a} python3-typeguard{a} python3-typing-extensions{a} python3-urllib3{a} python3-venv{a} python3-vtk9{a} python3-wheel{a} python3-zipp{a} python3.12{a} python3.12-dev{a} python3.12-minimal{a} python3.12-venv{a} python3.13{a} python3.13-dev{a} python3.13-minimal{a} qdoc-qt5{a} qhelpgenerator-qt5{a} qt5-assistant{a} qt5-qmake{a} qt5-qmake-bin{a} qt5-qmltooling-plugins{a} qtattributionsscanner-qt5{a} qtbase5-dev{a} qtbase5-dev-tools{a} qtchooser{a} qtdeclarative5-dev{a} qtdeclarative5-dev-tools{a} qttools5-dev{a} qttools5-dev-tools{a} qttools5-private-dev{a} readline-common{a} sensible-utils{a} sgml-base{a} shared-mime-info{a} sphinx-common{a} sphinx-rtd-theme-common{a} systemd{a} systemd-sysv{a} t1utils{a} tcl{a} tcl-dev{a} tcl8.6{a} tcl8.6-dev{a} tex-common{a} tex-gyre{a} texlive-base{a} texlive-binaries{a} texlive-fonts-recommended{a} texlive-latex-base{a} texlive-latex-extra{a} texlive-latex-recommended{a} texlive-pictures{a} tk{a} tk-dev{a} tk8.6{a} tk8.6-dev{a} tzdata{a} ucf{a} unixodbc-common{a} unixodbc-dev{a} uuid-dev{a} voro++-dev{a} vtk9{a} x11-common{a} x11proto-dev{a} xdg-utils{a} xfonts-encodings{a} xfonts-utils{a} xkb-data{a} xml-core{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: alsa-topology-conf alsa-ucm-conf apvlv aspell-am aspell-ar aspell-ar-large aspell-bg aspell-br aspell-ca aspell-cs aspell-cy aspell-da aspell-de aspell-de-1901 aspell-el aspell-en aspell-eo aspell-eo-cx7 aspell-es aspell-et aspell-eu aspell-fa aspell-fo aspell-fr aspell-ga aspell-gl-minimos aspell-he aspell-hr aspell-hsb aspell-hu aspell-hy aspell-is aspell-it aspell-kk aspell-ku aspell-lt aspell-lv aspell-nl aspell-no aspell-pl aspell-pt-br aspell-pt-pt aspell-ro aspell-ru aspell-sk aspell-sl aspell-sv aspell-tl aspell-uk aspell-uz at-spi2-core atril bzip2-doc chrony curl dvisvgm enchant-2 evince fonts-dejavu-extra fonts-liberation fonts-texgyre fonts-texgyre-math geoclue-2.0 ghostscript gnupg-utils gpg-wks-client gstreamer1.0-plugins-base gv i965-va-driver intel-media-va-driver javascript-common krb5-locales less libaacs0 libarchive-cpio-perl libatk-wrapper-java-jni libcfitsio-doc libcoarrays-openmpi-dev libfile-mimeinfo-perl libgdk-pixbuf2.0-bin libglib2.0-data libgtk-3-bin libgts-bin libheif-plugin-aomenc libheif-plugin-x265 libjson-xs-perl libkmod2 libldap-common libmail-sendmail-perl libnet-dbus-perl libnss-systemd libpam-cap libpng-tools libqt5svg5 librsvg2-common libsasl2-modules libspreadsheet-parseexcel-perl libtasn1-doc libvdpau-va-gl1 libx11-protocol-perl linux-sysctl-defaults lmodern lynx mesa-va-drivers mesa-vdpau-drivers mesa-vulkan-drivers mupdf ntpsec okular openntpd poppler-data proj-bin psmisc publicsuffix python3-pil qpdfview qpdfview-ps-plugin qt5-gtk-platformtheme qttranslations5-l10n qtwayland5 ruby systemd-cryptsetup systemd-timesyncd texlive-plain-generic tipa va-driver-all vdpau-driver-all viewpdf.app wget x11-utils x11-xserver-utils xauth xdg-user-dirs xpdf zathura-pdf-poppler zathura-ps 0 packages upgraded, 796 newly installed, 0 to remove and 0 not upgraded. Need to get 775 MB of archives. After unpacking 3180 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian unstable/main amd64 libapparmor1 amd64 3.1.7-1+b3 [42.1 kB] Get: 2 http://deb.debian.org/debian unstable/main amd64 libsystemd-shared amd64 257-2 [2136 kB] Get: 3 http://deb.debian.org/debian unstable/main amd64 systemd amd64 257-2 [3608 kB] Get: 4 http://deb.debian.org/debian unstable/main amd64 systemd-sysv amd64 257-2 [59.6 kB] Get: 5 http://deb.debian.org/debian unstable/main amd64 libdbus-1-3 amd64 1.15.92-1 [177 kB] Get: 6 http://deb.debian.org/debian unstable/main amd64 dbus-bin amd64 1.15.92-1 [78.7 kB] Get: 7 http://deb.debian.org/debian unstable/main amd64 dbus-session-bus-common all 1.15.92-1 [51.0 kB] Get: 8 http://deb.debian.org/debian unstable/main amd64 libexpat1 amd64 2.6.4-1 [106 kB] Get: 9 http://deb.debian.org/debian unstable/main amd64 dbus-daemon amd64 1.15.92-1 [157 kB] Get: 10 http://deb.debian.org/debian unstable/main amd64 dbus-system-bus-common all 1.15.92-1 [52.1 kB] Get: 11 http://deb.debian.org/debian unstable/main amd64 dbus amd64 1.15.92-1 [70.3 kB] Get: 12 http://deb.debian.org/debian unstable/main amd64 fonts-lato all 2.015-1 [2780 kB] Get: 13 http://deb.debian.org/debian unstable/main amd64 libglib2.0-0t64 amd64 2.82.3-2 [1501 kB] Get: 14 http://deb.debian.org/debian unstable/main amd64 libdrm-common all 2.4.123-1 [8084 B] Get: 15 http://deb.debian.org/debian unstable/main amd64 libdrm2 amd64 2.4.123-1 [38.7 kB] Get: 16 http://deb.debian.org/debian unstable/main amd64 libelf1t64 amd64 0.192-4 [189 kB] Get: 17 http://deb.debian.org/debian unstable/main amd64 libdw1t64 amd64 0.192-4 [255 kB] Get: 18 http://deb.debian.org/debian unstable/main amd64 libunwind8 amd64 1.7.2-1 [52.8 kB] Get: 19 http://deb.debian.org/debian unstable/main amd64 libcap2-bin amd64 1:2.66-5+b1 [35.3 kB] Get: 20 http://deb.debian.org/debian unstable/main amd64 libgstreamer1.0-0 amd64 1.24.10-2 [1403 kB] Get: 21 http://deb.debian.org/debian unstable/main amd64 liborc-0.4-0t64 amd64 1:0.4.40-1 [189 kB] Get: 22 http://deb.debian.org/debian unstable/main amd64 iso-codes all 4.17.0-1 [3055 kB] Get: 23 http://deb.debian.org/debian unstable/main amd64 libgstreamer-plugins-base1.0-0 amd64 1.24.10-1 [1003 kB] Get: 24 http://deb.debian.org/debian unstable/main amd64 libhyphen0 amd64 2.8.8-7+b2 [30.7 kB] Get: 25 http://deb.debian.org/debian unstable/main amd64 libicu72 amd64 72.1-5+b1 [9423 kB] Get: 26 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo amd64 1:2.1.5-3+b1 [168 kB] Get: 27 http://deb.debian.org/debian unstable/main amd64 libpng16-16t64 amd64 1.6.44-3 [280 kB] Get: 28 http://deb.debian.org/debian unstable/main amd64 libxml2 amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [699 kB] Get: 29 http://deb.debian.org/debian unstable/main amd64 shared-mime-info amd64 2.4-5+b1 [759 kB] Get: 30 http://deb.debian.org/debian unstable/main amd64 libdouble-conversion3 amd64 3.3.0-1+b2 [41.8 kB] Get: 31 http://deb.debian.org/debian unstable/main amd64 libpcre2-16-0 amd64 10.44-5 [260 kB] Get: 32 http://deb.debian.org/debian unstable/main amd64 libqt5core5t64 amd64 5.15.15+dfsg-2 [1866 kB] Get: 33 http://deb.debian.org/debian unstable/main amd64 libbrotli1 amd64 1.1.0-2+b6 [302 kB] Get: 34 http://deb.debian.org/debian unstable/main amd64 libfreetype6 amd64 2.13.3+dfsg-1 [452 kB] Get: 35 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-mono all 2.37-8 [489 kB] Get: 36 http://deb.debian.org/debian unstable/main amd64 fonts-dejavu-core all 2.37-8 [840 kB] Get: 37 http://deb.debian.org/debian unstable/main amd64 fontconfig-config amd64 2.15.0-1.1+b1 [318 kB] Get: 38 http://deb.debian.org/debian unstable/main amd64 libfontconfig1 amd64 2.15.0-1.1+b1 [391 kB] Get: 39 http://deb.debian.org/debian unstable/main amd64 fontconfig amd64 2.15.0-1.1+b1 [463 kB] Get: 40 http://deb.debian.org/debian unstable/main amd64 libglvnd0 amd64 1.7.0-1+b2 [52.0 kB] Get: 41 http://deb.debian.org/debian unstable/main amd64 libwayland-server0 amd64 1.23.0-1+b1 [34.2 kB] Get: 42 http://deb.debian.org/debian unstable/main amd64 libxau6 amd64 1:1.0.11-1 [20.4 kB] Get: 43 http://deb.debian.org/debian unstable/main amd64 libxdmcp6 amd64 1:1.1.5-1 [27.8 kB] Get: 44 http://deb.debian.org/debian unstable/main amd64 libxcb1 amd64 1.17.0-2+b1 [144 kB] Get: 45 http://deb.debian.org/debian unstable/main amd64 libxcb-randr0 amd64 1.17.0-2+b1 [117 kB] Get: 46 http://deb.debian.org/debian unstable/main amd64 libdrm-amdgpu1 amd64 2.4.123-1 [22.3 kB] Get: 47 http://deb.debian.org/debian unstable/main amd64 libpciaccess0 amd64 0.17-3+b2 [51.9 kB] Get: 48 http://deb.debian.org/debian unstable/main amd64 libdrm-intel1 amd64 2.4.123-1 [63.7 kB] Get: 49 http://deb.debian.org/debian unstable/main amd64 libdrm-radeon1 amd64 2.4.123-1 [22.3 kB] Get: 50 http://deb.debian.org/debian unstable/main amd64 libglapi-mesa amd64 24.2.8-1 [38.0 kB] Get: 51 http://deb.debian.org/debian unstable/main amd64 libedit2 amd64 3.1-20240808-1 [93.9 kB] Get: 52 http://deb.debian.org/debian unstable/main amd64 libz3-4 amd64 4.13.3-1 [8560 kB] Get: 53 http://deb.debian.org/debian unstable/main amd64 libllvm19 amd64 1:19.1.5-1 [26.0 MB] Get: 54 http://deb.debian.org/debian unstable/main amd64 libsensors-config all 1:3.6.0-10 [14.6 kB] Get: 55 http://deb.debian.org/debian unstable/main amd64 libsensors5 amd64 1:3.6.0-10+b1 [35.1 kB] Get: 56 http://deb.debian.org/debian unstable/main amd64 libx11-data all 2:1.8.10-2 [337 kB] Get: 57 http://deb.debian.org/debian unstable/main amd64 libx11-6 amd64 2:1.8.10-2 [813 kB] Get: 58 http://deb.debian.org/debian unstable/main amd64 libx11-xcb1 amd64 2:1.8.10-2 [241 kB] Get: 59 http://deb.debian.org/debian unstable/main amd64 libxcb-dri2-0 amd64 1.17.0-2+b1 [107 kB] Get: 60 http://deb.debian.org/debian unstable/main amd64 libxcb-dri3-0 amd64 1.17.0-2+b1 [107 kB] Get: 61 http://deb.debian.org/debian unstable/main amd64 libxcb-present0 amd64 1.17.0-2+b1 [106 kB] Get: 62 http://deb.debian.org/debian unstable/main amd64 libxcb-sync1 amd64 1.17.0-2+b1 [109 kB] Get: 63 http://deb.debian.org/debian unstable/main amd64 libxcb-xfixes0 amd64 1.17.0-2+b1 [109 kB] Get: 64 http://deb.debian.org/debian unstable/main amd64 libxshmfence1 amd64 1.3-1+b2 [8848 B] Get: 65 http://deb.debian.org/debian unstable/main amd64 mesa-libgallium amd64 24.2.8-1 [9185 kB] Get: 66 http://deb.debian.org/debian unstable/main amd64 libgbm1 amd64 24.2.8-1 [42.8 kB] Get: 67 http://deb.debian.org/debian unstable/main amd64 libwayland-client0 amd64 1.23.0-1+b1 [26.6 kB] Get: 68 http://deb.debian.org/debian unstable/main amd64 libxcb-shm0 amd64 1.17.0-2+b1 [105 kB] Get: 69 http://deb.debian.org/debian unstable/main amd64 libegl-mesa0 amd64 24.2.8-1 [133 kB] Get: 70 http://deb.debian.org/debian unstable/main amd64 libegl1 amd64 1.7.0-1+b2 [34.6 kB] Get: 71 http://deb.debian.org/debian unstable/main amd64 libxcb-glx0 amd64 1.17.0-2+b1 [122 kB] Get: 72 http://deb.debian.org/debian unstable/main amd64 libxext6 amd64 2:1.3.4-1+b2 [50.5 kB] Get: 73 http://deb.debian.org/debian unstable/main amd64 libxfixes3 amd64 1:6.0.0-2+b2 [20.3 kB] Get: 74 http://deb.debian.org/debian unstable/main amd64 libxxf86vm1 amd64 1:1.1.4-1+b3 [19.3 kB] Get: 75 http://deb.debian.org/debian unstable/main amd64 libvulkan1 amd64 1.3.296.0-1 [126 kB] Get: 76 http://deb.debian.org/debian unstable/main amd64 libgl1-mesa-dri amd64 24.2.8-1 [43.9 kB] Get: 77 http://deb.debian.org/debian unstable/main amd64 libglx-mesa0 amd64 24.2.8-1 [154 kB] Get: 78 http://deb.debian.org/debian unstable/main amd64 libglx0 amd64 1.7.0-1+b2 [34.9 kB] Get: 79 http://deb.debian.org/debian unstable/main amd64 libgl1 amd64 1.7.0-1+b2 [89.5 kB] Get: 80 http://deb.debian.org/debian unstable/main amd64 libgraphite2-3 amd64 1.3.14-2+b1 [75.4 kB] Get: 81 http://deb.debian.org/debian unstable/main amd64 libharfbuzz0b amd64 10.1.0-1 [478 kB] Get: 82 http://deb.debian.org/debian unstable/main amd64 x11-common all 1:7.7+23.1 [216 kB] Get: 83 http://deb.debian.org/debian unstable/main amd64 libice6 amd64 2:1.1.1-1 [65.4 kB] Get: 84 http://deb.debian.org/debian unstable/main amd64 libevdev2 amd64 1.13.3+dfsg-1 [32.2 kB] Get: 85 http://deb.debian.org/debian unstable/main amd64 libmtdev1t64 amd64 1.1.6-1.2+b1 [22.5 kB] Get: 86 http://deb.debian.org/debian unstable/main amd64 libgudev-1.0-0 amd64 238-5+b1 [14.8 kB] Get: 87 http://deb.debian.org/debian unstable/main amd64 libwacom-common all 2.13.0-1 [98.0 kB] Get: 88 http://deb.debian.org/debian unstable/main amd64 libwacom9 amd64 2.13.0-1 [24.0 kB] Get: 89 http://deb.debian.org/debian unstable/main amd64 libinput-bin amd64 1.26.2-1 [25.3 kB] Get: 90 http://deb.debian.org/debian unstable/main amd64 libinput10 amd64 1.26.2-1 [131 kB] Get: 91 http://deb.debian.org/debian unstable/main amd64 libmd4c0 amd64 0.5.2-2+b1 [49.0 kB] Get: 92 http://deb.debian.org/debian unstable/main amd64 libqt5dbus5t64 amd64 5.15.15+dfsg-2 [217 kB] Get: 93 http://deb.debian.org/debian unstable/main amd64 libkrb5support0 amd64 1.21.3-3 [32.5 kB] Get: 94 http://deb.debian.org/debian unstable/main amd64 libcom-err2 amd64 1.47.2~rc1-2 [23.8 kB] Get: 95 http://deb.debian.org/debian unstable/main amd64 libk5crypto3 amd64 1.21.3-3 [79.9 kB] Get: 96 http://deb.debian.org/debian unstable/main amd64 libkeyutils1 amd64 1.6.3-4 [9092 B] Get: 97 http://deb.debian.org/debian unstable/main amd64 libkrb5-3 amd64 1.21.3-3 [324 kB] Get: 98 http://deb.debian.org/debian unstable/main amd64 libgssapi-krb5-2 amd64 1.21.3-3 [136 kB] Get: 99 http://deb.debian.org/debian unstable/main amd64 libqt5network5t64 amd64 5.15.15+dfsg-2 [682 kB] Get: 100 http://deb.debian.org/debian unstable/main amd64 libsm6 amd64 2:1.2.4-1 [35.2 kB] Get: 101 http://deb.debian.org/debian unstable/main amd64 libxcb-icccm4 amd64 0.4.2-1 [27.5 kB] Get: 102 http://deb.debian.org/debian unstable/main amd64 libxcb-util1 amd64 0.4.0-1+b2 [22.5 kB] Get: 103 http://deb.debian.org/debian unstable/main amd64 libxcb-image0 amd64 0.4.0-2+b2 [22.2 kB] Get: 104 http://deb.debian.org/debian unstable/main amd64 libxcb-keysyms1 amd64 0.4.0-1+b3 [15.7 kB] Get: 105 http://deb.debian.org/debian unstable/main amd64 libxcb-render0 amd64 1.17.0-2+b1 [115 kB] Get: 106 http://deb.debian.org/debian unstable/main amd64 libxcb-render-util0 amd64 0.3.9-1+b2 [17.4 kB] Get: 107 http://deb.debian.org/debian unstable/main amd64 libxcb-shape0 amd64 1.17.0-2+b1 [106 kB] Get: 108 http://deb.debian.org/debian unstable/main amd64 libxcb-xinerama0 amd64 1.17.0-2+b1 [105 kB] Get: 109 http://deb.debian.org/debian unstable/main amd64 libxcb-xinput0 amd64 1.17.0-2+b1 [130 kB] Get: 110 http://deb.debian.org/debian unstable/main amd64 libxcb-xkb1 amd64 1.17.0-2+b1 [130 kB] Get: 111 http://deb.debian.org/debian unstable/main amd64 xkb-data all 2.42-1 [790 kB] Get: 112 http://deb.debian.org/debian unstable/main amd64 libxkbcommon0 amd64 1.7.0-1 [113 kB] Get: 113 http://deb.debian.org/debian unstable/main amd64 libxkbcommon-x11-0 amd64 1.7.0-1 [16.1 kB] Get: 114 http://deb.debian.org/debian unstable/main amd64 libxrender1 amd64 1:0.9.10-1.1+b2 [27.8 kB] Get: 115 http://deb.debian.org/debian unstable/main amd64 libqt5gui5t64 amd64 5.15.15+dfsg-2 [3498 kB] Get: 116 http://deb.debian.org/debian unstable/main amd64 libqt5positioning5 amd64 5.15.15+dfsg-2 [207 kB] Get: 117 http://deb.debian.org/debian unstable/main amd64 libavahi-common-data amd64 0.8-15 [112 kB] Get: 118 http://deb.debian.org/debian unstable/main amd64 libavahi-common3 amd64 0.8-15 [44.1 kB] Get: 119 http://deb.debian.org/debian unstable/main amd64 libavahi-client3 amd64 0.8-15 [48.1 kB] Get: 120 http://deb.debian.org/debian unstable/main amd64 libcups2t64 amd64 2.4.10-2 [251 kB] Get: 121 http://deb.debian.org/debian unstable/main amd64 libqt5widgets5t64 amd64 5.15.15+dfsg-2 [2400 kB] Get: 122 http://deb.debian.org/debian unstable/main amd64 libqt5printsupport5t64 amd64 5.15.15+dfsg-2 [206 kB] Get: 123 http://deb.debian.org/debian unstable/main amd64 libqt5qml5 amd64 5.15.15+dfsg-3 [1377 kB] Get: 124 http://deb.debian.org/debian unstable/main amd64 libqt5qmlmodels5 amd64 5.15.15+dfsg-3 [193 kB] Get: 125 http://deb.debian.org/debian unstable/main amd64 libqt5quick5 amd64 5.15.15+dfsg-3 [1610 kB] Get: 126 http://deb.debian.org/debian unstable/main amd64 libqt5sensors5 amd64 5.15.15-2 [113 kB] Get: 127 http://deb.debian.org/debian unstable/main amd64 libqt5webchannel5 amd64 5.15.15-2 [58.3 kB] Get: 128 http://deb.debian.org/debian unstable/main amd64 libsharpyuv0 amd64 1.4.0-0.1+b1 [113 kB] Get: 129 http://deb.debian.org/debian unstable/main amd64 libwebp7 amd64 1.4.0-0.1+b1 [313 kB] Get: 130 http://deb.debian.org/debian unstable/main amd64 libwoff1 amd64 1.0.2-2+b2 [44.3 kB] Get: 131 http://deb.debian.org/debian unstable/main amd64 libxslt1.1 amd64 1.1.35-1.1+b1 [233 kB] Get: 132 http://deb.debian.org/debian unstable/main amd64 libqt5webkit5 amd64 5.212.0~alpha4-41 [12.0 MB] Get: 133 http://deb.debian.org/debian unstable/main amd64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 134 http://deb.debian.org/debian unstable/main amd64 x11proto-dev all 2024.1-1 [603 kB] Get: 135 http://deb.debian.org/debian unstable/main amd64 libxau-dev amd64 1:1.0.11-1 [23.6 kB] Get: 136 http://deb.debian.org/debian unstable/main amd64 libxdmcp-dev amd64 1:1.1.5-1 [44.3 kB] Get: 137 http://deb.debian.org/debian unstable/main amd64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 138 http://deb.debian.org/debian unstable/main amd64 libxcb1-dev amd64 1.17.0-2+b1 [181 kB] Get: 139 http://deb.debian.org/debian unstable/main amd64 libx11-dev amd64 2:1.8.10-2 [891 kB] Get: 140 http://deb.debian.org/debian unstable/main amd64 libglx-dev amd64 1.7.0-1+b2 [15.8 kB] Get: 141 http://deb.debian.org/debian unstable/main amd64 libgl-dev amd64 1.7.0-1+b2 [101 kB] Get: 142 http://deb.debian.org/debian unstable/main amd64 libegl-dev amd64 1.7.0-1+b2 [19.5 kB] Get: 143 http://deb.debian.org/debian unstable/main amd64 libopengl0 amd64 1.7.0-1+b2 [30.9 kB] Get: 144 http://deb.debian.org/debian unstable/main amd64 libglu1-mesa amd64 9.0.2-1.1+b2 [185 kB] Get: 145 http://deb.debian.org/debian unstable/main amd64 libopengl-dev amd64 1.7.0-1+b2 [5388 B] Get: 146 http://deb.debian.org/debian unstable/main amd64 libglu1-mesa-dev amd64 9.0.2-1.1+b2 [223 kB] Get: 147 http://deb.debian.org/debian unstable/main amd64 libqt5concurrent5t64 amd64 5.15.15+dfsg-2 [44.6 kB] Get: 148 http://deb.debian.org/debian unstable/main amd64 libqt5sql5t64 amd64 5.15.15+dfsg-2 [125 kB] Get: 149 http://deb.debian.org/debian unstable/main amd64 libqt5test5t64 amd64 5.15.15+dfsg-2 [151 kB] Get: 150 http://deb.debian.org/debian unstable/main amd64 libqt5xml5t64 amd64 5.15.15+dfsg-2 [126 kB] Get: 151 http://deb.debian.org/debian unstable/main amd64 libpython3.12-minimal amd64 3.12.8-2 [816 kB] Get: 152 http://deb.debian.org/debian unstable/main amd64 python3.12-minimal amd64 3.12.8-2 [2163 kB] Get: 153 http://deb.debian.org/debian unstable/main amd64 python3-minimal amd64 3.12.7-1 [26.8 kB] Get: 154 http://deb.debian.org/debian unstable/main amd64 media-types all 10.1.0 [26.9 kB] Get: 155 http://deb.debian.org/debian unstable/main amd64 netbase all 6.4 [12.8 kB] Get: 156 http://deb.debian.org/debian unstable/main amd64 tzdata all 2024b-4 [256 kB] Get: 157 http://deb.debian.org/debian unstable/main amd64 libtirpc-common all 1.3.4+ds-1.3 [10.9 kB] Get: 158 http://deb.debian.org/debian unstable/main amd64 libtirpc3t64 amd64 1.3.4+ds-1.3+b1 [83.1 kB] Get: 159 http://deb.debian.org/debian unstable/main amd64 libnsl2 amd64 1.3.0-3+b3 [40.6 kB] Get: 160 http://deb.debian.org/debian unstable/main amd64 readline-common all 8.2-5 [69.3 kB] Get: 161 http://deb.debian.org/debian unstable/main amd64 libreadline8t64 amd64 8.2-5 [169 kB] Get: 162 http://deb.debian.org/debian unstable/main amd64 libpython3.12-stdlib amd64 3.12.8-2 [1970 kB] Get: 163 http://deb.debian.org/debian unstable/main amd64 python3.12 amd64 3.12.8-2 [677 kB] Get: 164 http://deb.debian.org/debian unstable/main amd64 libpython3-stdlib amd64 3.12.7-1 [9712 B] Get: 165 http://deb.debian.org/debian unstable/main amd64 python3 amd64 3.12.7-1 [27.8 kB] Get: 166 http://deb.debian.org/debian unstable/main amd64 libvulkan-dev amd64 1.3.296.0-1 [1397 kB] Get: 167 http://deb.debian.org/debian unstable/main amd64 libxext-dev amd64 2:1.3.4-1+b2 [104 kB] Get: 168 http://deb.debian.org/debian unstable/main amd64 qt5-qmake-bin amd64 5.15.15+dfsg-2 [1066 kB] Get: 169 http://deb.debian.org/debian unstable/main amd64 qtchooser amd64 66-2 [26.3 kB] Get: 170 http://deb.debian.org/debian unstable/main amd64 qt5-qmake amd64 5.15.15+dfsg-2 [224 kB] Get: 171 http://deb.debian.org/debian unstable/main amd64 qtbase5-dev-tools amd64 5.15.15+dfsg-2 [777 kB] Get: 172 http://deb.debian.org/debian unstable/main amd64 qtbase5-dev amd64 5.15.15+dfsg-2 [1122 kB] Get: 173 http://deb.debian.org/debian unstable/main amd64 libqt5qmlworkerscript5 amd64 5.15.15+dfsg-3 [35.4 kB] Get: 174 http://deb.debian.org/debian unstable/main amd64 libqt5quickparticles5 amd64 5.15.15+dfsg-3 [206 kB] Get: 175 http://deb.debian.org/debian unstable/main amd64 libqt5quickshapes5 amd64 5.15.15+dfsg-3 [97.9 kB] Get: 176 http://deb.debian.org/debian unstable/main amd64 libqt5quicktest5 amd64 5.15.15+dfsg-3 [57.2 kB] Get: 177 http://deb.debian.org/debian unstable/main amd64 libqt5quickwidgets5 amd64 5.15.15+dfsg-3 [40.2 kB] Get: 178 http://deb.debian.org/debian unstable/main amd64 qt5-qmltooling-plugins amd64 5.15.15+dfsg-3 [179 kB] Get: 179 http://deb.debian.org/debian unstable/main amd64 qtdeclarative5-dev-tools amd64 5.15.15+dfsg-3 [630 kB] Get: 180 http://deb.debian.org/debian unstable/main amd64 qtdeclarative5-dev amd64 5.15.15+dfsg-3 [461 kB] Get: 181 http://deb.debian.org/debian unstable/main amd64 libqt5webkit5-dev amd64 5.212.0~alpha4-41 [55.4 kB] Get: 182 http://deb.debian.org/debian unstable/main amd64 libpython3.13-minimal amd64 3.13.1-2 [858 kB] Get: 183 http://deb.debian.org/debian unstable/main amd64 python3.13-minimal amd64 3.13.1-2 [2198 kB] Get: 184 http://deb.debian.org/debian unstable/main amd64 sgml-base all 1.31 [15.4 kB] Get: 185 http://deb.debian.org/debian unstable/main amd64 libproc2-0 amd64 2:4.0.4-6 [64.8 kB] Get: 186 http://deb.debian.org/debian unstable/main amd64 procps amd64 2:4.0.4-6 [879 kB] Get: 187 http://deb.debian.org/debian unstable/main amd64 sensible-utils all 0.0.24 [24.8 kB] Get: 188 http://deb.debian.org/debian unstable/main amd64 openssl amd64 3.3.2-2 [1382 kB] Get: 189 http://deb.debian.org/debian unstable/main amd64 ca-certificates all 20240203 [158 kB] Get: 190 http://deb.debian.org/debian unstable/main amd64 libmagic-mgc amd64 1:5.45-3+b1 [314 kB] Get: 191 http://deb.debian.org/debian unstable/main amd64 libmagic1t64 amd64 1:5.45-3+b1 [108 kB] Get: 192 http://deb.debian.org/debian unstable/main amd64 file amd64 1:5.45-3+b1 [43.3 kB] Get: 193 http://deb.debian.org/debian unstable/main amd64 gettext-base amd64 0.22.5-2 [200 kB] Get: 194 http://deb.debian.org/debian unstable/main amd64 libuchardet0 amd64 0.0.8-1+b2 [68.9 kB] Get: 195 http://deb.debian.org/debian unstable/main amd64 groff-base amd64 1.23.0-6 [1184 kB] Get: 196 http://deb.debian.org/debian unstable/main amd64 libpam-systemd amd64 257-2 [292 kB] Get: 197 http://deb.debian.org/debian unstable/main amd64 bsdextrautils amd64 2.40.2-12 [92.0 kB] Get: 198 http://deb.debian.org/debian unstable/main amd64 libpipeline1 amd64 1.5.8-1 [42.0 kB] Get: 199 http://deb.debian.org/debian unstable/main amd64 man-db amd64 2.13.0-1 [1420 kB] Get: 200 http://deb.debian.org/debian unstable/main amd64 libcbor0.10 amd64 0.10.2-2 [28.3 kB] Get: 201 http://deb.debian.org/debian unstable/main amd64 libfido2-1 amd64 1.15.0-1+b1 [78.7 kB] Get: 202 http://deb.debian.org/debian unstable/main amd64 openssh-client amd64 1:9.9p1-3 [991 kB] Get: 203 http://deb.debian.org/debian unstable/main amd64 ucf all 3.0045 [45.2 kB] Get: 204 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf2.0-common all 2.42.12+dfsg-1 [311 kB] Get: 205 http://deb.debian.org/debian unstable/main amd64 libdeflate0 amd64 1.22-1 [47.3 kB] Get: 206 http://deb.debian.org/debian unstable/main amd64 libjbig0 amd64 2.1-6.1+b2 [32.1 kB] Get: 207 http://deb.debian.org/debian unstable/main amd64 liblerc4 amd64 4.0.0+ds-5 [183 kB] Get: 208 http://deb.debian.org/debian unstable/main amd64 libtiff6 amd64 4.5.1+git230720-5 [324 kB] Get: 209 http://deb.debian.org/debian unstable/main amd64 libgdk-pixbuf-2.0-0 amd64 2.42.12+dfsg-1+b1 [141 kB] Get: 210 http://deb.debian.org/debian unstable/main amd64 gtk-update-icon-cache amd64 4.16.7+ds-1 [50.2 kB] Get: 211 http://deb.debian.org/debian unstable/main amd64 hicolor-icon-theme all 0.18-1 [12.0 kB] Get: 212 http://deb.debian.org/debian unstable/main amd64 adwaita-icon-theme all 47.0-2 [463 kB] Get: 213 http://deb.debian.org/debian unstable/main amd64 at-spi2-common all 2.54.0-1 [170 kB] Get: 214 http://deb.debian.org/debian unstable/main amd64 m4 amd64 1.4.19-4 [287 kB] Get: 215 http://deb.debian.org/debian unstable/main amd64 autoconf all 2.72-3 [493 kB] Get: 216 http://deb.debian.org/debian unstable/main amd64 autotools-dev all 20220109.1 [51.6 kB] Get: 217 http://deb.debian.org/debian unstable/main amd64 automake all 1:1.16.5-1.3 [823 kB] Get: 218 http://deb.debian.org/debian unstable/main amd64 autopoint all 0.22.5-2 [723 kB] Get: 219 http://deb.debian.org/debian unstable/main amd64 ca-certificates-java all 20240118 [11.6 kB] Get: 220 http://deb.debian.org/debian unstable/main amd64 cfortran all 20210827-1 [67.7 kB] Get: 221 http://deb.debian.org/debian unstable/main amd64 cmake-data all 3.31.2-1 [2267 kB] Get: 222 http://deb.debian.org/debian unstable/main amd64 libarchive13t64 amd64 3.7.4-1.1 [349 kB] Get: 223 http://deb.debian.org/debian unstable/main amd64 libsasl2-modules-db amd64 2.1.28+dfsg1-8 [19.6 kB] Get: 224 http://deb.debian.org/debian unstable/main amd64 libsasl2-2 amd64 2.1.28+dfsg1-8 [57.3 kB] Get: 225 http://deb.debian.org/debian unstable/main amd64 libldap-2.5-0 amd64 2.5.18+dfsg-3+b1 [188 kB] Get: 226 http://deb.debian.org/debian unstable/main amd64 libnghttp2-14 amd64 1.64.0-1 [75.5 kB] Get: 227 http://deb.debian.org/debian unstable/main amd64 libpsl5t64 amd64 0.21.2-1.1+b1 [57.2 kB] Get: 228 http://deb.debian.org/debian unstable/main amd64 librtmp1 amd64 2.4+20151223.gitfa8646d.1-2+b5 [58.8 kB] Get: 229 http://deb.debian.org/debian unstable/main amd64 libssh2-1t64 amd64 1.11.1-1 [245 kB] Get: 230 http://deb.debian.org/debian unstable/main amd64 libcurl4t64 amd64 8.11.1-1 [351 kB] Get: 231 http://deb.debian.org/debian unstable/main amd64 libjsoncpp26 amd64 1.9.6-3 [81.7 kB] Get: 232 http://deb.debian.org/debian unstable/main amd64 librhash1 amd64 1.4.5-1 [132 kB] Get: 233 http://deb.debian.org/debian unstable/main amd64 libuv1t64 amd64 1.48.0-7 [148 kB] Get: 234 http://deb.debian.org/debian unstable/main amd64 cmake amd64 3.31.2-1 [11.9 MB] Get: 235 http://deb.debian.org/debian unstable/main amd64 comerr-dev amd64 2.1-1.47.2~rc1-2 [55.4 kB] Get: 236 http://deb.debian.org/debian unstable/main amd64 dbus-user-session amd64 1.15.92-1 [50.9 kB] Get: 237 http://deb.debian.org/debian unstable/main amd64 libdconf1 amd64 0.40.0-4+b3 [41.9 kB] Get: 238 http://deb.debian.org/debian unstable/main amd64 dconf-service amd64 0.40.0-4+b3 [32.6 kB] Get: 239 http://deb.debian.org/debian unstable/main amd64 dconf-gsettings-backend amd64 0.40.0-4+b3 [28.8 kB] Get: 240 http://deb.debian.org/debian unstable/main amd64 libdebhelper-perl all 13.20 [89.7 kB] Get: 241 http://deb.debian.org/debian unstable/main amd64 libtool all 2.4.7-8 [517 kB] Get: 242 http://deb.debian.org/debian unstable/main amd64 dh-autoreconf all 20 [17.1 kB] Get: 243 http://deb.debian.org/debian unstable/main amd64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 244 http://deb.debian.org/debian unstable/main amd64 libfile-stripnondeterminism-perl all 1.14.0-1 [19.5 kB] Get: 245 http://deb.debian.org/debian unstable/main amd64 dh-strip-nondeterminism all 1.14.0-1 [8448 B] Get: 246 http://deb.debian.org/debian unstable/main amd64 dwz amd64 0.15-1+b1 [110 kB] Get: 247 http://deb.debian.org/debian unstable/main amd64 gettext amd64 0.22.5-2 [1601 kB] Get: 248 http://deb.debian.org/debian unstable/main amd64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 249 http://deb.debian.org/debian unstable/main amd64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 250 http://deb.debian.org/debian unstable/main amd64 debhelper all 13.20 [915 kB] Get: 251 http://deb.debian.org/debian unstable/main amd64 java-common all 0.76 [6776 B] Get: 252 http://deb.debian.org/debian unstable/main amd64 liblcms2-2 amd64 2.16-2 [160 kB] Get: 253 http://deb.debian.org/debian unstable/main amd64 libnspr4 amd64 2:4.36-1 [110 kB] Get: 254 http://deb.debian.org/debian unstable/main amd64 libnss3 amd64 2:3.106-1 [1392 kB] Get: 255 http://deb.debian.org/debian unstable/main amd64 libpcsclite1 amd64 2.3.0-3 [55.8 kB] Get: 256 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jre-headless amd64 21.0.5+11-1 [41.8 MB] Get: 257 http://deb.debian.org/debian unstable/main amd64 default-jre-headless amd64 2:1.21-76 [3192 B] Get: 258 http://deb.debian.org/debian unstable/main amd64 libatk1.0-0t64 amd64 2.54.0-1 [51.2 kB] Get: 259 http://deb.debian.org/debian unstable/main amd64 libxi6 amd64 2:1.8.2-1 [78.9 kB] Get: 260 http://deb.debian.org/debian unstable/main amd64 libatspi2.0-0t64 amd64 2.54.0-1 [76.4 kB] Get: 261 http://deb.debian.org/debian unstable/main amd64 libatk-bridge2.0-0t64 amd64 2.54.0-1 [67.6 kB] Get: 262 http://deb.debian.org/debian unstable/main amd64 libpixman-1-0 amd64 0.44.0-3 [248 kB] Get: 263 http://deb.debian.org/debian unstable/main amd64 libcairo2 amd64 1.18.2-2 [535 kB] Get: 264 http://deb.debian.org/debian unstable/main amd64 libcairo-gobject2 amd64 1.18.2-2 [130 kB] Get: 265 http://deb.debian.org/debian unstable/main amd64 libcloudproviders0 amd64 0.3.6-1+b1 [29.2 kB] Get: 266 http://deb.debian.org/debian unstable/main amd64 libcolord2 amd64 1.4.7-1+b2 [140 kB] Get: 267 http://deb.debian.org/debian unstable/main amd64 libepoxy0 amd64 1.5.10-2 [193 kB] Get: 268 http://deb.debian.org/debian unstable/main amd64 libfribidi0 amd64 1.0.16-1 [26.5 kB] Get: 269 http://deb.debian.org/debian unstable/main amd64 libthai-data all 0.1.29-2 [168 kB] Get: 270 http://deb.debian.org/debian unstable/main amd64 libdatrie1 amd64 0.2.13-3+b1 [38.1 kB] Get: 271 http://deb.debian.org/debian unstable/main amd64 libthai0 amd64 0.1.29-2+b1 [49.4 kB] Get: 272 http://deb.debian.org/debian unstable/main amd64 libpango-1.0-0 amd64 1.55.0+ds-3 [225 kB] Get: 273 http://deb.debian.org/debian unstable/main amd64 libpangoft2-1.0-0 amd64 1.55.0+ds-3 [54.6 kB] Get: 274 http://deb.debian.org/debian unstable/main amd64 libpangocairo-1.0-0 amd64 1.55.0+ds-3 [35.4 kB] Get: 275 http://deb.debian.org/debian unstable/main amd64 libwayland-cursor0 amd64 1.23.0-1+b1 [11.7 kB] Get: 276 http://deb.debian.org/debian unstable/main amd64 libwayland-egl1 amd64 1.23.0-1+b1 [5664 B] Get: 277 http://deb.debian.org/debian unstable/main amd64 libxcomposite1 amd64 1:0.4.6-1 [16.3 kB] Get: 278 http://deb.debian.org/debian unstable/main amd64 libxcursor1 amd64 1:1.2.2-1+b1 [37.6 kB] Get: 279 http://deb.debian.org/debian unstable/main amd64 libxdamage1 amd64 1:1.1.6-1+b2 [15.5 kB] Get: 280 http://deb.debian.org/debian unstable/main amd64 libxinerama1 amd64 2:1.1.4-3+b2 [16.0 kB] Get: 281 http://deb.debian.org/debian unstable/main amd64 libxrandr2 amd64 2:1.5.4-1+b1 [36.3 kB] Get: 282 http://deb.debian.org/debian unstable/main amd64 libgtk-3-common all 3.24.43-4 [4657 kB] Get: 283 http://deb.debian.org/debian unstable/main amd64 libgtk-3-0t64 amd64 3.24.43-4 [2754 kB] Get: 284 http://deb.debian.org/debian unstable/main amd64 libasound2-data all 1.2.12-1 [21.0 kB] Get: 285 http://deb.debian.org/debian unstable/main amd64 libasound2t64 amd64 1.2.12-1+b1 [371 kB] Get: 286 http://deb.debian.org/debian unstable/main amd64 libgif7 amd64 5.2.2-1+b1 [44.2 kB] Get: 287 http://deb.debian.org/debian unstable/main amd64 libxtst6 amd64 2:1.2.3-1.1+b2 [25.9 kB] Get: 288 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jre amd64 21.0.5+11-1 [205 kB] Get: 289 http://deb.debian.org/debian unstable/main amd64 default-jre amd64 2:1.21-76 [1068 B] Get: 290 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jdk-headless amd64 21.0.5+11-1 [82.8 MB] Get: 291 http://deb.debian.org/debian unstable/main amd64 default-jdk-headless amd64 2:1.21-76 [1124 B] Get: 292 http://deb.debian.org/debian unstable/main amd64 openjdk-21-jdk amd64 21.0.5+11-1 [3360 kB] Get: 293 http://deb.debian.org/debian unstable/main amd64 default-jdk amd64 2:1.21-76 [1076 B] Get: 294 http://deb.debian.org/debian unstable/main amd64 mysql-common all 5.8+1.1.1 [6784 B] Get: 295 http://deb.debian.org/debian unstable/main amd64 mariadb-common all 1:11.4.3-1 [27.1 kB] Get: 296 http://deb.debian.org/debian unstable/main amd64 libmariadb3 amd64 1:11.4.3-1 [181 kB] Get: 297 http://deb.debian.org/debian unstable/main amd64 libssl-dev amd64 3.3.2-2 [2742 kB] Get: 298 http://deb.debian.org/debian unstable/main amd64 zlib1g-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [920 kB] Get: 299 http://deb.debian.org/debian unstable/main amd64 libmariadb-dev amd64 1:11.4.3-1 [272 kB] Get: 300 http://deb.debian.org/debian unstable/main amd64 libmariadb-dev-compat amd64 1:11.4.3-1 [25.9 kB] Get: 301 http://deb.debian.org/debian unstable/main amd64 default-libmysqlclient-dev amd64 1.1.1 [3252 B] Get: 302 http://deb.debian.org/debian unstable/main amd64 python3-autocommand all 2.2.2-3 [13.6 kB] Get: 303 http://deb.debian.org/debian unstable/main amd64 python3-more-itertools all 10.5.0-1 [63.8 kB] Get: 304 http://deb.debian.org/debian unstable/main amd64 python3-typing-extensions all 4.12.2-2 [73.0 kB] Get: 305 http://deb.debian.org/debian unstable/main amd64 python3-zipp all 3.21.0-1 [10.6 kB] Get: 306 http://deb.debian.org/debian unstable/main amd64 python3-importlib-metadata all 8.5.0-1 [21.0 kB] Get: 307 http://deb.debian.org/debian unstable/main amd64 python3-typeguard all 4.4.1-1 [37.0 kB] Get: 308 http://deb.debian.org/debian unstable/main amd64 python3-inflect all 7.3.1-2 [32.4 kB] Get: 309 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.context all 6.0.0-1 [7984 B] Get: 310 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.functools all 4.1.0-1 [12.0 kB] Get: 311 http://deb.debian.org/debian unstable/main amd64 python3-pkg-resources all 75.2.0-1 [213 kB] Get: 312 http://deb.debian.org/debian unstable/main amd64 python3-jaraco.text all 4.0.0-1 [11.4 kB] Get: 313 http://deb.debian.org/debian unstable/main amd64 python3-setuptools all 75.2.0-1 [731 kB] Get: 314 http://deb.debian.org/debian unstable/main amd64 dh-python all 6.20241024 [109 kB] Get: 315 http://deb.debian.org/debian unstable/main amd64 libtext-iconv-perl amd64 1.7-8+b4 [14.4 kB] Get: 316 http://deb.debian.org/debian unstable/main amd64 emacsen-common all 3.0.5 [12.3 kB] Get: 317 http://deb.debian.org/debian unstable/main amd64 dictionaries-common all 1.30.2 [172 kB] Get: 318 http://deb.debian.org/debian unstable/main amd64 libassuan9 amd64 3.0.1-2 [60.6 kB] Get: 319 http://deb.debian.org/debian unstable/main amd64 gpgconf amd64 2.2.45-2 [120 kB] Get: 320 http://deb.debian.org/debian unstable/main amd64 libksba8 amd64 1.6.7-2+b1 [136 kB] Get: 321 http://deb.debian.org/debian unstable/main amd64 libnpth0t64 amd64 1.8-1 [22.8 kB] Get: 322 http://deb.debian.org/debian unstable/main amd64 dirmngr amd64 2.2.45-2 [368 kB] Get: 323 http://deb.debian.org/debian unstable/main amd64 xml-core all 0.19 [20.1 kB] Get: 324 http://deb.debian.org/debian unstable/main amd64 docutils-common all 0.21.2+dfsg-2 [128 kB] Get: 325 http://deb.debian.org/debian unstable/main amd64 libclang-cpp19 amd64 1:19.1.5-1 [13.2 MB] Get: 326 http://deb.debian.org/debian unstable/main amd64 libclang1-19 amd64 1:19.1.5-1 [7615 kB] Get: 327 http://deb.debian.org/debian unstable/main amd64 libfmt10 amd64 10.1.1+ds1-4 [127 kB] Get: 328 http://deb.debian.org/debian unstable/main amd64 doxygen amd64 1.9.8+ds-2+b3 [5011 kB] Get: 329 http://deb.debian.org/debian unstable/main amd64 fonts-font-awesome all 5.0.10+really4.7.0~dfsg-4.1 [517 kB] Get: 330 http://deb.debian.org/debian unstable/main amd64 fonts-lmodern all 2.005-1 [4540 kB] Get: 331 http://deb.debian.org/debian unstable/main amd64 fonts-mathjax all 2.7.9+dfsg-1 [2210 kB] Get: 332 http://deb.debian.org/debian unstable/main amd64 gdal-data all 3.9.3+dfsg-1 [564 kB] Get: 333 http://deb.debian.org/debian unstable/main amd64 gdal-plugins amd64 3.9.3+dfsg-1+b2 [343 kB] Get: 334 http://deb.debian.org/debian unstable/main amd64 libgfortran5 amd64 14.2.0-8 [836 kB] Get: 335 http://deb.debian.org/debian unstable/main amd64 libgfortran-14-dev amd64 14.2.0-8 [878 kB] Get: 336 http://deb.debian.org/debian unstable/main amd64 gfortran-14-x86-64-linux-gnu amd64 14.2.0-8 [11.7 MB] Get: 337 http://deb.debian.org/debian unstable/main amd64 gfortran-14 amd64 14.2.0-8 [12.2 kB] Get: 338 http://deb.debian.org/debian unstable/main amd64 gfortran-x86-64-linux-gnu amd64 4:14.2.0-1 [1284 B] Get: 339 http://deb.debian.org/debian unstable/main amd64 gfortran amd64 4:14.2.0-1 [1436 B] Get: 340 http://deb.debian.org/debian unstable/main amd64 libnghttp3-9 amd64 1.6.0-2 [64.8 kB] Get: 341 http://deb.debian.org/debian unstable/main amd64 libngtcp2-16 amd64 1.9.1-1 [119 kB] Get: 342 http://deb.debian.org/debian unstable/main amd64 libngtcp2-crypto-gnutls8 amd64 1.9.1-1 [18.5 kB] Get: 343 http://deb.debian.org/debian unstable/main amd64 libcurl3t64-gnutls amd64 8.11.1-1 [360 kB] Get: 344 http://deb.debian.org/debian unstable/main amd64 liberror-perl all 0.17029-2 [29.0 kB] Get: 345 http://deb.debian.org/debian unstable/main amd64 git-man all 1:2.45.2-1.2 [2159 kB] Get: 346 http://deb.debian.org/debian unstable/main amd64 git amd64 1:2.45.2-1.2 [8662 kB] Get: 347 http://deb.debian.org/debian unstable/main amd64 gnupg-l10n all 2.2.45-2 [705 kB] Get: 348 http://deb.debian.org/debian unstable/main amd64 gpg amd64 2.2.45-2 [531 kB] Get: 349 http://deb.debian.org/debian unstable/main amd64 pinentry-curses amd64 1.2.1-4+b1 [79.7 kB] Get: 350 http://deb.debian.org/debian unstable/main amd64 gpg-agent amd64 2.2.45-2 [251 kB] Get: 351 http://deb.debian.org/debian unstable/main amd64 gpgsm amd64 2.2.45-2 [255 kB] Get: 352 http://deb.debian.org/debian unstable/main amd64 gnupg all 2.2.45-2 [376 kB] Get: 353 http://deb.debian.org/debian unstable/main amd64 libann0 amd64 1.1.2+doc-9+b1 [25.1 kB] Get: 354 http://deb.debian.org/debian unstable/main amd64 libcdt5 amd64 2.42.4-2+b1 [40.5 kB] Get: 355 http://deb.debian.org/debian unstable/main amd64 libcgraph6 amd64 2.42.4-2+b1 [64.2 kB] Get: 356 http://deb.debian.org/debian unstable/main amd64 libaom3 amd64 3.11.0-1 [1879 kB] Get: 357 http://deb.debian.org/debian unstable/main amd64 libdav1d7 amd64 1.5.0-1+b1 [550 kB] Get: 358 http://deb.debian.org/debian unstable/main amd64 libabsl20230802 amd64 20230802.1-4 [464 kB] Get: 359 http://deb.debian.org/debian unstable/main amd64 libgav1-1 amd64 0.19.0-2+b2 [350 kB] Get: 360 http://deb.debian.org/debian unstable/main amd64 librav1e0.7 amd64 0.7.1-7+b2 [936 kB] Get: 361 http://deb.debian.org/debian unstable/main amd64 libsvtav1enc2 amd64 2.2.1+dfsg-2 [2173 kB] Get: 362 http://deb.debian.org/debian unstable/main amd64 libyuv0 amd64 0.0.1898.20241125-1 [172 kB] Get: 363 http://deb.debian.org/debian unstable/main amd64 libavif16 amd64 1.1.1-1 [117 kB] Get: 364 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-dav1d amd64 1.19.3-1 [11.2 kB] Get: 365 http://deb.debian.org/debian unstable/main amd64 libde265-0 amd64 1.0.15-1+b2 [189 kB] Get: 366 http://deb.debian.org/debian unstable/main amd64 libheif-plugin-libde265 amd64 1.19.3-1 [15.0 kB] Get: 367 http://deb.debian.org/debian unstable/main amd64 libheif1 amd64 1.19.3-1 [489 kB] Get: 368 http://deb.debian.org/debian unstable/main amd64 libimagequant0 amd64 2.18.0-1+b2 [35.2 kB] Get: 369 http://deb.debian.org/debian unstable/main amd64 libraqm0 amd64 0.10.2-1 [13.9 kB] Get: 370 http://deb.debian.org/debian unstable/main amd64 libxpm4 amd64 1:3.5.17-1+b2 [56.3 kB] Get: 371 http://deb.debian.org/debian unstable/main amd64 libgd3 amd64 2.3.3-12+b1 [126 kB] Get: 372 http://deb.debian.org/debian unstable/main amd64 libgts-0.7-5t64 amd64 0.7.6+darcs121130-5.2+b1 [160 kB] Get: 373 http://deb.debian.org/debian unstable/main amd64 libltdl7 amd64 2.4.7-8 [393 kB] Get: 374 http://deb.debian.org/debian unstable/main amd64 libpathplan4 amd64 2.42.4-2+b1 [42.8 kB] Get: 375 http://deb.debian.org/debian unstable/main amd64 libgvc6 amd64 2.42.4-2+b1 [685 kB] Get: 376 http://deb.debian.org/debian unstable/main amd64 libgvpr2 amd64 2.42.4-2+b1 [193 kB] Get: 377 http://deb.debian.org/debian unstable/main amd64 liblab-gamut1 amd64 2.42.4-2+b1 [198 kB] Get: 378 http://deb.debian.org/debian unstable/main amd64 libxt6t64 amd64 1:1.2.1-1.2+b1 [188 kB] Get: 379 http://deb.debian.org/debian unstable/main amd64 libxmu6 amd64 2:1.1.3-3+b3 [58.8 kB] Get: 380 http://deb.debian.org/debian unstable/main amd64 libxaw7 amd64 2:1.0.16-1 [212 kB] Get: 381 http://deb.debian.org/debian unstable/main amd64 graphviz amd64 2.42.4-2+b1 [616 kB] Get: 382 http://deb.debian.org/debian unstable/main amd64 hdf5-helpers amd64 1.14.5+repack-1 [26.3 kB] Get: 383 http://deb.debian.org/debian unstable/main amd64 htmldoc-common all 1.9.20-1 [1994 kB] Get: 384 http://deb.debian.org/debian unstable/main amd64 libxft2 amd64 2.3.6-1+b2 [54.5 kB] Get: 385 http://deb.debian.org/debian unstable/main amd64 libfltk1.3t64 amd64 1.3.8-6.1+b1 [556 kB] Get: 386 http://deb.debian.org/debian unstable/main amd64 libfltk-images1.3t64 amd64 1.3.8-6.1+b1 [50.2 kB] Get: 387 http://deb.debian.org/debian unstable/main amd64 htmldoc amd64 1.9.20-1 [160 kB] Get: 388 http://deb.debian.org/debian unstable/main amd64 hunspell-en-us all 1:2020.12.07-3 [559 kB] Get: 389 http://deb.debian.org/debian unstable/main amd64 libnl-3-200 amd64 3.7.0-0.3+b1 [59.4 kB] Get: 390 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-200 amd64 3.7.0-0.3+b1 [182 kB] Get: 391 http://deb.debian.org/debian unstable/main amd64 libibverbs1 amd64 52.0-2+b1 [62.2 kB] Get: 392 http://deb.debian.org/debian unstable/main amd64 ibverbs-providers amd64 52.0-2+b1 [343 kB] Get: 393 http://deb.debian.org/debian unstable/main amd64 icu-devtools amd64 72.1-5+b1 [210 kB] Get: 394 http://deb.debian.org/debian unstable/main amd64 libgssrpc4t64 amd64 1.21.3-3 [59.5 kB] Get: 395 http://deb.debian.org/debian unstable/main amd64 libkadm5clnt-mit12 amd64 1.21.3-3 [41.7 kB] Get: 396 http://deb.debian.org/debian unstable/main amd64 libkdb5-10t64 amd64 1.21.3-3 [42.0 kB] Get: 397 http://deb.debian.org/debian unstable/main amd64 libkadm5srv-mit12 amd64 1.21.3-3 [53.5 kB] Get: 398 http://deb.debian.org/debian unstable/main amd64 krb5-multidev amd64 1.21.3-3 [126 kB] Get: 399 http://deb.debian.org/debian unstable/main amd64 tex-common all 6.18 [32.5 kB] Get: 400 http://deb.debian.org/debian unstable/main amd64 libpaper1 amd64 1.1.29+b2 [12.8 kB] Get: 401 http://deb.debian.org/debian unstable/main amd64 libpaper-utils amd64 1.1.29+b2 [9236 B] Get: 402 http://deb.debian.org/debian unstable/main amd64 libkpathsea6 amd64 2024.20240313.70630+ds-5 [157 kB] Get: 403 http://deb.debian.org/debian unstable/main amd64 libptexenc1 amd64 2024.20240313.70630+ds-5 [49.1 kB] Get: 404 http://deb.debian.org/debian unstable/main amd64 libsynctex2 amd64 2024.20240313.70630+ds-5 [62.7 kB] Get: 405 http://deb.debian.org/debian unstable/main amd64 libtexlua53-5 amd64 2024.20240313.70630+ds-5 [114 kB] Get: 406 http://deb.debian.org/debian unstable/main amd64 t1utils amd64 1.41-4 [62.1 kB] Get: 407 http://deb.debian.org/debian unstable/main amd64 libmpfi0 amd64 1.5.4+ds-4 [35.5 kB] Get: 408 http://deb.debian.org/debian unstable/main amd64 libpotrace0 amd64 1.16-2+b2 [25.6 kB] Get: 409 http://deb.debian.org/debian unstable/main amd64 libteckit0 amd64 2.5.12+ds1-1+b1 [341 kB] Get: 410 http://deb.debian.org/debian unstable/main amd64 libzzip-0-13t64 amd64 0.13.72+dfsg.1-1.3 [56.2 kB] Get: 411 http://deb.debian.org/debian unstable/main amd64 texlive-binaries amd64 2024.20240313.70630+ds-5 [8492 kB] Get: 412 http://deb.debian.org/debian unstable/main amd64 xdg-utils all 1.2.1-2 [75.8 kB] Get: 413 http://deb.debian.org/debian unstable/main amd64 texlive-base all 2024.20241115-1 [22.7 MB] Get: 414 http://deb.debian.org/debian unstable/main amd64 texlive-latex-base all 2024.20241115-1 [1278 kB] Get: 415 http://deb.debian.org/debian unstable/main amd64 latexmk all 1:4.85-1 [501 kB] Get: 416 http://deb.debian.org/debian unstable/main amd64 libaec0 amd64 1.1.3-1+b1 [23.8 kB] Get: 417 http://deb.debian.org/debian unstable/main amd64 libsz2 amd64 1.1.3-1+b1 [8080 B] Get: 418 http://deb.debian.org/debian unstable/main amd64 libaec-dev amd64 1.1.3-1+b1 [21.5 kB] Get: 419 http://deb.debian.org/debian unstable/main amd64 libllvm17t64 amd64 1:17.0.6-18 [23.6 MB] Get: 420 http://deb.debian.org/debian unstable/main amd64 libamd-comgr2 amd64 6.0+git20231212.4510c28+dfsg-3+b2 [13.0 MB] Get: 421 http://deb.debian.org/debian unstable/main amd64 libnuma1 amd64 2.0.18-1+b1 [22.3 kB] Get: 422 http://deb.debian.org/debian unstable/main amd64 libhsakmt1 amd64 6.1.2+ds-1 [59.8 kB] Get: 423 http://deb.debian.org/debian unstable/main amd64 libhsa-runtime64-1 amd64 6.1.2-2 [535 kB] Get: 424 http://deb.debian.org/debian unstable/main amd64 libamdhip64-5 amd64 5.7.1-5 [8877 kB] Get: 425 http://deb.debian.org/debian unstable/main amd64 libapache-pom-java all 33-2 [5852 B] Get: 426 http://deb.debian.org/debian unstable/main amd64 libblas3 amd64 3.12.0-4 [152 kB] Get: 427 http://deb.debian.org/debian unstable/main amd64 liblapack3 amd64 3.12.0-4 [2450 kB] Get: 428 http://deb.debian.org/debian unstable/main amd64 libarpack2t64 amd64 3.9.1-4 [104 kB] Get: 429 http://deb.debian.org/debian unstable/main amd64 libarmadillo14 amd64 1:14.2.1+dfsg-1+b1 [102 kB] Get: 430 http://deb.debian.org/debian unstable/main amd64 libblas-dev amd64 3.12.0-4 [161 kB] Get: 431 http://deb.debian.org/debian unstable/main amd64 liblapack-dev amd64 3.12.0-4 [4991 kB] Get: 432 http://deb.debian.org/debian unstable/main amd64 libarpack2-dev amd64 3.9.1-4 [120 kB] Get: 433 http://deb.debian.org/debian unstable/main amd64 libhdf5-310 amd64 1.14.5+repack-1 [1340 kB] Get: 434 http://deb.debian.org/debian unstable/main amd64 libhdf5-fortran-310 amd64 1.14.5+repack-1 [112 kB] Get: 435 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-310 amd64 1.14.5+repack-1 [69.0 kB] Get: 436 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-fortran-310 amd64 1.14.5+repack-1 [43.6 kB] Get: 437 http://deb.debian.org/debian unstable/main amd64 libhdf5-cpp-310 amd64 1.14.5+repack-1 [133 kB] Get: 438 http://deb.debian.org/debian unstable/main amd64 libhdf5-hl-cpp-310 amd64 1.14.5+repack-1 [24.1 kB] Get: 439 http://deb.debian.org/debian unstable/main amd64 libjpeg62-turbo-dev amd64 1:2.1.5-3+b1 [292 kB] Get: 440 http://deb.debian.org/debian unstable/main amd64 libjpeg-dev amd64 1:2.1.5-3+b1 [72.2 kB] Get: 441 http://deb.debian.org/debian unstable/main amd64 libbrotli-dev amd64 1.1.0-2+b6 [316 kB] Get: 442 http://deb.debian.org/debian unstable/main amd64 libidn2-dev amd64 2.3.7-2+b1 [123 kB] Get: 443 http://deb.debian.org/debian unstable/main amd64 libkrb5-dev amd64 1.21.3-3 [15.7 kB] Get: 444 http://deb.debian.org/debian unstable/main amd64 libldap-dev amd64 2.5.18+dfsg-3+b1 [303 kB] Get: 445 http://deb.debian.org/debian unstable/main amd64 libpkgconf3 amd64 1.8.1-4 [36.4 kB] Get: 446 http://deb.debian.org/debian unstable/main amd64 pkgconf-bin amd64 1.8.1-4 [30.2 kB] Get: 447 http://deb.debian.org/debian unstable/main amd64 pkgconf amd64 1.8.1-4 [26.2 kB] Get: 448 http://deb.debian.org/debian unstable/main amd64 libnghttp2-dev amd64 1.64.0-1 [115 kB] Get: 449 http://deb.debian.org/debian unstable/main amd64 libpsl-dev amd64 0.21.2-1.1+b1 [77.6 kB] Get: 450 http://deb.debian.org/debian unstable/main amd64 libgmpxx4ldbl amd64 2:6.3.0+dfsg-3 [329 kB] Get: 451 http://deb.debian.org/debian unstable/main amd64 libgmp-dev amd64 2:6.3.0+dfsg-3 [642 kB] Get: 452 http://deb.debian.org/debian unstable/main amd64 libevent-2.1-7t64 amd64 2.1.12-stable-10+b1 [182 kB] Get: 453 http://deb.debian.org/debian unstable/main amd64 libunbound8 amd64 1.22.0-1 [598 kB] Get: 454 http://deb.debian.org/debian unstable/main amd64 libgnutls-dane0t64 amd64 3.8.8-2 [449 kB] Get: 455 http://deb.debian.org/debian unstable/main amd64 libgnutls-openssl27t64 amd64 3.8.8-2 [449 kB] Get: 456 http://deb.debian.org/debian unstable/main amd64 libp11-kit-dev amd64 0.25.5-2+b1 [208 kB] Get: 457 http://deb.debian.org/debian unstable/main amd64 libtasn1-6-dev amd64 4.19.0-3+b3 [98.9 kB] Get: 458 http://deb.debian.org/debian unstable/main amd64 nettle-dev amd64 3.10-1+b1 [1317 kB] Get: 459 http://deb.debian.org/debian unstable/main amd64 libgnutls28-dev amd64 3.8.8-2 [1391 kB] Get: 460 http://deb.debian.org/debian unstable/main amd64 librtmp-dev amd64 2.4+20151223.gitfa8646d.1-2+b5 [68.0 kB] Get: 461 http://deb.debian.org/debian unstable/main amd64 libssh2-1-dev amd64 1.11.1-1 [393 kB] Get: 462 http://deb.debian.org/debian unstable/main amd64 libzstd-dev amd64 1.5.6+dfsg-1+b1 [365 kB] Get: 463 http://deb.debian.org/debian unstable/main amd64 libcurl4-openssl-dev amd64 8.11.1-1 [464 kB] Get: 464 http://deb.debian.org/debian unstable/main amd64 libhdf5-dev amd64 1.14.5+repack-1 [3165 kB] Get: 465 http://deb.debian.org/debian unstable/main amd64 libsuperlu7 amd64 7.0.0+dfsg1-2 [174 kB] Get: 466 http://deb.debian.org/debian unstable/main amd64 libsuperlu-dev amd64 7.0.0+dfsg1-2 [21.9 kB] Get: 467 http://deb.debian.org/debian unstable/main amd64 libarmadillo-dev amd64 1:14.2.1+dfsg-1+b1 [414 kB] Get: 468 http://deb.debian.org/debian unstable/main amd64 libaspell15 amd64 0.60.8.1-2 [337 kB] Get: 469 http://deb.debian.org/debian unstable/main amd64 libva2 amd64 2.22.0-1+b1 [79.1 kB] Get: 470 http://deb.debian.org/debian unstable/main amd64 libva-drm2 amd64 2.22.0-1+b1 [18.6 kB] Get: 471 http://deb.debian.org/debian unstable/main amd64 libva-x11-2 amd64 2.22.0-1+b1 [23.4 kB] Get: 472 http://deb.debian.org/debian unstable/main amd64 libvdpau1 amd64 1.5-3+b1 [27.2 kB] Get: 473 http://deb.debian.org/debian unstable/main amd64 libvpl2 amd64 1:2.13.0-1 [128 kB] Get: 474 http://deb.debian.org/debian unstable/main amd64 ocl-icd-libopencl1 amd64 2.3.2-1+b2 [40.2 kB] Get: 475 http://deb.debian.org/debian unstable/main amd64 libavutil59 amd64 7:7.1-3 [409 kB] Get: 476 http://deb.debian.org/debian unstable/main amd64 libcodec2-1.2 amd64 1.2.0-2+b2 [8179 kB] Get: 477 http://deb.debian.org/debian unstable/main amd64 libgsm1 amd64 1.0.22-1+b2 [29.3 kB] Get: 478 http://deb.debian.org/debian unstable/main amd64 libhwy1t64 amd64 1.2.0-2+b1 [676 kB] Get: 479 http://deb.debian.org/debian unstable/main amd64 libimath-3-1-29t64 amd64 3.1.12-1+b1 [42.0 kB] Get: 480 http://deb.debian.org/debian unstable/main amd64 libopenexr-3-1-30 amd64 3.1.5-5.1+b3 [934 kB] Get: 481 http://deb.debian.org/debian unstable/main amd64 libjxl0.9 amd64 0.9.2-10+b1 [1052 kB] Get: 482 http://deb.debian.org/debian unstable/main amd64 libmp3lame0 amd64 3.100-6+b3 [363 kB] Get: 483 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7 amd64 2.5.0-2+b4 [199 kB] Get: 484 http://deb.debian.org/debian unstable/main amd64 libopus0 amd64 1.5.2-2 [2852 kB] Get: 485 http://deb.debian.org/debian unstable/main amd64 librsvg2-2 amd64 2.59.2+dfsg-1 [1854 kB] Get: 486 http://deb.debian.org/debian unstable/main amd64 libshine3 amd64 3.1.1-2+b2 [23.1 kB] Get: 487 http://deb.debian.org/debian unstable/main amd64 libsnappy1v5 amd64 1.2.1-1+b1 [29.6 kB] Get: 488 http://deb.debian.org/debian unstable/main amd64 libspeex1 amd64 1.2.1-3 [56.8 kB] Get: 489 http://deb.debian.org/debian unstable/main amd64 libsoxr0 amd64 0.1.3-4+b2 [81.0 kB] Get: 490 http://deb.debian.org/debian unstable/main amd64 libswresample5 amd64 7:7.1-3 [92.7 kB] Get: 491 http://deb.debian.org/debian unstable/main amd64 libogg0 amd64 1.3.5-3+b2 [23.8 kB] Get: 492 http://deb.debian.org/debian unstable/main amd64 libtheora0 amd64 1.1.1+dfsg.1-17 [155 kB] Get: 493 http://deb.debian.org/debian unstable/main amd64 libtwolame0 amd64 0.4.0-2+b2 [51.3 kB] Get: 494 http://deb.debian.org/debian unstable/main amd64 libvorbis0a amd64 1.3.7-2+b1 [91.1 kB] Get: 495 http://deb.debian.org/debian unstable/main amd64 libvorbisenc2 amd64 1.3.7-2+b1 [76.1 kB] Get: 496 http://deb.debian.org/debian unstable/main amd64 libvpx9 amd64 1.14.1-1+b1 [1105 kB] Get: 497 http://deb.debian.org/debian unstable/main amd64 libwebpmux3 amd64 1.4.0-0.1+b1 [123 kB] Get: 498 http://deb.debian.org/debian unstable/main amd64 libx264-164 amd64 2:0.164.3108+git31e19f9-2 [558 kB] Get: 499 http://deb.debian.org/debian unstable/main amd64 libx265-209 amd64 3.6-3+b1 [1191 kB] Get: 500 http://deb.debian.org/debian unstable/main amd64 libxvidcore4 amd64 2:1.3.7-1+b2 [252 kB] Get: 501 http://deb.debian.org/debian unstable/main amd64 libzvbi-common all 0.2.43-2 [71.2 kB] Get: 502 http://deb.debian.org/debian unstable/main amd64 libzvbi0t64 amd64 0.2.43-2 [278 kB] Get: 503 http://deb.debian.org/debian unstable/main amd64 libavcodec61 amd64 7:7.1-3 [5811 kB] Get: 504 http://deb.debian.org/debian unstable/main amd64 libavutil-dev amd64 7:7.1-3 [564 kB] Get: 505 http://deb.debian.org/debian unstable/main amd64 libswresample-dev amd64 7:7.1-3 [107 kB] Get: 506 http://deb.debian.org/debian unstable/main amd64 libavcodec-dev amd64 7:7.1-3 [6428 kB] Get: 507 http://deb.debian.org/debian unstable/main amd64 libudfread0 amd64 1.1.2-1+b2 [17.7 kB] Get: 508 http://deb.debian.org/debian unstable/main amd64 libbluray2 amd64 1:1.3.4-1+b2 [138 kB] Get: 509 http://deb.debian.org/debian unstable/main amd64 libchromaprint1 amd64 1.5.1-6 [42.8 kB] Get: 510 http://deb.debian.org/debian unstable/main amd64 libdvdread8t64 amd64 6.1.3-2 [86.2 kB] Get: 511 http://deb.debian.org/debian unstable/main amd64 libdvdnav4 amd64 6.1.1-3+b1 [44.5 kB] Get: 512 http://deb.debian.org/debian unstable/main amd64 libgme0 amd64 0.6.3-7+b2 [131 kB] Get: 513 http://deb.debian.org/debian unstable/main amd64 libmpg123-0t64 amd64 1.32.9-1 [149 kB] Get: 514 http://deb.debian.org/debian unstable/main amd64 libvorbisfile3 amd64 1.3.7-2+b1 [21.5 kB] Get: 515 http://deb.debian.org/debian unstable/main amd64 libopenmpt0t64 amd64 0.7.12-1 [854 kB] Get: 516 http://deb.debian.org/debian unstable/main amd64 librabbitmq4 amd64 0.15.0-1 [41.8 kB] Get: 517 http://deb.debian.org/debian unstable/main amd64 libcjson1 amd64 1.7.18-3+b1 [29.9 kB] Get: 518 http://deb.debian.org/debian unstable/main amd64 libmbedcrypto16 amd64 3.6.2-3 [355 kB] Get: 519 http://deb.debian.org/debian unstable/main amd64 librist4 amd64 0.2.11+dfsg-1 [72.1 kB] Get: 520 http://deb.debian.org/debian unstable/main amd64 libsrt1.5-gnutls amd64 1.5.4-1 [345 kB] Get: 521 http://deb.debian.org/debian unstable/main amd64 libssh-4 amd64 0.11.1-1 [208 kB] Get: 522 http://deb.debian.org/debian unstable/main amd64 libnorm1t64 amd64 1.5.9+dfsg-3.1+b1 [221 kB] Get: 523 http://deb.debian.org/debian unstable/main amd64 libpgm-5.3-0t64 amd64 5.3.128~dfsg-2.1+b1 [162 kB] Get: 524 http://deb.debian.org/debian unstable/main amd64 libsodium23 amd64 1.0.18-1+b2 [165 kB] Get: 525 http://deb.debian.org/debian unstable/main amd64 libzmq5 amd64 4.3.5-1+b3 [283 kB] Get: 526 http://deb.debian.org/debian unstable/main amd64 libavformat61 amd64 7:7.1-3 [1182 kB] Get: 527 http://deb.debian.org/debian unstable/main amd64 libavformat-dev amd64 7:7.1-3 [1390 kB] Get: 528 http://deb.debian.org/debian unstable/main amd64 libblosc1 amd64 1.21.5+ds-1+b2 [49.5 kB] Get: 529 http://deb.debian.org/debian unstable/main amd64 libblosc-dev amd64 1.21.5+ds-1+b2 [61.5 kB] Get: 530 http://deb.debian.org/debian unstable/main amd64 libboost1.83-dev amd64 1.83.0-4 [10.6 MB] Get: 531 http://deb.debian.org/debian unstable/main amd64 libboost-dev amd64 1.83.0.2+b2 [3836 B] Get: 532 http://deb.debian.org/debian unstable/main amd64 libbz2-dev amd64 1.0.8-6 [31.4 kB] Get: 533 http://deb.debian.org/debian unstable/main amd64 libcfitsio10t64 amd64 4.5.0-5 [575 kB] Get: 534 http://deb.debian.org/debian unstable/main amd64 libcfitsio-dev amd64 4.5.0-5 [640 kB] Get: 535 http://deb.debian.org/debian unstable/main amd64 libcommons-parent-java all 56-1 [10.8 kB] Get: 536 http://deb.debian.org/debian unstable/main amd64 libcommons-logging-java all 1.3.0-1 [68.6 kB] Get: 537 http://deb.debian.org/debian unstable/main amd64 libdeflate-dev amd64 1.22-1 [55.8 kB] Get: 538 http://deb.debian.org/debian unstable/main amd64 libdouble-conversion-dev amd64 3.3.0-1+b2 [61.7 kB] Get: 539 http://deb.debian.org/debian unstable/main amd64 pkg-config amd64 1.8.1-4 [14.0 kB] Get: 540 http://deb.debian.org/debian unstable/main amd64 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 541 http://deb.debian.org/debian unstable/main amd64 libhunspell-1.7-0 amd64 1.7.2+really1.7.2-10+b3 [237 kB] Get: 542 http://deb.debian.org/debian unstable/main amd64 libenchant-2-2 amd64 2.3.3-2+b3 [47.9 kB] Get: 543 http://deb.debian.org/debian unstable/main amd64 libevent-core-2.1-7t64 amd64 2.1.12-stable-10+b1 [132 kB] Get: 544 http://deb.debian.org/debian unstable/main amd64 libevent-extra-2.1-7t64 amd64 2.1.12-stable-10+b1 [108 kB] Get: 545 http://deb.debian.org/debian unstable/main amd64 libevent-pthreads-2.1-7t64 amd64 2.1.12-stable-10+b1 [54.3 kB] Get: 546 http://deb.debian.org/debian unstable/main amd64 libevent-openssl-2.1-7t64 amd64 2.1.12-stable-10+b1 [61.1 kB] Get: 547 http://deb.debian.org/debian unstable/main amd64 libevent-dev amd64 2.1.12-stable-10+b1 [305 kB] Get: 548 http://deb.debian.org/debian unstable/main amd64 libexpat1-dev amd64 2.6.4-1 [158 kB] Get: 549 http://deb.debian.org/debian unstable/main amd64 libpsm-infinipath1 amd64 3.3+20.604758e7-6.3 [170 kB] Get: 550 http://deb.debian.org/debian unstable/main amd64 libpsm2-2 amd64 11.2.185-2.1 [181 kB] Get: 551 http://deb.debian.org/debian unstable/main amd64 librdmacm1t64 amd64 52.0-2+b1 [70.4 kB] Get: 552 http://deb.debian.org/debian unstable/main amd64 libfabric1 amd64 1.17.0-3.1 [631 kB] Get: 553 http://deb.debian.org/debian unstable/main amd64 libfftw3-double3 amd64 3.3.10-2+b1 [781 kB] Get: 554 http://deb.debian.org/debian unstable/main amd64 libfftw3-long3 amd64 3.3.10-2+b1 [347 kB] Get: 555 http://deb.debian.org/debian unstable/main amd64 libfftw3-quad3 amd64 3.3.10-2+b1 [618 kB] Get: 556 http://deb.debian.org/debian unstable/main amd64 libfftw3-single3 amd64 3.3.10-2+b1 [809 kB] Get: 557 http://deb.debian.org/debian unstable/main amd64 libfftw3-bin amd64 3.3.10-2+b1 [51.3 kB] Get: 558 http://deb.debian.org/debian unstable/main amd64 libfftw3-dev amd64 3.3.10-2+b1 [2118 kB] Get: 559 http://deb.debian.org/debian unstable/main amd64 libfontbox-java all 1:1.8.16-5 [211 kB] Get: 560 http://deb.debian.org/debian unstable/main amd64 libpng-dev amd64 1.6.44-3 [366 kB] Get: 561 http://deb.debian.org/debian unstable/main amd64 libfreetype-dev amd64 2.13.3+dfsg-1 [622 kB] Get: 562 http://deb.debian.org/debian unstable/main amd64 uuid-dev amd64 2.40.2-12 [47.3 kB] Get: 563 http://deb.debian.org/debian unstable/main amd64 libfontconfig-dev amd64 2.15.0-1.1+b1 [414 kB] Get: 564 http://deb.debian.org/debian unstable/main amd64 libfontconfig1-dev amd64 2.15.0-1.1+b1 [269 kB] Get: 565 http://deb.debian.org/debian unstable/main amd64 libfontenc1 amd64 1:1.1.8-1+b1 [23.3 kB] Get: 566 http://deb.debian.org/debian unstable/main amd64 libminizip1t64 amd64 1:1.3.dfsg+really1.3.1-1+b1 [53.3 kB] Get: 567 http://deb.debian.org/debian unstable/main amd64 libfreexl1 amd64 2.0.0-1+b3 [40.0 kB] Get: 568 http://deb.debian.org/debian unstable/main amd64 libminizip-dev amd64 1:1.3.dfsg+really1.3.1-1+b1 [61.0 kB] Get: 569 http://deb.debian.org/debian unstable/main amd64 libfreexl-dev amd64 2.0.0-1+b3 [42.1 kB] Get: 570 http://deb.debian.org/debian unstable/main amd64 libfyba0t64 amd64 4.1.1-11+b1 [113 kB] Get: 571 http://deb.debian.org/debian unstable/main amd64 libfyba-dev amd64 4.1.1-11+b1 [169 kB] Get: 572 http://deb.debian.org/debian unstable/main amd64 libgeos3.13.0 amd64 3.13.0-1 [968 kB] Get: 573 http://deb.debian.org/debian unstable/main amd64 libgeos-c1t64 amd64 3.13.0-1 [102 kB] Get: 574 http://deb.debian.org/debian unstable/main amd64 proj-data all 9.5.1-1 [6284 kB] Get: 575 http://deb.debian.org/debian unstable/main amd64 libproj25 amd64 9.5.1-1 [1420 kB] Get: 576 http://deb.debian.org/debian unstable/main amd64 libgeotiff5 amd64 1.7.3-1+b1 [68.7 kB] Get: 577 http://deb.debian.org/debian unstable/main amd64 libhdf4-0-alt amd64 4.3.0-1+b1 [269 kB] Get: 578 http://deb.debian.org/debian unstable/main amd64 libjson-c5 amd64 0.18+ds-1 [46.0 kB] Get: 579 http://deb.debian.org/debian unstable/main amd64 liburiparser1 amd64 0.9.8+dfsg-2 [45.5 kB] Get: 580 http://deb.debian.org/debian unstable/main amd64 libkmlbase1t64 amd64 1.3.0-12+b1 [50.4 kB] Get: 581 http://deb.debian.org/debian unstable/main amd64 libkmldom1t64 amd64 1.3.0-12+b1 [158 kB] Get: 582 http://deb.debian.org/debian unstable/main amd64 libkmlengine1t64 amd64 1.3.0-12+b1 [80.2 kB] Get: 583 http://deb.debian.org/debian unstable/main amd64 libnetcdf19t64 amd64 1:4.9.2-7+b1 [477 kB] Get: 584 http://deb.debian.org/debian unstable/main amd64 libodbc2 amd64 2.3.12-1+b3 [151 kB] Get: 585 http://deb.debian.org/debian unstable/main amd64 unixodbc-common all 2.3.12-1 [8496 B] Get: 586 http://deb.debian.org/debian unstable/main amd64 libodbcinst2 amd64 2.3.12-1+b3 [35.3 kB] Get: 587 http://deb.debian.org/debian unstable/main amd64 libogdi4.1 amd64 4.1.1+ds-5 [217 kB] Get: 588 http://deb.debian.org/debian unstable/main amd64 libgpgme11t64 amd64 1.24.0-2 [344 kB] Get: 589 http://deb.debian.org/debian unstable/main amd64 libgpgmepp6t64 amd64 1.24.0-2 [339 kB] Get: 590 http://deb.debian.org/debian unstable/main amd64 libpoppler140 amd64 24.08.0-3 [1965 kB] Get: 591 http://deb.debian.org/debian unstable/main amd64 libpq5 amd64 17.2-1 [223 kB] Get: 592 http://deb.debian.org/debian unstable/main amd64 libqhull-r8.0 amd64 2020.2-6+b2 [248 kB] Get: 593 http://deb.debian.org/debian unstable/main amd64 librttopo1 amd64 1.1.0-3+b2 [179 kB] Get: 594 http://deb.debian.org/debian unstable/main amd64 libspatialite8t64 amd64 5.1.0-3+b2 [1864 kB] Get: 595 http://deb.debian.org/debian unstable/main amd64 libxerces-c3.2t64 amd64 3.2.4+debian-1.3+b1 [900 kB] Get: 596 http://deb.debian.org/debian unstable/main amd64 libgdal35 amd64 3.9.3+dfsg-1+b2 [9219 kB] Get: 597 http://deb.debian.org/debian unstable/main amd64 libgeos-dev amd64 3.13.0-1 [58.3 kB] Get: 598 http://deb.debian.org/debian unstable/main amd64 libsqlite3-dev amd64 3.46.1-1 [1107 kB] Get: 599 http://deb.debian.org/debian unstable/main amd64 libjbig-dev amd64 2.1-6.1+b2 [31.4 kB] Get: 600 http://deb.debian.org/debian unstable/main amd64 liblzma-dev amd64 5.6.3-1+b1 [316 kB] Get: 601 http://deb.debian.org/debian unstable/main amd64 libwebpdemux2 amd64 1.4.0-0.1+b1 [111 kB] Get: 602 http://deb.debian.org/debian unstable/main amd64 libwebpdecoder3 amd64 1.4.0-0.1+b1 [204 kB] Get: 603 http://deb.debian.org/debian unstable/main amd64 libsharpyuv-dev amd64 1.4.0-0.1+b1 [117 kB] Get: 604 http://deb.debian.org/debian unstable/main amd64 libwebp-dev amd64 1.4.0-0.1+b1 [442 kB] Get: 605 http://deb.debian.org/debian unstable/main amd64 libtiffxx6 amd64 4.5.1+git230720-5 [149 kB] Get: 606 http://deb.debian.org/debian unstable/main amd64 liblerc-dev amd64 4.0.0+ds-5 [183 kB] Get: 607 http://deb.debian.org/debian unstable/main amd64 libtiff-dev amd64 4.5.1+git230720-5 [463 kB] Get: 608 http://deb.debian.org/debian unstable/main amd64 libproj-dev amd64 9.5.1-1 [135 kB] Get: 609 http://deb.debian.org/debian unstable/main amd64 libgeotiff-dev amd64 1.7.3-1+b1 [97.6 kB] Get: 610 http://deb.debian.org/debian unstable/main amd64 libgif-dev amd64 5.2.2-1+b1 [47.0 kB] Get: 611 http://deb.debian.org/debian unstable/main amd64 libicu-dev amd64 72.1-5+b1 [10.4 MB] Get: 612 http://deb.debian.org/debian unstable/main amd64 libxml2-dev amd64 2.12.7+dfsg+really2.9.14-0.2+b1 [795 kB] Get: 613 http://deb.debian.org/debian unstable/main amd64 libnetcdf-dev amd64 1:4.9.2-7+b1 [104 kB] Get: 614 http://deb.debian.org/debian unstable/main amd64 libhdf4-alt-dev amd64 4.3.0-1+b1 [324 kB] Get: 615 http://deb.debian.org/debian unstable/main amd64 libheif-dev amd64 1.19.3-1 [50.8 kB] Get: 616 http://deb.debian.org/debian unstable/main amd64 libjson-c-dev amd64 0.18+ds-1 [74.8 kB] Get: 617 http://deb.debian.org/debian unstable/main amd64 libkmlconvenience1t64 amd64 1.3.0-12+b1 [49.7 kB] Get: 618 http://deb.debian.org/debian unstable/main amd64 libkmlregionator1t64 amd64 1.3.0-12+b1 [22.7 kB] Get: 619 http://deb.debian.org/debian unstable/main amd64 libkmlxsd1t64 amd64 1.3.0-12+b1 [31.1 kB] Get: 620 http://deb.debian.org/debian unstable/main amd64 liburiparser-dev amd64 0.9.8+dfsg-2 [26.7 kB] Get: 621 http://deb.debian.org/debian unstable/main amd64 libkml-dev amd64 1.3.0-12+b1 [662 kB] Get: 622 http://deb.debian.org/debian unstable/main amd64 libltdl-dev amd64 2.4.7-8 [165 kB] Get: 623 http://deb.debian.org/debian unstable/main amd64 liblz4-dev amd64 1.9.4-3+b1 [83.2 kB] Get: 624 http://deb.debian.org/debian unstable/main amd64 libtirpc-dev amd64 1.3.4+ds-1.3+b1 [190 kB] Get: 625 http://deb.debian.org/debian unstable/main amd64 libogdi-dev amd64 4.1.1+ds-5 [35.5 kB] Get: 626 http://deb.debian.org/debian unstable/main amd64 libopenjp2-7-dev amd64 2.5.0-2+b4 [273 kB] Get: 627 http://deb.debian.org/debian unstable/main amd64 libpcre2-32-0 amd64 10.44-5 [248 kB] Get: 628 http://deb.debian.org/debian unstable/main amd64 libpcre2-posix3 amd64 10.44-5 [60.4 kB] Get: 629 http://deb.debian.org/debian unstable/main amd64 libpcre2-dev amd64 10.44-5 [790 kB] Get: 630 http://deb.debian.org/debian unstable/main amd64 libpoppler-dev amd64 24.08.0-3 [8484 B] Get: 631 http://deb.debian.org/debian unstable/main amd64 libpoppler-private-dev amd64 24.08.0-3 [193 kB] Get: 632 http://deb.debian.org/debian unstable/main amd64 libpq-dev amd64 17.2-1 [147 kB] Get: 633 http://deb.debian.org/debian unstable/main amd64 libqhull8.0 amd64 2020.2-6+b2 [246 kB] Get: 634 http://deb.debian.org/debian unstable/main amd64 libqhullcpp8.0 amd64 2020.2-6+b2 [108 kB] Get: 635 http://deb.debian.org/debian unstable/main amd64 libqhull-dev amd64 2020.2-6+b2 [522 kB] Get: 636 http://deb.debian.org/debian unstable/main amd64 librttopo-dev amd64 1.1.0-3+b2 [221 kB] Get: 637 http://deb.debian.org/debian unstable/main amd64 libspatialite-dev amd64 5.1.0-3+b2 [2025 kB] Get: 638 http://deb.debian.org/debian unstable/main amd64 libxerces-c-dev amd64 3.2.4+debian-1.3+b1 [1708 kB] Get: 639 http://deb.debian.org/debian unstable/main amd64 libodbccr2 amd64 2.3.12-1+b3 [18.3 kB] Get: 640 http://deb.debian.org/debian unstable/main amd64 unixodbc-dev amd64 2.3.12-1+b3 [234 kB] Get: 641 http://deb.debian.org/debian unstable/main amd64 libgdal-dev amd64 3.9.3+dfsg-1+b2 [537 kB] Get: 642 http://deb.debian.org/debian unstable/main amd64 libgl2ps1.4 amd64 1.4.2+dfsg1-2 [41.3 kB] Get: 643 http://deb.debian.org/debian unstable/main amd64 libgl2ps-dev amd64 1.4.2+dfsg1-2 [24.8 kB] Get: 644 http://deb.debian.org/debian unstable/main amd64 libglew2.2 amd64 2.2.0-4+b2 [168 kB] Get: 645 http://deb.debian.org/debian unstable/main amd64 libglew-dev amd64 2.2.0-4+b2 [246 kB] Get: 646 http://deb.debian.org/debian unstable/main amd64 libhwloc15 amd64 2.11.2-1 [164 kB] Get: 647 http://deb.debian.org/debian unstable/main amd64 libmunge2 amd64 0.5.15-4+b1 [20.0 kB] Get: 648 http://deb.debian.org/debian unstable/main amd64 libxnvctrl0 amd64 535.171.04-1+b1 [14.2 kB] Get: 649 http://deb.debian.org/debian unstable/main amd64 libhwloc-plugins amd64 2.11.2-1 [18.1 kB] Get: 650 http://deb.debian.org/debian unstable/main amd64 libpmix2t64 amd64 5.0.4-1 [661 kB] Get: 651 http://deb.debian.org/debian unstable/main amd64 libibumad3 amd64 52.0-2+b1 [28.2 kB] Get: 652 http://deb.debian.org/debian unstable/main amd64 libibmad5 amd64 52.0-2+b1 [43.4 kB] Get: 653 http://deb.debian.org/debian unstable/main amd64 libucx0 amd64 1.17.0+ds-3 [1130 kB] Get: 654 http://deb.debian.org/debian unstable/main amd64 libopenmpi40 amd64 5.0.6-3 [2360 kB] Get: 655 http://deb.debian.org/debian unstable/main amd64 libhdf5-openmpi-310 amd64 1.14.5+repack-1 [1395 kB] Get: 656 http://deb.debian.org/debian unstable/main amd64 libhdf5-openmpi-fortran-310 amd64 1.14.5+repack-1 [113 kB] Get: 657 http://deb.debian.org/debian unstable/main amd64 libhdf5-openmpi-hl-310 amd64 1.14.5+repack-1 [69.1 kB] Get: 658 http://deb.debian.org/debian unstable/main amd64 libhdf5-openmpi-hl-fortran-310 amd64 1.14.5+repack-1 [43.7 kB] Get: 659 http://deb.debian.org/debian unstable/main amd64 libhdf5-openmpi-cpp-310 amd64 1.14.5+repack-1 [133 kB] Get: 660 http://deb.debian.org/debian unstable/main amd64 libhdf5-openmpi-hl-cpp-310 amd64 1.14.5+repack-1 [24.1 kB] Get: 661 http://deb.debian.org/debian unstable/main amd64 openmpi-common all 5.0.6-3 [97.0 kB] Get: 662 http://deb.debian.org/debian unstable/main amd64 libnl-3-dev amd64 3.7.0-0.3+b1 [100 kB] Get: 663 http://deb.debian.org/debian unstable/main amd64 libnl-route-3-dev amd64 3.7.0-0.3+b1 [200 kB] Get: 664 http://deb.debian.org/debian unstable/main amd64 libibverbs-dev amd64 52.0-2+b1 [636 kB] Get: 665 http://deb.debian.org/debian unstable/main amd64 libnuma-dev amd64 2.0.18-1+b1 [36.6 kB] Get: 666 http://deb.debian.org/debian unstable/main amd64 libhwloc-dev amd64 2.11.2-1 [254 kB] Get: 667 http://deb.debian.org/debian unstable/main amd64 python3-defusedxml all 0.7.1-3 [43.4 kB] Get: 668 http://deb.debian.org/debian unstable/main amd64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 669 http://deb.debian.org/debian unstable/main amd64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 670 http://deb.debian.org/debian unstable/main amd64 libjs-sphinxdoc all 8.1.3-2 [30.3 kB] Get: 671 http://deb.debian.org/debian unstable/main amd64 libjson-perl all 4.10000-1 [87.5 kB] Get: 672 http://deb.debian.org/debian unstable/main amd64 sphinx-common all 8.1.3-2 [616 kB] Get: 673 http://deb.debian.org/debian unstable/main amd64 python3-alabaster all 0.7.16-0.1 [27.9 kB] Get: 674 http://deb.debian.org/debian unstable/main amd64 python-babel-localedata all 2.16.0-1 [5696 kB] Get: 675 http://deb.debian.org/debian unstable/main amd64 python3-babel all 2.16.0-1 [114 kB] Get: 676 http://deb.debian.org/debian unstable/main amd64 python3-roman all 4.2-1 [10.4 kB] Get: 677 http://deb.debian.org/debian unstable/main amd64 python3-docutils all 0.21.2+dfsg-2 [403 kB] Get: 678 http://deb.debian.org/debian unstable/main amd64 python3-imagesize all 1.4.1-1 [6688 B] Get: 679 http://deb.debian.org/debian unstable/main amd64 python3-markupsafe amd64 2.1.5-1+b2 [13.9 kB] Get: 680 http://deb.debian.org/debian unstable/main amd64 python3-jinja2 all 3.1.3-1 [119 kB] Get: 681 http://deb.debian.org/debian unstable/main amd64 python3-packaging all 24.2-1 [55.3 kB] Get: 682 http://deb.debian.org/debian unstable/main amd64 python3-pygments all 2.18.0+dfsg-1 [836 kB] Get: 683 http://deb.debian.org/debian unstable/main amd64 python3-certifi all 2024.8.30+dfsg-1 [9576 B] Get: 684 http://deb.debian.org/debian unstable/main amd64 python3-charset-normalizer amd64 3.4.0-1+b1 [140 kB] Get: 685 http://deb.debian.org/debian unstable/main amd64 python3-idna all 3.8-2 [41.6 kB] Get: 686 http://deb.debian.org/debian unstable/main amd64 python3-urllib3 all 2.2.3-4 [112 kB] Get: 687 http://deb.debian.org/debian unstable/main amd64 python3-chardet all 5.2.0+dfsg-1 [107 kB] Get: 688 http://deb.debian.org/debian unstable/main amd64 python3-requests all 2.32.3+dfsg-1 [71.9 kB] Get: 689 http://deb.debian.org/debian unstable/main amd64 python3-snowballstemmer all 2.2.0-4 [58.0 kB] Get: 690 http://deb.debian.org/debian unstable/main amd64 python3-sphinx all 8.1.3-2 [468 kB] Get: 691 http://deb.debian.org/debian unstable/main amd64 libpmix-dev amd64 5.0.4-1 [3972 kB] Get: 692 http://deb.debian.org/debian unstable/main amd64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 693 http://deb.debian.org/debian unstable/main amd64 openmpi-bin amd64 5.0.6-3 [188 kB] Get: 694 http://deb.debian.org/debian unstable/main amd64 libopenmpi-dev amd64 5.0.6-3 [1088 kB] Get: 695 http://deb.debian.org/debian unstable/main amd64 libhdf5-openmpi-dev amd64 1.14.5+repack-1 [3268 kB] Get: 696 http://deb.debian.org/debian unstable/main amd64 mpi-default-dev amd64 1.17 [3148 B] Get: 697 http://deb.debian.org/debian unstable/main amd64 libhdf5-mpi-dev amd64 1.14.5+repack-1 [18.5 kB] Get: 698 http://deb.debian.org/debian unstable/main amd64 libice-dev amd64 2:1.1.1-1 [73.8 kB] Get: 699 http://deb.debian.org/debian unstable/main amd64 libjs-mathjax all 2.7.9+dfsg-1 [5667 kB] Get: 700 http://deb.debian.org/debian unstable/main amd64 libjsoncpp-dev amd64 1.9.6-3 [25.0 kB] Get: 701 http://deb.debian.org/debian unstable/main amd64 libkim-api2 amd64 2.3.0-1+b2 [577 kB] Get: 702 http://deb.debian.org/debian unstable/main amd64 libkim-api-dev amd64 2.3.0-1+b2 [107 kB] Get: 703 http://deb.debian.org/debian unstable/main amd64 libogg-dev amd64 1.3.5-3+b2 [200 kB] Get: 704 http://deb.debian.org/debian unstable/main amd64 libpdfbox-java all 1:1.8.16-5 [5527 kB] Get: 705 http://deb.debian.org/debian unstable/main amd64 libpnetcdf6 amd64 1.14.0-2 [920 kB] Get: 706 http://deb.debian.org/debian unstable/main amd64 libpnetcdf-dev amd64 1.14.0-2 [1106 kB] Get: 707 http://deb.debian.org/debian unstable/main amd64 libpython3.12t64 amd64 3.12.8-2 [2151 kB] Get: 708 http://deb.debian.org/debian unstable/main amd64 libpython3.12-dev amd64 3.12.8-2 [5135 kB] Get: 709 http://deb.debian.org/debian unstable/main amd64 libpython3-dev amd64 3.12.7-1 [9976 B] Get: 710 http://deb.debian.org/debian unstable/main amd64 libpython3.13-stdlib amd64 3.13.1-2 [1975 kB] Get: 711 http://deb.debian.org/debian unstable/main amd64 libpython3.13 amd64 3.13.1-2 [2151 kB] Get: 712 http://deb.debian.org/debian unstable/main amd64 libpython3.13-dev amd64 3.13.1-2 [5009 kB] Get: 713 http://deb.debian.org/debian unstable/main amd64 libpython3-all-dev amd64 3.12.7-1 [1072 B] Get: 714 http://deb.debian.org/debian unstable/main amd64 libqt5designer5 amd64 5.15.15-4 [2759 kB] Get: 715 http://deb.debian.org/debian unstable/main amd64 libqt5designercomponents5 amd64 5.15.15-4 [738 kB] Get: 716 http://deb.debian.org/debian unstable/main amd64 libqt5help5 amd64 5.15.15-4 [151 kB] Get: 717 http://deb.debian.org/debian unstable/main amd64 libqt5opengl5t64 amd64 5.15.15+dfsg-2 [150 kB] Get: 718 http://deb.debian.org/debian unstable/main amd64 libqt5opengl5-dev amd64 5.15.15+dfsg-2 [51.5 kB] Get: 719 http://deb.debian.org/debian unstable/main amd64 libqt5sql5-sqlite amd64 5.15.15+dfsg-2 [59.1 kB] Get: 720 http://deb.debian.org/debian unstable/main amd64 libsm-dev amd64 2:1.2.4-1 [37.7 kB] Get: 721 http://deb.debian.org/debian unstable/main amd64 libswscale8 amd64 7:7.1-3 [224 kB] Get: 722 http://deb.debian.org/debian unstable/main amd64 libswscale-dev amd64 7:7.1-3 [254 kB] Get: 723 http://deb.debian.org/debian unstable/main amd64 libsymspg2 amd64 2.5.0-1+b1 [197 kB] Get: 724 http://deb.debian.org/debian unstable/main amd64 libsymspg-dev amd64 2.5.0-1+b1 [37.2 kB] Get: 725 http://deb.debian.org/debian unstable/main amd64 libtbbmalloc2 amd64 2021.12.0-1 [48.9 kB] Get: 726 http://deb.debian.org/debian unstable/main amd64 libtbbbind-2-5 amd64 2021.12.0-1 [14.4 kB] Get: 727 http://deb.debian.org/debian unstable/main amd64 libtbb12 amd64 2021.12.0-1 [87.8 kB] Get: 728 http://deb.debian.org/debian unstable/main amd64 libtbb-dev amd64 2021.12.0-1 [193 kB] Get: 729 http://deb.debian.org/debian unstable/main amd64 libtcl8.6 amd64 8.6.15+dfsg-2 [1042 kB] Get: 730 http://deb.debian.org/debian unstable/main amd64 libtheora-dev amd64 1.1.1+dfsg.1-17 [175 kB] Get: 731 http://deb.debian.org/debian unstable/main amd64 libxss1 amd64 1:1.2.3-1+b2 [17.0 kB] Get: 732 http://deb.debian.org/debian unstable/main amd64 libtk8.6 amd64 8.6.15-1 [791 kB] Get: 733 http://deb.debian.org/debian unstable/main amd64 libutfcpp-dev all 4.0.5-1 [12.9 kB] Get: 734 http://deb.debian.org/debian unstable/main amd64 libvoro++1 amd64 0.5+revert-to-0.4.6+dfsg1-1 [127 kB] Get: 735 http://deb.debian.org/debian unstable/main amd64 libvtk9.3 amd64 9.3.0+dfsg1-1.1+b2 [23.2 MB] Get: 736 http://deb.debian.org/debian unstable/main amd64 libvtk9.3-qt amd64 9.3.0+dfsg1-1.1+b2 [173 kB] Get: 737 http://deb.debian.org/debian unstable/main amd64 libvtk9-java amd64 9.3.0+dfsg1-1.1+b2 [6393 kB] Get: 738 http://deb.debian.org/debian unstable/main amd64 libxrender-dev amd64 1:0.9.10-1.1+b2 [35.8 kB] Get: 739 http://deb.debian.org/debian unstable/main amd64 libxft-dev amd64 2.3.6-1+b2 [73.2 kB] Get: 740 http://deb.debian.org/debian unstable/main amd64 libxss-dev amd64 1:1.2.3-1+b2 [22.7 kB] Get: 741 http://deb.debian.org/debian unstable/main amd64 libxt-dev amd64 1:1.2.1-1.2+b1 [407 kB] Get: 742 http://deb.debian.org/debian unstable/main amd64 mpi-default-bin amd64 1.17 [2372 B] Get: 743 http://deb.debian.org/debian unstable/main amd64 python3-mpi4py amd64 4.0.1-6+b1 [1000 kB] Get: 744 http://deb.debian.org/debian unstable/main amd64 python3-vtk9 amd64 9.3.0+dfsg1-1.1+b2 [7224 kB] Get: 745 http://deb.debian.org/debian unstable/main amd64 tcl8.6 amd64 8.6.15+dfsg-2 [120 kB] Get: 746 http://deb.debian.org/debian unstable/main amd64 tcl8.6-dev amd64 8.6.15+dfsg-2 [1029 kB] Get: 747 http://deb.debian.org/debian unstable/main amd64 tcl amd64 8.6.14 [4032 B] Get: 748 http://deb.debian.org/debian unstable/main amd64 tcl-dev amd64 8.6.14 [6580 B] Get: 749 http://deb.debian.org/debian unstable/main amd64 tk8.6 amd64 8.6.15-1 [69.6 kB] Get: 750 http://deb.debian.org/debian unstable/main amd64 tk8.6-dev amd64 8.6.15-1 [791 kB] Get: 751 http://deb.debian.org/debian unstable/main amd64 tk amd64 8.6.14 [4076 B] Get: 752 http://deb.debian.org/debian unstable/main amd64 tk-dev amd64 8.6.14 [3896 B] Get: 753 http://deb.debian.org/debian unstable/main amd64 vtk9 amd64 9.3.0+dfsg1-1.1+b2 [20.0 kB] Get: 754 http://deb.debian.org/debian unstable/main amd64 libvtk9-dev amd64 9.3.0+dfsg1-1.1+b2 [3052 kB] Get: 755 http://deb.debian.org/debian unstable/main amd64 qdoc-qt5 amd64 5.15.15-4 [593 kB] Get: 756 http://deb.debian.org/debian unstable/main amd64 qhelpgenerator-qt5 amd64 5.15.15-4 [61.1 kB] Get: 757 http://deb.debian.org/debian unstable/main amd64 qt5-assistant amd64 5.15.15-4 [353 kB] Get: 758 http://deb.debian.org/debian unstable/main amd64 qtattributionsscanner-qt5 amd64 5.15.15-4 [32.9 kB] Get: 759 http://deb.debian.org/debian unstable/main amd64 qttools5-dev-tools amd64 5.15.15-4 [1048 kB] Get: 760 http://deb.debian.org/debian unstable/main amd64 qttools5-dev amd64 5.15.15-4 [193 kB] Get: 761 http://deb.debian.org/debian unstable/main amd64 qttools5-private-dev amd64 5.15.15-4 [73.9 kB] Get: 762 http://deb.debian.org/debian unstable/main amd64 libvtk9-qt-dev amd64 9.3.0+dfsg1-1.1+b2 [32.4 kB] Get: 763 http://deb.debian.org/debian unstable/main amd64 opencl-c-headers all 3.0~2024.10.24-2 [46.8 kB] Get: 764 http://deb.debian.org/debian unstable/main amd64 opencl-clhpp-headers all 3.0~2024.10.24-2 [50.7 kB] Get: 765 http://deb.debian.org/debian unstable/main amd64 ocl-icd-opencl-dev amd64 2.3.2-1+b2 [8672 B] Get: 766 http://deb.debian.org/debian unstable/main amd64 preview-latex-style all 13.2-1 [350 kB] Get: 767 http://deb.debian.org/debian unstable/main amd64 python3-pyproject-hooks all 1.2.0-1 [11.7 kB] Get: 768 http://deb.debian.org/debian unstable/main amd64 python3-toml all 0.10.2-1 [16.2 kB] Get: 769 http://deb.debian.org/debian unstable/main amd64 python3-wheel all 0.45.1-1 [56.7 kB] Get: 770 http://deb.debian.org/debian unstable/main amd64 python3-build all 1.2.2-1 [36.0 kB] Get: 771 http://deb.debian.org/debian unstable/main amd64 python3-installer all 0.7.0+dfsg1-3 [18.6 kB] Get: 772 http://deb.debian.org/debian unstable/main amd64 pybuild-plugin-pyproject all 6.20241024 [11.4 kB] Get: 773 http://deb.debian.org/debian unstable/main amd64 python3.13 amd64 3.13.1-2 [740 kB] Get: 774 http://deb.debian.org/debian unstable/main amd64 python3-all amd64 3.12.7-1 [1052 B] Get: 775 http://deb.debian.org/debian unstable/main amd64 python3.12-dev amd64 3.12.8-2 [505 kB] Get: 776 http://deb.debian.org/debian unstable/main amd64 python3-dev amd64 3.12.7-1 [26.1 kB] Get: 777 http://deb.debian.org/debian unstable/main amd64 python3.13-dev amd64 3.13.1-2 [504 kB] Get: 778 http://deb.debian.org/debian unstable/main amd64 python3-all-dev amd64 3.12.7-1 [1076 B] Get: 779 http://deb.debian.org/debian unstable/main amd64 python3-breathe all 4.35.0-3 [78.2 kB] Get: 780 http://deb.debian.org/debian unstable/main amd64 python3-enchant all 3.2.2-1 [39.2 kB] Get: 781 http://deb.debian.org/debian unstable/main amd64 python3-pip-whl all 24.3.1+dfsg-1 [1501 kB] Get: 782 http://deb.debian.org/debian unstable/main amd64 python3-setuptools-whl all 75.2.0-1 [1249 kB] Get: 783 http://deb.debian.org/debian unstable/main amd64 python3-sphinx-tabs all 3.4.7-1 [14.7 kB] Get: 784 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.jquery all 4.1-5 [7348 B] Get: 785 http://deb.debian.org/debian unstable/main amd64 python3-sphinxcontrib.spelling all 7.7.0-1 [34.3 kB] Get: 786 http://deb.debian.org/debian unstable/main amd64 python3.12-venv amd64 3.12.8-2 [5832 B] Get: 787 http://deb.debian.org/debian unstable/main amd64 python3-venv amd64 3.12.7-1 [1180 B] Get: 788 http://deb.debian.org/debian unstable/main amd64 sphinx-rtd-theme-common all 3.0.2+dfsg-1 [1023 kB] Get: 789 http://deb.debian.org/debian unstable/main amd64 xfonts-encodings all 1:1.0.4-2.2 [577 kB] Get: 790 http://deb.debian.org/debian unstable/main amd64 xfonts-utils amd64 1:7.7+7 [93.3 kB] Get: 791 http://deb.debian.org/debian unstable/main amd64 tex-gyre all 20180621-6 [6209 kB] Get: 792 http://deb.debian.org/debian unstable/main amd64 texlive-fonts-recommended all 2024.20241115-1 [4991 kB] Get: 793 http://deb.debian.org/debian unstable/main amd64 texlive-latex-recommended all 2024.20241115-1 [8757 kB] Get: 794 http://deb.debian.org/debian unstable/main amd64 texlive-pictures all 2024.20241115-1 [17.0 MB] Get: 795 http://deb.debian.org/debian unstable/main amd64 texlive-latex-extra all 2024.20241115-1 [24.6 MB] Get: 796 http://deb.debian.org/debian unstable/main amd64 voro++-dev amd64 0.5+revert-to-0.4.6+dfsg1-1 [155 kB] Fetched 775 MB in 9s (84.3 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libapparmor1:amd64. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 19965 files and directories currently installed.) Preparing to unpack .../libapparmor1_3.1.7-1+b3_amd64.deb ... Unpacking libapparmor1:amd64 (3.1.7-1+b3) ... Selecting previously unselected package libsystemd-shared:amd64. Preparing to unpack .../libsystemd-shared_257-2_amd64.deb ... Unpacking libsystemd-shared:amd64 (257-2) ... Selecting previously unselected package systemd. Preparing to unpack .../systemd_257-2_amd64.deb ... Unpacking systemd (257-2) ... Setting up libapparmor1:amd64 (3.1.7-1+b3) ... Setting up libsystemd-shared:amd64 (257-2) ... Setting up systemd (257-2) ... Created symlink '/etc/systemd/system/getty.target.wants/getty@tty1.service' -> '/usr/lib/systemd/system/getty@.service'. Created symlink '/etc/systemd/system/multi-user.target.wants/remote-fs.target' -> '/usr/lib/systemd/system/remote-fs.target'. Created symlink '/etc/systemd/system/sysinit.target.wants/systemd-pstore.service' -> '/usr/lib/systemd/system/systemd-pstore.service'. Initializing machine ID from random generator. Creating group 'systemd-journal' with GID 999. Creating group 'systemd-network' with GID 998. Creating user 'systemd-network' (systemd Network Management) with UID 998 and GID 998. /usr/lib/tmpfiles.d/legacy.conf:14: Duplicate line for path "/run/lock", ignoring. Selecting previously unselected package systemd-sysv. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 20921 files and directories currently installed.) Preparing to unpack .../000-systemd-sysv_257-2_amd64.deb ... Unpacking systemd-sysv (257-2) ... Selecting previously unselected package libdbus-1-3:amd64. Preparing to unpack .../001-libdbus-1-3_1.15.92-1_amd64.deb ... Unpacking libdbus-1-3:amd64 (1.15.92-1) ... Selecting previously unselected package dbus-bin. Preparing to unpack .../002-dbus-bin_1.15.92-1_amd64.deb ... Unpacking dbus-bin (1.15.92-1) ... Selecting previously unselected package dbus-session-bus-common. Preparing to unpack .../003-dbus-session-bus-common_1.15.92-1_all.deb ... Unpacking dbus-session-bus-common (1.15.92-1) ... Selecting previously unselected package libexpat1:amd64. Preparing to unpack .../004-libexpat1_2.6.4-1_amd64.deb ... Unpacking libexpat1:amd64 (2.6.4-1) ... Selecting previously unselected package dbus-daemon. Preparing to unpack .../005-dbus-daemon_1.15.92-1_amd64.deb ... Unpacking dbus-daemon (1.15.92-1) ... Selecting previously unselected package dbus-system-bus-common. Preparing to unpack .../006-dbus-system-bus-common_1.15.92-1_all.deb ... Unpacking dbus-system-bus-common (1.15.92-1) ... Selecting previously unselected package dbus. Preparing to unpack .../007-dbus_1.15.92-1_amd64.deb ... Unpacking dbus (1.15.92-1) ... Selecting previously unselected package fonts-lato. Preparing to unpack .../008-fonts-lato_2.015-1_all.deb ... Unpacking fonts-lato (2.015-1) ... Selecting previously unselected package libglib2.0-0t64:amd64. Preparing to unpack .../009-libglib2.0-0t64_2.82.3-2_amd64.deb ... Unpacking libglib2.0-0t64:amd64 (2.82.3-2) ... Selecting previously unselected package libdrm-common. Preparing to unpack .../010-libdrm-common_2.4.123-1_all.deb ... Unpacking libdrm-common (2.4.123-1) ... Selecting previously unselected package libdrm2:amd64. Preparing to unpack .../011-libdrm2_2.4.123-1_amd64.deb ... Unpacking libdrm2:amd64 (2.4.123-1) ... Selecting previously unselected package libelf1t64:amd64. Preparing to unpack .../012-libelf1t64_0.192-4_amd64.deb ... Unpacking libelf1t64:amd64 (0.192-4) ... Selecting previously unselected package libdw1t64:amd64. Preparing to unpack .../013-libdw1t64_0.192-4_amd64.deb ... Unpacking libdw1t64:amd64 (0.192-4) ... Selecting previously unselected package libunwind8:amd64. Preparing to unpack .../014-libunwind8_1.7.2-1_amd64.deb ... Unpacking libunwind8:amd64 (1.7.2-1) ... Selecting previously unselected package libcap2-bin. Preparing to unpack .../015-libcap2-bin_1%3a2.66-5+b1_amd64.deb ... Unpacking libcap2-bin (1:2.66-5+b1) ... Selecting previously unselected package libgstreamer1.0-0:amd64. Preparing to unpack .../016-libgstreamer1.0-0_1.24.10-2_amd64.deb ... Unpacking libgstreamer1.0-0:amd64 (1.24.10-2) ... Selecting previously unselected package liborc-0.4-0t64:amd64. Preparing to unpack .../017-liborc-0.4-0t64_1%3a0.4.40-1_amd64.deb ... Unpacking liborc-0.4-0t64:amd64 (1:0.4.40-1) ... Selecting previously unselected package iso-codes. Preparing to unpack .../018-iso-codes_4.17.0-1_all.deb ... Unpacking iso-codes (4.17.0-1) ... Selecting previously unselected package libgstreamer-plugins-base1.0-0:amd64. Preparing to unpack .../019-libgstreamer-plugins-base1.0-0_1.24.10-1_amd64.deb ... Unpacking libgstreamer-plugins-base1.0-0:amd64 (1.24.10-1) ... Selecting previously unselected package libhyphen0:amd64. Preparing to unpack .../020-libhyphen0_2.8.8-7+b2_amd64.deb ... Unpacking libhyphen0:amd64 (2.8.8-7+b2) ... Selecting previously unselected package libicu72:amd64. Preparing to unpack .../021-libicu72_72.1-5+b1_amd64.deb ... Unpacking libicu72:amd64 (72.1-5+b1) ... Selecting previously unselected package libjpeg62-turbo:amd64. Preparing to unpack .../022-libjpeg62-turbo_1%3a2.1.5-3+b1_amd64.deb ... Unpacking libjpeg62-turbo:amd64 (1:2.1.5-3+b1) ... Selecting previously unselected package libpng16-16t64:amd64. Preparing to unpack .../023-libpng16-16t64_1.6.44-3_amd64.deb ... Unpacking libpng16-16t64:amd64 (1.6.44-3) ... Selecting previously unselected package libxml2:amd64. Preparing to unpack .../024-libxml2_2.12.7+dfsg+really2.9.14-0.2+b1_amd64.deb ... Unpacking libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Selecting previously unselected package shared-mime-info. Preparing to unpack .../025-shared-mime-info_2.4-5+b1_amd64.deb ... Unpacking shared-mime-info (2.4-5+b1) ... Selecting previously unselected package libdouble-conversion3:amd64. Preparing to unpack .../026-libdouble-conversion3_3.3.0-1+b2_amd64.deb ... Unpacking libdouble-conversion3:amd64 (3.3.0-1+b2) ... Selecting previously unselected package libpcre2-16-0:amd64. Preparing to unpack .../027-libpcre2-16-0_10.44-5_amd64.deb ... Unpacking libpcre2-16-0:amd64 (10.44-5) ... Selecting previously unselected package libqt5core5t64:amd64. Preparing to unpack .../028-libqt5core5t64_5.15.15+dfsg-2_amd64.deb ... Unpacking libqt5core5t64:amd64 (5.15.15+dfsg-2) ... Selecting previously unselected package libbrotli1:amd64. Preparing to unpack .../029-libbrotli1_1.1.0-2+b6_amd64.deb ... Unpacking libbrotli1:amd64 (1.1.0-2+b6) ... Selecting previously unselected package libfreetype6:amd64. Preparing to unpack .../030-libfreetype6_2.13.3+dfsg-1_amd64.deb ... Unpacking libfreetype6:amd64 (2.13.3+dfsg-1) ... Selecting previously unselected package fonts-dejavu-mono. Preparing to unpack .../031-fonts-dejavu-mono_2.37-8_all.deb ... Unpacking fonts-dejavu-mono (2.37-8) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../032-fonts-dejavu-core_2.37-8_all.deb ... Unpacking fonts-dejavu-core (2.37-8) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../033-fontconfig-config_2.15.0-1.1+b1_amd64.deb ... Unpacking fontconfig-config (2.15.0-1.1+b1) ... Selecting previously unselected package libfontconfig1:amd64. Preparing to unpack .../034-libfontconfig1_2.15.0-1.1+b1_amd64.deb ... Unpacking libfontconfig1:amd64 (2.15.0-1.1+b1) ... Selecting previously unselected package fontconfig. Preparing to unpack .../035-fontconfig_2.15.0-1.1+b1_amd64.deb ... Unpacking fontconfig (2.15.0-1.1+b1) ... Selecting previously unselected package libglvnd0:amd64. Preparing to unpack .../036-libglvnd0_1.7.0-1+b2_amd64.deb ... Unpacking libglvnd0:amd64 (1.7.0-1+b2) ... Selecting previously unselected package libwayland-server0:amd64. Preparing to unpack .../037-libwayland-server0_1.23.0-1+b1_amd64.deb ... Unpacking libwayland-server0:amd64 (1.23.0-1+b1) ... Selecting previously unselected package libxau6:amd64. Preparing to unpack .../038-libxau6_1%3a1.0.11-1_amd64.deb ... Unpacking libxau6:amd64 (1:1.0.11-1) ... Selecting previously unselected package libxdmcp6:amd64. Preparing to unpack .../039-libxdmcp6_1%3a1.1.5-1_amd64.deb ... Unpacking libxdmcp6:amd64 (1:1.1.5-1) ... Selecting previously unselected package libxcb1:amd64. Preparing to unpack .../040-libxcb1_1.17.0-2+b1_amd64.deb ... Unpacking libxcb1:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libxcb-randr0:amd64. Preparing to unpack .../041-libxcb-randr0_1.17.0-2+b1_amd64.deb ... Unpacking libxcb-randr0:amd64 (1.17.0-2+b1) ... Selecting previously unselected package libdrm-amdgpu1:amd64. Preparing to unpack .../042-libdrm-amdgpu1_2.4.123-1_amd64.deb ... Unpacking libdrm-amdgpu1:amd64 (2.4.123-1) ... Selecting previously unselected package libpciaccess0:amd64. Preparing to unpack .../043-libpciaccess0_0.17-3+b2_amd64.deb ... Unpacking libpciaccess0:amd64 (0.17-3+b2) ... Selecting previously unselected package libdrm-intel1:amd64. Preparing to unpack .../044-libdrm-intel1_2.4.123-1_amd64.deb ... Unpacking libdrm-intel1:amd64 (2.4.123-1) ... Selecting previously unselected package libdrm-radeon1:amd64. Preparing to unpack .../045-libdrm-radeon1_2.4.123-1_amd64.deb ... Unpacking libdrm-radeon1:amd64 (2.4.123-1) ... Selecting previously unselected package libglapi-mesa:amd64. Preparing to unpack .../046-libglapi-mesa_24.2.8-1_amd64.deb ... Unpacking libglapi-mesa:amd64 (24.2.8-1) ... Selecting previously unselected package libedit2:amd64. Preparing to unpack .../047-libedit2_3.1-20240808-1_amd64.deb ... Unpacking libedit2:amd64 (3.1-20240808-1) ... Selecting previously unselected package libz3-4:amd64. 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Setting up libsharpyuv-dev:amd64 (1.4.0-0.1+b1) ... Setting up libkmlbase1t64:amd64 (1.3.0-12+b1) ... Setting up libvoro++1 (0.5+revert-to-0.4.6+dfsg1-1) ... Setting up libtasn1-6-dev:amd64 (4.19.0-3+b3) ... Setting up openssl (3.3.2-2) ... Setting up libwebpmux3:amd64 (1.4.0-0.1+b1) ... Setting up libtiffxx6:amd64 (4.5.1+git230720-5) ... Setting up libdeflate-dev:amd64 (1.22-1) ... Setting up libdrm-common (2.4.123-1) ... Setting up libyuv0:amd64 (0.0.1898.20241125-1) ... Setting up libxcomposite1:amd64 (1:0.4.6-1) ... Setting up libjson-c5:amd64 (0.18+ds-1) ... Setting up libevdev2:amd64 (1.13.3+dfsg-1) ... Setting up readline-common (8.2-5) ... Setting up libicu-dev:amd64 (72.1-5+b1) ... Setting up libxml2:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-4.1) ... Setting up sphinx-rtd-theme-common (3.0.2+dfsg-1) ... Setting up xdg-utils (1.2.1-2) ... update-alternatives: using /usr/bin/xdg-open to provide /usr/bin/open (open) in auto mode Setting up iso-codes (4.17.0-1) ... Setting up dbus-bin (1.15.92-1) ... Setting up libbrotli-dev:amd64 (1.1.0-2+b6) ... Setting up libgudev-1.0-0:amd64 (238-5+b1) ... Setting up libfmt10:amd64 (10.1.1+ds1-4) ... Setting up libzvbi-common (0.2.43-2) ... Setting up libngtcp2-crypto-gnutls8:amd64 (1.9.1-1) ... Setting up qtchooser (66-2) ... Setting up libgstreamer1.0-0:amd64 (1.24.10-2) ... Setcap worked! gst-ptp-helper is not suid! Setting up libp11-kit-dev:amd64 (0.25.5-2+b1) ... Setting up libmp3lame0:amd64 (3.100-6+b3) ... Setting up libblas-dev:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/blas/libblas.so to provide /usr/lib/x86_64-linux-gnu/libblas.so (libblas.so-x86_64-linux-gnu) in auto mode Setting up libsz2:amd64 (1.1.3-1+b1) ... Setting up libvorbisenc2:amd64 (1.3.7-2+b1) ... Setting up libsynctex2:amd64 (2024.20240313.70630+ds-5) ... Setting up libdvdnav4:amd64 (6.1.1-3+b1) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libodbccr2:amd64 (2.3.12-1+b3) ... Setting up gdal-plugins:amd64 (3.9.3+dfsg-1+b2) ... Setting up libwacom-common (2.13.0-1) ... Setting up libbz2-dev:amd64 (1.0.8-6) ... Setting up libxkbcommon0:amd64 (1.7.0-1) ... Setting up libpotrace0:amd64 (1.16-2+b2) ... Setting up libwayland-client0:amd64 (1.23.0-1+b1) ... Setting up automake (1:1.16.5-1.3) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up libgfortran-14-dev:amd64 (14.2.0-8) ... Setting up pinentry-curses (1.2.1-4+b1) ... Setting up x11proto-dev (2024.1-1) ... Setting up libfile-stripnondeterminism-perl (1.14.0-1) ... Setting up libxcb-dri3-0:amd64 (1.17.0-2+b1) ... Setting up libllvm19:amd64 (1:19.1.5-1) ... Setting up libx11-xcb1:amd64 (2:1.8.10-2) ... Setting up libice6:amd64 (2:1.1.1-1) ... Setting up libjsoncpp-dev:amd64 (1.9.6-3) ... Setting up libodbcinst2:amd64 (2.3.12-1+b3) ... Setting up tcl8.6 (8.6.15+dfsg-2) ... Setting up liblapack3:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/x86_64-linux-gnu/liblapack.so.3 (liblapack.so.3-x86_64-linux-gnu) in auto mode Setting up libkmlxsd1t64:amd64 (1.3.0-12+b1) ... Setting up gettext (0.22.5-2) ... Setting up libarpack2t64:amd64 (3.9.1-4) ... Setting up libxdamage1:amd64 (1:1.1.6-1+b2) ... Setting up libgmp-dev:amd64 (2:6.3.0+dfsg-3) ... Setting up libatk1.0-0t64:amd64 (2.54.0-1) ... Setting up libclang1-19 (1:19.1.5-1) ... Setting up libpdfbox-java (1:1.8.16-5) ... Setting up libxau-dev:amd64 (1:1.0.11-1) ... Setting up libxpm4:amd64 (1:3.5.17-1+b2) ... Setting up libsymspg-dev:amd64 (2.5.0-1+b1) ... Setting up qt5-qmake:amd64 (5.15.15+dfsg-2) ... Setting up libpcre2-dev:amd64 (10.44-5) ... Setting up libzvbi0t64:amd64 (0.2.43-2) ... Setting up nettle-dev:amd64 (3.10-1+b1) ... Setting up libwoff1:amd64 (1.0.2-2+b2) ... Setting up libxrender1:amd64 (1:0.9.10-1.1+b2) ... Setting up libice-dev:amd64 (2:1.1.1-1) ... Setting up dictionaries-common (1.30.2) ... Setting up voro++-dev (0.5+revert-to-0.4.6+dfsg1-1) ... Setting up libtool (2.4.7-8) ... Setting up libblosc-dev:amd64 (1.21.5+ds-1+b2) ... Setting up libfftw3-bin (3.3.10-2+b1) ... Setting up libwacom9:amd64 (2.13.0-1) ... Setting up libevent-pthreads-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up fontconfig-config (2.15.0-1.1+b1) ... Setting up libjson-c-dev:amd64 (0.18+ds-1) ... Setting up libgeos-c1t64:amd64 (3.13.0-1) ... Setting up libfyba-dev:amd64 (4.1.1-11+b1) ... Setting up libwebpdemux2:amd64 (1.4.0-0.1+b1) ... Setting up tcl8.6-dev:amd64 (8.6.15+dfsg-2) ... Setting up libevent-openssl-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libpng-dev:amd64 (1.6.44-3) ... Setting up libcommons-parent-java (56-1) ... Setting up libaec-dev:amd64 (1.1.3-1+b1) ... Setting up libavahi-common3:amd64 (0.8-15) ... Setting up libjpeg-dev:amd64 (1:2.1.5-3+b1) ... Setting up libjbig-dev:amd64 (2.1-6.1+b2) ... Setting up libcloudproviders0:amd64 (0.3.6-1+b1) ... Setting up libcommons-logging-java (1.3.0-1) ... Setting up libxext6:amd64 (2:1.3.4-1+b2) ... Setting up libnss3:amd64 (2:3.106-1) ... Setting up dbus-daemon (1.15.92-1) ... Setting up libkim-api2:amd64 (2.3.0-1+b2) ... Setting up libkim-api-dev (2.3.0-1+b2) ... Setting up libldap-2.5-0:amd64 (2.5.18+dfsg-3+b1) ... Setting up libcolord2:amd64 (1.4.7-1+b2) ... Setting up libsuperlu7:amd64 (7.0.0+dfsg1-2) ... Setting up gfortran-14-x86-64-linux-gnu (14.2.0-8) ... Setting up pkgconf:amd64 (1.8.1-4) ... Setting up libxxf86vm1:amd64 (1:1.1.4-1+b3) ... Setting up libinput-bin (1.26.2-1) ... Setting up libtbbbind-2-5:amd64 (2021.12.0-1) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up liburiparser-dev (0.9.8+dfsg-2) ... Setting up libnuma-dev:amd64 (2.0.18-1+b1) ... Setting up libnl-route-3-200:amd64 (3.7.0-0.3+b1) ... Setting up libxnvctrl0:amd64 (535.171.04-1+b1) ... Setting up librist4:amd64 (0.2.11+dfsg-1) ... Setting up libdconf1:amd64 (0.40.0-4+b3) ... Setting up libkmldom1t64:amd64 (1.3.0-12+b1) ... Setting up dh-autoreconf (20) ... Setting up libminizip-dev:amd64 (1:1.3.dfsg+really1.3.1-1+b1) ... Setting up libltdl-dev:amd64 (2.4.7-8) ... Setting up libthai0:amd64 (0.1.29-2+b1) ... Setting up ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 146 added, 0 removed; done. Setting up libvorbisfile3:amd64 (1.3.7-2+b1) ... Setting up libxdmcp-dev:amd64 (1:1.1.5-1) ... Setting up libxml2-dev:amd64 (2.12.7+dfsg+really2.9.14-0.2+b1) ... Setting up libwebp-dev:amd64 (1.4.0-0.1+b1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libptexenc1:amd64 (2024.20240313.70630+ds-5) ... Setting up libllvm17t64:amd64 (1:17.0.6-18) ... Setting up libfreetype6:amd64 (2.13.3+dfsg-1) ... Setting up libtiff-dev:amd64 (4.5.1+git230720-5) ... Setting up libopenjp2-7-dev:amd64 (2.5.0-2+b4) ... Setting up libxfixes3:amd64 (1:6.0.0-2+b2) ... Setting up libldap-dev:amd64 (2.5.18+dfsg-3+b1) ... Setting up libgeos-dev (3.13.0-1) ... Setting up dbus (1.15.92-1) ... Running in chroot, ignoring request. invoke-rc.d: policy-rc.d denied execution of start. Setting up libopenexr-3-1-30:amd64 (3.1.5-5.1+b3) ... Setting up shared-mime-info (2.4-5+b1) ... Setting up libxinerama1:amd64 (2:1.1.4-3+b2) ... Setting up opencl-clhpp-headers (3.0~2024.10.24-2) ... Setting up libx265-209:amd64 (3.6-3+b1) ... Setting up libxkbcommon-x11-0:amd64 (1.7.0-1) ... Setting up liblapack-dev:amd64 (3.12.0-4) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/lapack/liblapack.so to provide /usr/lib/x86_64-linux-gnu/liblapack.so (liblapack.so-x86_64-linux-gnu) in auto mode Setting up libeigen3-dev (3.4.0-4) ... Setting up libgssapi-krb5-2:amd64 (1.21.3-3) ... Setting up libxrandr2:amd64 (2:1.5.4-1+b1) ... Setting up pkg-config:amd64 (1.8.1-4) ... Setting up libgav1-1:amd64 (0.19.0-2+b2) ... Setting up ucf (3.0045) ... Setting up libssh2-1-dev:amd64 (1.11.1-1) ... Setting up libjs-sphinxdoc (8.1.3-2) ... Setting up ocl-icd-opencl-dev:amd64 (2.3.2-1+b2) ... Setting up libssh-4:amd64 (0.11.1-1) ... Setting up libevent-extra-2.1-7t64:amd64 (2.1.12-stable-10+b1) ... Setting up libhdf4-0-alt:amd64 (4.3.0-1+b1) ... Setting up libmariadb-dev (1:11.4.3-1) ... Setting up libreadline8t64:amd64 (8.2-5) ... Setting up dh-strip-nondeterminism (1.14.0-1) ... Setting up libgvpr2:amd64 (2.42.4-2+b1) ... Setting up libdrm2:amd64 (2.4.123-1) ... Setting up librttopo1:amd64 (1.1.0-3+b2) ... Setting up libnl-3-dev:amd64 (3.7.0-0.3+b1) ... Setting up libfreexl1:amd64 (2.0.0-1+b3) ... Setting up libva-drm2:amd64 (2.22.0-1+b1) ... Setting up groff-base (1.23.0-6) ... Setting up libvdpau1:amd64 (1.5-3+b1) ... Setting up libwayland-cursor0:amd64 (1.23.0-1+b1) ... Setting up xml-core (0.19) ... Setting up tcl (8.6.14) ... Setting up libxslt1.1:amd64 (1.1.35-1.1+b1) ... Setting up gpgconf (2.2.45-2) ... Setting up hunspell-en-us (1:2020.12.07-3) ... Setting up libpam-systemd:amd64 (257-2) ... Setting up libharfbuzz0b:amd64 (10.1.0-1) ... Setting up libgdk-pixbuf-2.0-0:amd64 (2.42.12+dfsg-1+b1) ... Setting up libarmadillo14 (1:14.2.1+dfsg-1+b1) ... Setting up libhwloc-dev:amd64 (2.11.2-1) ... Setting up libamd-comgr2:amd64 (6.0+git20231212.4510c28+dfsg-3+b2) ... Setting up libxss1:amd64 (1:1.2.3-1+b2) ... Setting up libfontconfig1:amd64 (2.15.0-1.1+b1) ... Setting up ca-certificates-java (20240118) ... No JRE found. Skipping Java certificates setup. Setting up libbluray2:amd64 (1:1.3.4-1+b2) ... Setting up gfortran-14 (14.2.0-8) ... Setting up libsuperlu-dev:amd64 (7.0.0+dfsg1-2) ... Setting up libva-x11-2:amd64 (2.22.0-1+b1) ... Setting up libsm6:amd64 (2:1.2.4-1) ... Setting up libarchive13t64:amd64 (3.7.4-1.1) ... Setting up libpython3.13-stdlib:amd64 (3.13.1-2) ... Setting up libfftw3-dev:amd64 (3.3.10-2+b1) ... Setting up unixodbc-dev:amd64 (2.3.12-1+b3) ... Setting up libopenmpt0t64:amd64 (0.7.12-1) ... Setting up libavahi-client3:amd64 (0.8-15) ... Setting up gpg (2.2.45-2) ... Setting up libclang-cpp19 (1:19.1.5-1) ... Setting up libdrm-amdgpu1:amd64 (2.4.123-1) ... Setting up libpython3.13:amd64 (3.13.1-2) ... Setting up libgnutls28-dev:amd64 (3.8.8-2) ... Setting up libmariadb-dev-compat (1:11.4.3-1) ... Setting up libinput10:amd64 (1.26.2-1) ... Setting up libpaper1:amd64 (1.1.29+b2) ... Creating config file /etc/papersize with new version Setting up gtk-update-icon-cache (4.16.7+ds-1) ... Setting up librttopo-dev:amd64 (1.1.0-3+b2) ... Setting up libnghttp2-dev:amd64 (1.64.0-1) ... Setting up libibverbs1:amd64 (52.0-2+b1) ... Setting up fontconfig (2.15.0-1.1+b1) ... Regenerating fonts cache... done. Setting up libavif16:amd64 (1.1.1-1) ... Setting up libxft2:amd64 (2.3.6-1+b2) ... Setting up libarpack2-dev:amd64 (3.9.1-4) ... Setting up gpg-agent (2.2.45-2) ... Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-browser.socket' -> '/usr/lib/systemd/user/gpg-agent-browser.socket'. Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-extra.socket' -> '/usr/lib/systemd/user/gpg-agent-extra.socket'. Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent-ssh.socket' -> '/usr/lib/systemd/user/gpg-agent-ssh.socket'. Created symlink '/etc/systemd/user/sockets.target.wants/gpg-agent.socket' -> '/usr/lib/systemd/user/gpg-agent.socket'. Setting up libxcb1-dev:amd64 (1.17.0-2+b1) ... Setting up libzmq5:amd64 (4.3.5-1+b3) ... Setting up openjdk-21-jre-headless:amd64 (21.0.5+11-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/java to provide /usr/bin/java (java) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jpackage to provide /usr/bin/jpackage (jpackage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/keytool to provide /usr/bin/keytool (keytool) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/rmiregistry to provide /usr/bin/rmiregistry (rmiregistry) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/lib/jexec to provide /usr/bin/jexec (jexec) in auto mode Setting up libxi6:amd64 (2:1.8.2-1) ... Setting up libcurl4t64:amd64 (8.11.1-1) ... Setting up libtirpc3t64:amd64 (1.3.4+ds-1.3+b1) ... Setting up ibverbs-providers:amd64 (52.0-2+b1) ... Setting up libogdi4.1:amd64 (4.1.1+ds-5) ... Setting up libenchant-2-2:amd64 (2.3.3-2+b3) ... Setting up python3.13 (3.13.1-2) ... Setting up python3-pip-whl (24.3.1+dfsg-1) ... Setting up libsm-dev:amd64 (2:1.2.4-1) ... Setting up libdrm-radeon1:amd64 (2.4.123-1) ... Setting up openssh-client (1:9.9p1-3) ... Setting up libfreexl-dev:amd64 (2.0.0-1+b3) ... Setting up libxtst6:amd64 (2:1.2.3-1.1+b2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libtk8.6:amd64 (8.6.15-1) ... Setting up libxcursor1:amd64 (1:1.2.2-1+b1) ... Setting up gpgsm (2.2.45-2) ... Setting up libpango-1.0-0:amd64 (1.55.0+ds-3) ... Setting up libdrm-intel1:amd64 (2.4.123-1) ... Setting up libpq5:amd64 (17.2-1) ... Setting up libx11-dev:amd64 (2:1.8.10-2) ... Setting up libcurl3t64-gnutls:amd64 (8.11.1-1) ... Setting up libjxl0.9:amd64 (0.9.2-10+b1) ... Setting up libgstreamer-plugins-base1.0-0:amd64 (1.24.10-1) ... Setting up libpq-dev (17.2-1) ... Setting up libtbb12:amd64 (2021.12.0-1) ... Setting up libkmlengine1t64:amd64 (1.3.0-12+b1) ... Setting up libpaper-utils (1.1.29+b2) ... Setting up libxerces-c3.2t64:amd64 (3.2.4+debian-1.3+b1) ... Setting up xfonts-utils (1:7.7+7) ... Setting up libhwloc-plugins:amd64 (2.11.2-1) ... Setting up man-db (2.13.0-1) ... Not building database; man-db/auto-update is not 'true'. Created symlink '/etc/systemd/system/timers.target.wants/man-db.timer' -> '/usr/lib/systemd/system/man-db.timer'. Setting up gfortran-x86-64-linux-gnu (4:14.2.0-1) ... Setting up libavutil59:amd64 (7:7.1-3) ... Setting up gfortran (4:14.2.0-1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libcairo2:amd64 (1.18.2-2) ... Setting up libfreetype-dev:amd64 (2.13.3+dfsg-1) ... Setting up tex-common (6.18) ... update-language: texlive-base not installed and configured, doing nothing! Setting up libnl-route-3-dev:amd64 (3.7.0-0.3+b1) ... Setting up dirmngr (2.2.45-2) ... Created symlink '/etc/systemd/user/sockets.target.wants/dirmngr.socket' -> '/usr/lib/systemd/user/dirmngr.socket'. Setting up dbus-user-session (1.15.92-1) ... Setting up libswresample5:amd64 (7:7.1-3) ... Setting up libqt5core5t64:amd64 (5.15.15+dfsg-2) ... Setting up libswscale8:amd64 (7:7.1-3) ... Setting up doxygen (1.9.8+ds-2+b3) ... Setting up libtirpc-dev:amd64 (1.3.4+ds-1.3+b1) ... Setting up libcfitsio10t64:amd64 (4.5.0-5) ... Setting up adwaita-icon-theme (47.0-2) ... update-alternatives: using /usr/share/icons/Adwaita/cursor.theme to provide /usr/share/icons/default/index.theme (x-cursor-theme) in auto mode Setting up libxerces-c-dev:amd64 (3.2.4+debian-1.3+b1) ... Setting up libgssrpc4t64:amd64 (1.21.3-3) ... Setting up libatspi2.0-0t64:amd64 (2.54.0-1) ... Setting up libraqm0:amd64 (0.10.2-1) ... Setting up libpython3.13-dev:amd64 (3.13.1-2) ... Setting up sphinx-common (8.1.3-2) ... Setting up libxt6t64:amd64 (1:1.2.1-1.2+b1) ... Setting up librtmp-dev:amd64 (2.4+20151223.gitfa8646d.1-2+b5) ... Setting up qtattributionsscanner-qt5 (5.15.15-4) ... Setting up libevent-dev (2.1.12-stable-10+b1) ... Setting up libpmix2t64:amd64 (5.0.4-1) ... Setting up git (1:2.45.2-1.2) ... Setting up tcl-dev:amd64 (8.6.14) ... Setting up libxext-dev:amd64 (2:1.3.4-1+b2) ... Setting up libhdf5-310:amd64 (1.14.5+repack-1) ... Setting up libtheora0:amd64 (1.1.1+dfsg.1-17) ... Setting up libnsl2:amd64 (1.3.0-3+b3) ... Setting up gnupg (2.2.45-2) ... Setting up libqt5sql5t64:amd64 (5.15.15+dfsg-2) ... Setting up cmake (3.31.2-1) ... Setting up librdmacm1t64:amd64 (52.0-2+b1) ... Setting up libcairo-gobject2:amd64 (1.18.2-2) ... Setting up libgpgme11t64:amd64 (1.24.0-2) ... Setting up libtbb-dev:amd64 (2021.12.0-1) ... Setting up libkmlconvenience1t64:amd64 (1.3.0-12+b1) ... Setting up libpangoft2-1.0-0:amd64 (1.55.0+ds-3) ... Setting up libhdf5-fortran-310:amd64 (1.14.5+repack-1) ... Setting up libxrender-dev:amd64 (1:0.9.10-1.1+b2) ... Setting up libogdi-dev (4.1.1+ds-5) ... Setting up libfltk1.3t64:amd64 (1.3.8-6.1+b1) ... Setting up libcups2t64:amd64 (2.4.10-2) ... Setting up tex-gyre (20180621-6) ... Setting up libhsakmt1:amd64 (6.1.2+ds-1) ... Setting up libpangocairo-1.0-0:amd64 (1.55.0+ds-3) ... Setting up libkadm5clnt-mit12:amd64 (1.21.3-3) ... Setting up libhdf5-cpp-310:amd64 (1.14.5+repack-1) ... Setting up default-libmysqlclient-dev:amd64 (1.1.1) ... Setting up libavutil-dev:amd64 (7:7.1-3) ... Setting up libatk-bridge2.0-0t64:amd64 (2.54.0-1) ... Setting up tk8.6 (8.6.15-1) ... Setting up libfabric1:amd64 (1.17.0-3.1) ... Setting up libgpgmepp6t64:amd64 (1.24.0-2) ... Setting up libfltk-images1.3t64:amd64 (1.3.8-6.1+b1) ... Setting up libhdf5-hl-310:amd64 (1.14.5+repack-1) ... Setting up mesa-libgallium:amd64 (24.2.8-1) ... Setting up libnetcdf19t64:amd64 (1:4.9.2-7+b1) ... Setting up libxmu6:amd64 (2:1.1.3-3+b3) ... Setting up libqt5dbus5t64:amd64 (5.15.15+dfsg-2) ... Setting up libcfitsio-dev:amd64 (4.5.0-5) ... Setting up libkmlregionator1t64:amd64 (1.3.0-12+b1) ... Setting up libpython3.12-stdlib:amd64 (3.12.8-2) ... Setting up libqt5sql5-sqlite:amd64 (5.15.15+dfsg-2) ... Setting up libproj25:amd64 (9.5.1-1) ... Setting up libkdb5-10t64:amd64 (1.21.3-3) ... Setting up libgbm1:amd64 (24.2.8-1) ... Setting up libswresample-dev:amd64 (7:7.1-3) ... Setting up libfontconfig-dev:amd64 (2.15.0-1.1+b1) ... Setting up python3.13-dev (3.13.1-2) ... Setting up qdoc-qt5 (5.15.15-4) ... Setting up libqt5concurrent5t64:amd64 (5.15.15+dfsg-2) ... Setting up preview-latex-style (13.2-1) ... Setting up python3.12 (3.12.8-2) ... Setting up libqt5positioning5:amd64 (5.15.15+dfsg-2) ... Setting up libgl1-mesa-dri:amd64 (24.2.8-1) ... Setting up libqt5network5t64:amd64 (5.15.15+dfsg-2) ... Setting up libqt5xml5t64:amd64 (5.15.15+dfsg-2) ... Setting up debhelper (13.20) ... Setting up dconf-service (0.40.0-4+b3) ... Setting up libxaw7:amd64 (2:1.0.16-1) ... Setting up libqt5test5t64:amd64 (5.15.15+dfsg-2) ... Setting up libibverbs-dev:amd64 (52.0-2+b1) ... Setting up libxss-dev:amd64 (1:1.2.3-1+b2) ... Setting up libgeotiff5:amd64 (1.7.3-1+b1) ... Setting up librsvg2-2:amd64 (2.59.2+dfsg-1) ... Setting up libpython3.12t64:amd64 (3.12.8-2) ... Setting up qtbase5-dev-tools (5.15.15+dfsg-2) ... Setting up libegl-mesa0:amd64 (24.2.8-1) ... Setting up libtheora-dev:amd64 (1.1.1+dfsg.1-17) ... Setting up libxt-dev:amd64 (1:1.2.1-1.2+b1) ... Setting up libqt5qml5:amd64 (5.15.15+dfsg-3) ... Setting up libswscale-dev:amd64 (7:7.1-3) ... Setting up libavcodec61:amd64 (7:7.1-3) ... Setting up libqt5webchannel5:amd64 (5.15.15-2) ... Setting up texlive-binaries (2024.20240313.70630+ds-5) ... update-alternatives: using /usr/bin/xdvi-xaw to provide /usr/bin/xdvi.bin (xdvi.bin) in auto mode update-alternatives: using /usr/bin/bibtex.original to provide /usr/bin/bibtex (bibtex) in auto mode Setting up libhsa-runtime64-1:amd64 (6.1.2-2) ... Setting up libkadm5srv-mit12:amd64 (1.21.3-3) ... Setting up libegl1:amd64 (1.7.0-1+b2) ... Setting up libpoppler140:amd64 (24.08.0-3) ... Setting up libqt5sensors5:amd64 (5.15.15-2) ... Setting up htmldoc (1.9.20-1) ... Setting up tk (8.6.14) ... Setting up texlive-base (2024.20241115-1) ... tl-paper: setting paper size for dvips to a4: /var/lib/texmf/dvips/config/config-paper.ps tl-paper: setting paper size for dvipdfmx to a4: /var/lib/texmf/dvipdfmx/dvipdfmx-paper.cfg tl-paper: setting paper size for xdvi to a4: /var/lib/texmf/xdvi/XDvi-paper tl-paper: setting paper size for pdftex to a4: /var/lib/texmf/tex/generic/tex-ini-files/pdftexconfig.tex Setting up libpython3-stdlib:amd64 (3.12.7-1) ... Setting up libxft-dev:amd64 (2.3.6-1+b2) ... Setting up libspatialite8t64:amd64 (5.1.0-3+b2) ... Setting up krb5-multidev:amd64 (1.21.3-3) ... Setting up libpoppler-dev:amd64 (24.08.0-3) ... Setting up libhdf5-hl-cpp-310:amd64 (1.14.5+repack-1) ... Setting up libkml-dev:amd64 (1.3.0-12+b1) ... Setting up libhdf5-hl-fortran-310:amd64 (1.14.5+repack-1) ... Setting up libqt5qmlmodels5:amd64 (5.15.15+dfsg-3) ... Setting up libfontconfig1-dev:amd64 (2.15.0-1.1+b1) ... Setting up libglx-mesa0:amd64 (24.2.8-1) ... Setting up libglx0:amd64 (1.7.0-1+b2) ... Setting up dconf-gsettings-backend:amd64 (0.40.0-4+b3) ... Setting up python3.12-venv (3.12.8-2) ... Setting up libavcodec-dev:amd64 (7:7.1-3) ... Setting up libpoppler-private-dev:amd64 (24.08.0-3) ... Setting up python3 (3.12.7-1) ... Setting up libpython3.12-dev:amd64 (3.12.8-2) ... Setting up python3-zipp (3.21.0-1) ... Setting up python3-autocommand (2.2.2-3) ... Setting up python3-markupsafe (2.1.5-1+b2) ... Setting up python3-wheel (0.45.1-1) ... Setting up libavformat61:amd64 (7:7.1-3) ... Setting up libqt5qmlworkerscript5:amd64 (5.15.15+dfsg-3) ... Setting up libkrb5-dev:amd64 (1.21.3-3) ... Setting up python3-roman (4.2-1) ... Setting up python3-jinja2 (3.1.3-1) ... Setting up python3-packaging (24.2-1) ... Setting up libgl1:amd64 (1.7.0-1+b2) ... Setting up python3-venv (3.12.7-1) ... Setting up libamdhip64-5 (5.7.1-5) ... Setting up python3-pyproject-hooks (1.2.0-1) ... Setting up python3-enchant (3.2.2-1) ... Setting up texlive-latex-base (2024.20241115-1) ... Setting up python3-certifi (2024.8.30+dfsg-1) ... Setting up libcurl4-openssl-dev:amd64 (8.11.1-1) ... Setting up python3-snowballstemmer (2.2.0-4) ... Setting up texlive-latex-recommended (2024.20241115-1) ... Setting up libhdf5-dev (1.14.5+repack-1) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-serial.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up libproj-dev:amd64 (9.5.1-1) ... Setting up python3-idna (3.8-2) ... Setting up python3.12-dev (3.12.8-2) ... Setting up libnetcdf-dev (1:4.9.2-7+b1) ... Setting up python3-typing-extensions (4.12.2-2) ... Setting up libspatialite-dev:amd64 (5.1.0-3+b2) ... Setting up libglew2.2:amd64 (2.2.0-4+b2) ... Setting up python3-toml (0.10.2-1) ... Setting up texlive-pictures (2024.20241115-1) ... Setting up python3-installer (0.7.0+dfsg1-3) ... Setting up python3-urllib3 (2.2.3-4) ... Setting up tk8.6-dev:amd64 (8.6.15-1) ... Setting up texlive-fonts-recommended (2024.20241115-1) ... Setting up libglx-dev:amd64 (1.7.0-1+b2) ... Setting up python3-build (1.2.2-1) ... Setting up libgl-dev:amd64 (1.7.0-1+b2) ... Setting up libgtk-3-common (3.24.43-4) ... Setting up python3-imagesize (1.4.1-1) ... Setting up python3-more-itertools (10.5.0-1) ... Setting up libucx0:amd64 (1.17.0+ds-3) ... Setting up libvulkan-dev:amd64 (1.3.296.0-1) ... Setting up libpython3-dev:amd64 (3.12.7-1) ... Setting up python3-importlib-metadata (8.5.0-1) ... Setting up python3-jaraco.functools (4.1.0-1) ... Setting up python3-jaraco.context (6.0.0-1) ... Setting up libegl-dev:amd64 (1.7.0-1+b2) ... Setting up libgeotiff-dev:amd64 (1.7.3-1+b1) ... Setting up python3-defusedxml (0.7.1-3) ... Setting up python3-charset-normalizer (3.4.0-1+b1) ... Setting up python3-alabaster (0.7.16-0.1) ... Setting up python3-typeguard (4.4.1-1) ... Setting up latexmk (1:4.85-1) ... Setting up python3-all (3.12.7-1) ... Setting up texlive-latex-extra (2024.20241115-1) ... Setting up libavformat-dev:amd64 (7:7.1-3) ... Setting up libgl2ps1.4 (1.4.2+dfsg1-2) ... Setting up libarmadillo-dev (1:14.2.1+dfsg-1+b1) ... Setting up python3-inflect (7.3.1-2) ... Setting up libqt5gui5t64:amd64 (5.15.15+dfsg-2) ... Setting up tk-dev:amd64 (8.6.14) ... Setting up libpython3-all-dev:amd64 (3.12.7-1) ... Setting up python3-jaraco.text (4.0.0-1) ... Setting up python3-dev (3.12.7-1) ... Setting up libgtk-3-0t64:amd64 (3.24.43-4) ... Setting up libhdf4-alt-dev (4.3.0-1+b1) ... Setting up libglu1-mesa-dev:amd64 (9.0.2-1.1+b2) ... Setting up libqt5quick5:amd64 (5.15.15+dfsg-3) ... Setting up python3-pkg-resources (75.2.0-1) ... Setting up python3-all-dev (3.12.7-1) ... Setting up libqt5quickshapes5:amd64 (5.15.15+dfsg-3) ... Setting up libopenmpi40:amd64 (5.0.6-3) ... Setting up python3-setuptools (75.2.0-1) ... Setting up python3-babel (2.16.0-1) ... update-alternatives: using /usr/bin/pybabel-python3 to provide /usr/bin/pybabel (pybabel) in auto mode Setting up libqt5widgets5t64:amd64 (5.15.15+dfsg-2) ... Setting up libpnetcdf6:amd64 (1.14.0-2) ... Setting up libgl2ps-dev (1.4.2+dfsg1-2) ... Setting up libhdf5-openmpi-310:amd64 (1.14.5+repack-1) ... Setting up libqt5help5:amd64 (5.15.15-4) ... Setting up qt5-qmltooling-plugins:amd64 (5.15.15+dfsg-3) ... Setting up libqt5quickwidgets5:amd64 (5.15.15+dfsg-3) ... Setting up libhdf5-openmpi-fortran-310:amd64 (1.14.5+repack-1) ... Setting up libglew-dev:amd64 (2.2.0-4+b2) ... Setting up python3-pygments (2.18.0+dfsg-1) ... Setting up python3-chardet (5.2.0+dfsg-1) ... Setting up libvtk9.3:amd64 (9.3.0+dfsg1-1.1+b2) ... Setting up python3-requests (2.32.3+dfsg-1) ... Setting up vtk9 (9.3.0+dfsg1-1.1+b2) ... Setting up libpnetcdf-dev:amd64 (1.14.0-2) ... Setting up libqt5opengl5t64:amd64 (5.15.15+dfsg-2) ... Setting up libqt5quickparticles5:amd64 (5.15.15+dfsg-3) ... Setting up openmpi-bin (5.0.6-3) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: warning: skip creation of /usr/share/man/man1/mpiexec.1.gz because associated file /usr/share/man/man1/mpiexec.openmpi.1.gz (of link group mpirun) doesn't exist update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up libqt5printsupport5t64:amd64 (5.15.15+dfsg-2) ... Setting up dh-python (6.20241024) ... Setting up libhdf5-openmpi-hl-310:amd64 (1.14.5+repack-1) ... Setting up libqt5quicktest5:amd64 (5.15.15+dfsg-3) ... Setting up libhdf5-openmpi-hl-fortran-310:amd64 (1.14.5+repack-1) ... Setting up libvtk9.3-qt:amd64 (9.3.0+dfsg1-1.1+b2) ... Setting up libqt5designer5:amd64 (5.15.15-4) ... Setting up libhdf5-openmpi-hl-cpp-310:amd64 (1.14.5+repack-1) ... Setting up pybuild-plugin-pyproject (6.20241024) ... Setting up qtdeclarative5-dev-tools (5.15.15+dfsg-3) ... Setting up libhdf5-openmpi-cpp-310:amd64 (1.14.5+repack-1) ... Setting up mpi-default-bin (1.17) ... Setting up qhelpgenerator-qt5 (5.15.15-4) ... Setting up libqt5webkit5:amd64 (5.212.0~alpha4-41) ... Setting up libqt5designercomponents5:amd64 (5.15.15-4) ... Setting up python3-mpi4py (4.0.1-6+b1) ... Setting up libvtk9-java (9.3.0+dfsg1-1.1+b2) ... Setting up qtbase5-dev:amd64 (5.15.15+dfsg-2) ... Setting up qt5-assistant (5.15.15-4) ... Setting up qttools5-dev-tools (5.15.15-4) ... Setting up qtdeclarative5-dev:amd64 (5.15.15+dfsg-3) ... Setting up python3-vtk9 (9.3.0+dfsg1-1.1+b2) ... /usr/lib/python3/dist-packages/vtkmodules/util/vtkMethodParser.py:304: SyntaxWarning: invalid escape sequence '\S' patn = re.compile (" \S") /usr/lib/python3/dist-packages/vtkmodules/util/vtkMethodParser.py:304: SyntaxWarning: invalid escape sequence '\S' patn = re.compile (" \S") Setting up libqt5opengl5-dev:amd64 (5.15.15+dfsg-2) ... Setting up libqt5webkit5-dev:amd64 (5.212.0~alpha4-41) ... Setting up qttools5-dev:amd64 (5.15.15-4) ... Setting up qttools5-private-dev:amd64 (5.15.15-4) ... Setting up libheif-plugin-dav1d:amd64 (1.19.3-1) ... Setting up libheif-plugin-libde265:amd64 (1.19.3-1) ... Setting up libheif1:amd64 (1.19.3-1) ... Setting up libheif-dev:amd64 (1.19.3-1) ... Setting up libgd3:amd64 (2.3.3-12+b1) ... Setting up libgvc6 (2.42.4-2+b1) ... Setting up libgdal35:amd64 (3.9.3+dfsg-1+b2) ... Setting up graphviz (2.42.4-2+b1) ... Setting up libgdal-dev (3.9.3+dfsg-1+b2) ... Processing triggers for libc-bin (2.40-4) ... Processing triggers for systemd (257-2) ... Processing triggers for ca-certificates-java (20240118) ... Adding debian:ACCVRAIZ1.pem Adding debian:AC_RAIZ_FNMT-RCM.pem Adding debian:AC_RAIZ_FNMT-RCM_SERVIDORES_SEGUROS.pem Adding debian:ANF_Secure_Server_Root_CA.pem Adding debian:Actalis_Authentication_Root_CA.pem Adding debian:AffirmTrust_Commercial.pem Adding debian:AffirmTrust_Networking.pem Adding debian:AffirmTrust_Premium.pem Adding debian:AffirmTrust_Premium_ECC.pem Adding debian:Amazon_Root_CA_1.pem Adding debian:Amazon_Root_CA_2.pem Adding debian:Amazon_Root_CA_3.pem Adding debian:Amazon_Root_CA_4.pem Adding debian:Atos_TrustedRoot_2011.pem Adding debian:Atos_TrustedRoot_Root_CA_ECC_TLS_2021.pem Adding debian:Atos_TrustedRoot_Root_CA_RSA_TLS_2021.pem Adding debian:Autoridad_de_Certificacion_Firmaprofesional_CIF_A62634068.pem Adding debian:BJCA_Global_Root_CA1.pem Adding debian:BJCA_Global_Root_CA2.pem Adding debian:Baltimore_CyberTrust_Root.pem Adding debian:Buypass_Class_2_Root_CA.pem Adding debian:Buypass_Class_3_Root_CA.pem Adding debian:CA_Disig_Root_R2.pem Adding debian:CFCA_EV_ROOT.pem Adding debian:COMODO_Certification_Authority.pem Adding debian:COMODO_ECC_Certification_Authority.pem Adding debian:COMODO_RSA_Certification_Authority.pem Adding debian:Certainly_Root_E1.pem Adding debian:Certainly_Root_R1.pem Adding debian:Certigna.pem Adding debian:Certigna_Root_CA.pem Adding debian:Certum_EC-384_CA.pem Adding debian:Certum_Trusted_Network_CA.pem Adding debian:Certum_Trusted_Network_CA_2.pem Adding debian:Certum_Trusted_Root_CA.pem Adding debian:CommScope_Public_Trust_ECC_Root-01.pem Adding debian:CommScope_Public_Trust_ECC_Root-02.pem Adding debian:CommScope_Public_Trust_RSA_Root-01.pem Adding debian:CommScope_Public_Trust_RSA_Root-02.pem Adding debian:Comodo_AAA_Services_root.pem Adding debian:D-TRUST_BR_Root_CA_1_2020.pem Adding debian:D-TRUST_EV_Root_CA_1_2020.pem Adding debian:D-TRUST_Root_Class_3_CA_2_2009.pem Adding debian:D-TRUST_Root_Class_3_CA_2_EV_2009.pem Adding debian:DigiCert_Assured_ID_Root_CA.pem Adding debian:DigiCert_Assured_ID_Root_G2.pem Adding debian:DigiCert_Assured_ID_Root_G3.pem Adding debian:DigiCert_Global_Root_CA.pem Adding debian:DigiCert_Global_Root_G2.pem Adding debian:DigiCert_Global_Root_G3.pem Adding debian:DigiCert_High_Assurance_EV_Root_CA.pem Adding debian:DigiCert_TLS_ECC_P384_Root_G5.pem Adding debian:DigiCert_TLS_RSA4096_Root_G5.pem Adding debian:DigiCert_Trusted_Root_G4.pem Adding debian:Entrust.net_Premium_2048_Secure_Server_CA.pem Adding debian:Entrust_Root_Certification_Authority.pem Adding debian:Entrust_Root_Certification_Authority_-_EC1.pem Adding debian:Entrust_Root_Certification_Authority_-_G2.pem Adding debian:Entrust_Root_Certification_Authority_-_G4.pem Adding debian:GDCA_TrustAUTH_R5_ROOT.pem Adding debian:GLOBALTRUST_2020.pem Adding debian:GTS_Root_R1.pem Adding debian:GTS_Root_R2.pem Adding debian:GTS_Root_R3.pem Adding debian:GTS_Root_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R4.pem Adding debian:GlobalSign_ECC_Root_CA_-_R5.pem Adding debian:GlobalSign_Root_CA.pem Adding debian:GlobalSign_Root_CA_-_R3.pem Adding debian:GlobalSign_Root_CA_-_R6.pem Adding debian:GlobalSign_Root_E46.pem Adding debian:GlobalSign_Root_R46.pem Adding debian:Go_Daddy_Class_2_CA.pem Adding debian:Go_Daddy_Root_Certificate_Authority_-_G2.pem Adding debian:HARICA_TLS_ECC_Root_CA_2021.pem Adding debian:HARICA_TLS_RSA_Root_CA_2021.pem Adding debian:Hellenic_Academic_and_Research_Institutions_ECC_RootCA_2015.pem Adding debian:Hellenic_Academic_and_Research_Institutions_RootCA_2015.pem Adding debian:HiPKI_Root_CA_-_G1.pem Adding debian:Hongkong_Post_Root_CA_3.pem Adding debian:ISRG_Root_X1.pem Adding debian:ISRG_Root_X2.pem Adding debian:IdenTrust_Commercial_Root_CA_1.pem Adding debian:IdenTrust_Public_Sector_Root_CA_1.pem Adding debian:Izenpe.com.pem Adding debian:Microsec_e-Szigno_Root_CA_2009.pem Adding debian:Microsoft_ECC_Root_Certificate_Authority_2017.pem Adding debian:Microsoft_RSA_Root_Certificate_Authority_2017.pem Adding debian:NAVER_Global_Root_Certification_Authority.pem Adding debian:NetLock_Arany_=Class_Gold=_Főtanúsítvány.pem Adding debian:OISTE_WISeKey_Global_Root_GB_CA.pem Adding debian:OISTE_WISeKey_Global_Root_GC_CA.pem Adding debian:QuoVadis_Root_CA_1_G3.pem Adding debian:QuoVadis_Root_CA_2.pem Adding debian:QuoVadis_Root_CA_2_G3.pem Adding debian:QuoVadis_Root_CA_3.pem Adding debian:QuoVadis_Root_CA_3_G3.pem Adding debian:SSL.com_EV_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_EV_Root_Certification_Authority_RSA_R2.pem Adding debian:SSL.com_Root_Certification_Authority_ECC.pem Adding debian:SSL.com_Root_Certification_Authority_RSA.pem Adding debian:SSL.com_TLS_ECC_Root_CA_2022.pem Adding debian:SSL.com_TLS_RSA_Root_CA_2022.pem Adding debian:SZAFIR_ROOT_CA2.pem Adding debian:Sectigo_Public_Server_Authentication_Root_E46.pem Adding debian:Sectigo_Public_Server_Authentication_Root_R46.pem Adding debian:SecureSign_RootCA11.pem Adding debian:SecureTrust_CA.pem Adding debian:Secure_Global_CA.pem Adding debian:Security_Communication_ECC_RootCA1.pem Adding debian:Security_Communication_RootCA2.pem Adding debian:Security_Communication_RootCA3.pem Adding debian:Security_Communication_Root_CA.pem Adding debian:Starfield_Class_2_CA.pem Adding debian:Starfield_Root_Certificate_Authority_-_G2.pem Adding debian:Starfield_Services_Root_Certificate_Authority_-_G2.pem Adding debian:SwissSign_Gold_CA_-_G2.pem Adding debian:SwissSign_Silver_CA_-_G2.pem Adding debian:T-TeleSec_GlobalRoot_Class_2.pem Adding debian:T-TeleSec_GlobalRoot_Class_3.pem Adding debian:TUBITAK_Kamu_SM_SSL_Kok_Sertifikasi_-_Surum_1.pem Adding debian:TWCA_Global_Root_CA.pem Adding debian:TWCA_Root_Certification_Authority.pem Adding debian:TeliaSonera_Root_CA_v1.pem Adding debian:Telia_Root_CA_v2.pem Adding debian:TrustAsia_Global_Root_CA_G3.pem Adding debian:TrustAsia_Global_Root_CA_G4.pem Adding debian:Trustwave_Global_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P256_Certification_Authority.pem Adding debian:Trustwave_Global_ECC_P384_Certification_Authority.pem Adding debian:TunTrust_Root_CA.pem Adding debian:UCA_Extended_Validation_Root.pem Adding debian:UCA_Global_G2_Root.pem Adding debian:USERTrust_ECC_Certification_Authority.pem Adding debian:USERTrust_RSA_Certification_Authority.pem Adding debian:XRamp_Global_CA_Root.pem Adding debian:certSIGN_ROOT_CA.pem Adding debian:certSIGN_Root_CA_G2.pem Adding debian:e-Szigno_Root_CA_2017.pem Adding debian:ePKI_Root_Certification_Authority.pem Adding debian:emSign_ECC_Root_CA_-_C3.pem Adding debian:emSign_ECC_Root_CA_-_G3.pem Adding debian:emSign_Root_CA_-_C1.pem Adding debian:emSign_Root_CA_-_G1.pem Adding debian:vTrus_ECC_Root_CA.pem Adding debian:vTrus_Root_CA.pem done. Setting up openjdk-21-jre:amd64 (21.0.5+11-1) ... Setting up openjdk-21-jdk-headless:amd64 (21.0.5+11-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jar to provide /usr/bin/jar (jar) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jarsigner to provide /usr/bin/jarsigner (jarsigner) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javac to provide /usr/bin/javac (javac) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javadoc to provide /usr/bin/javadoc (javadoc) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/javap to provide /usr/bin/javap (javap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jcmd to provide /usr/bin/jcmd (jcmd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdb to provide /usr/bin/jdb (jdb) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeprscan to provide /usr/bin/jdeprscan (jdeprscan) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jdeps to provide /usr/bin/jdeps (jdeps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jfr to provide /usr/bin/jfr (jfr) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jimage to provide /usr/bin/jimage (jimage) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jinfo to provide /usr/bin/jinfo (jinfo) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jlink to provide /usr/bin/jlink (jlink) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmap to provide /usr/bin/jmap (jmap) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jmod to provide /usr/bin/jmod (jmod) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jps to provide /usr/bin/jps (jps) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jrunscript to provide /usr/bin/jrunscript (jrunscript) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jshell to provide /usr/bin/jshell (jshell) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstack to provide /usr/bin/jstack (jstack) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstat to provide /usr/bin/jstat (jstat) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jstatd to provide /usr/bin/jstatd (jstatd) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jwebserver to provide /usr/bin/jwebserver (jwebserver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/serialver to provide /usr/bin/serialver (serialver) in auto mode update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jhsdb to provide /usr/bin/jhsdb (jhsdb) in auto mode Setting up default-jre-headless (2:1.21-76) ... Setting up default-jre (2:1.21-76) ... Setting up openjdk-21-jdk:amd64 (21.0.5+11-1) ... update-alternatives: using /usr/lib/jvm/java-21-openjdk-amd64/bin/jconsole to provide /usr/bin/jconsole (jconsole) in auto mode Setting up default-jdk-headless (2:1.21-76) ... Setting up default-jdk (2:1.21-76) ... Processing triggers for sgml-base (1.31) ... Setting up docutils-common (0.21.2+dfsg-2) ... Processing triggers for sgml-base (1.31) ... Setting up python3-docutils (0.21.2+dfsg-2) ... Setting up python3-sphinx (8.1.3-2) ... Setting up libpmix-dev:amd64 (5.0.4-1) ... Setting up python3-sphinxcontrib.spelling (7.7.0-1) ... Setting up python3-breathe (4.35.0-3) ... Setting up python3-sphinxcontrib.jquery (4.1-5) ... Setting up python3-sphinx-tabs (3.4.7-1) ... Setting up libopenmpi-dev:amd64 (5.0.6-3) ... update-alternatives: using /usr/lib/x86_64-linux-gnu/openmpi/include to provide /usr/include/x86_64-linux-gnu/mpi (mpi-x86_64-linux-gnu) in auto mode Setting up libhdf5-openmpi-dev (1.14.5+repack-1) ... update-alternatives: using /usr/bin/h5pcc.openmpi to provide /usr/bin/h5pcc (h5pcc) in auto mode update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-openmpi.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode update-alternatives: updating alternative /usr/bin/mpicc.openmpi because link group mpi has changed slave links update-alternatives: using /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5-mpi.pc to provide /usr/lib/x86_64-linux-gnu/pkgconfig/hdf5.pc (hdf5.pc) in auto mode Setting up mpi-default-dev (1.17) ... Setting up libhdf5-mpi-dev:amd64 (1.14.5+repack-1) ... Setting up libvtk9-dev:amd64 (9.3.0+dfsg1-1.1+b2) ... Setting up libvtk9-qt-dev:amd64 (9.3.0+dfsg1-1.1+b2) ... Processing triggers for dictionaries-common (1.30.2) ... Processing triggers for ca-certificates (20240203) ... Updating certificates in /etc/ssl/certs... 0 added, 0 removed; done. Running hooks in /etc/ca-certificates/update.d... done. Processing triggers for tex-common (6.18) ... Running updmap-sys. This may take some time... done. Running mktexlsr /var/lib/texmf ... done. Building format(s) --all. This may take some time... done. Processing triggers for ca-certificates-java (20240118) ... done. Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.36-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/reproducible-path/lammps-20240207+dfsg/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../lammps_20240207+dfsg-2_source.changes dpkg-buildpackage: info: source package lammps dpkg-buildpackage: info: source version 20240207+dfsg-2 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Anton Gladky dpkg-source --before-build . dpkg-buildpackage: info: host architecture amd64 fakeroot debian/rules clean dh clean --with python3,sphinxdoc --sourcedirectory=cmake --builddirectory=/build/reproducible-path/lammps-20240207+dfsg/debian/build dh_auto_clean -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build debian/rules execute_after_dh_auto_clean make[1]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg' rm -rf /build/reproducible-path/lammps-20240207+dfsg/debian/build rm -rf .pybuild rm -rf python/build rm -rf python/lammps.egg-info rm -f python/examples/log.lammps if [ -d doc/html.orig ]; then \ rm -rf doc/html; \ mv doc/html.orig doc/html; \ fi rm -rf doc/docenv doc/doctrees doc/utils/sphinx-config/conf.py rm -rf doc/doxygen/xml doc/doxygen-warn.log doc/doxygen/Doxyfile make[1]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg' dh_autoreconf_clean -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build dh_clean -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build debian/rules build dh build --with python3,sphinxdoc --sourcedirectory=cmake --builddirectory=/build/reproducible-path/lammps-20240207+dfsg/debian/build dh_update_autotools_config -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build dh_autoreconf -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg' dh_auto_configure -- \ -DBUILD_SHARED_LIBS=ON \ -DCMAKE_SKIP_INSTALL_RPATH=TRUE \ -DPKG_ASPHERE=ON \ -DPKG_ATC=ON \ -DPKG_AWPMD=ON \ -DPKG_BOCS=ON \ -DPKG_BODY=ON \ -DPKG_CG-DNA=ON \ -DPKG_CG-SPICA=ON \ -DPKG_CLASS2=ON \ -DPKG_COLLOID=ON \ -DPKG_COMPRESS=ON \ -DPKG_CORESHELL=ON \ -DPKG_EXTRA-PAIR=ON \ -DPKG_DIELECTRIC=ON \ -DPKG_DIFFRACTION=ON \ -DPKG_DIPOLE=ON \ -DPKG_DPD-BASIC=ON \ -DPKG_DRUDE=ON \ -DPKG_EFF=ON \ -DPKG_ELECTRODE=ON \ -DUSE_INTERNAL_LINALG=no \ -DPKG_FEP=ON \ -DPKG_GPU=OFF \ -DPKG_GRANULAR=ON \ -DPKG_H5MD=ON \ -DPKG_KIM=ON \ -DPKG_KSPACE=ON \ -DPKG_LATBOLTZ=ON \ -DPKG_MANIFOLD=ON \ -DPKG_MANYBODY=ON \ -DPKG_MC=ON \ -DPKG_MEAM=ON \ -DPKG_MGPT=ON \ -DPKG_MISC=ON \ -DPKG_MOFFF=ON \ -DPKG_MOLFILE=ON \ -DPKG_MPIIO=ON \ -DPKG_MOLECULE=ON \ -DPKG_NETCDF=ON \ -DPKG_OPENMP==ON \ -DPKG_OPT=ON \ -DPKG_ORIENT=ON \ -DPKG_PERI=ON \ -DPKG_PHONON=ON \ -DPKG_POEMS=ON \ -DPKG_PYTHON=ON \ -DPKG_QEQ=ON \ -DPKG_QTB=ON \ -DPKG_REAXFF=OFF \ -DPKG_REPLICA=ON \ -DPKG_RIGID=ON \ -DPKG_SHOCK=ON \ -DPKG_SMTBQ=ON \ -DPKG_SNAP=ON \ -DPKG_SPH=ON \ -DPKG_SRD=ON \ -DPKG_TALLY=ON \ -DPKG_UEF=ON \ -DPKG_VTK=ON \ -DPKG_VORONOI=ON cd debian/build && DEB_PYTHON_INSTALL_LAYOUT=deb PKG_CONFIG=/usr/bin/pkg-config cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/x86_64-linux-gnu -DBUILD_SHARED_LIBS=ON -DCMAKE_SKIP_INSTALL_RPATH=TRUE -DPKG_ASPHERE=ON -DPKG_ATC=ON -DPKG_AWPMD=ON -DPKG_BOCS=ON -DPKG_BODY=ON -DPKG_CG-DNA=ON -DPKG_CG-SPICA=ON -DPKG_CLASS2=ON -DPKG_COLLOID=ON -DPKG_COMPRESS=ON -DPKG_CORESHELL=ON -DPKG_EXTRA-PAIR=ON -DPKG_DIELECTRIC=ON -DPKG_DIFFRACTION=ON -DPKG_DIPOLE=ON -DPKG_DPD-BASIC=ON -DPKG_DRUDE=ON -DPKG_EFF=ON -DPKG_ELECTRODE=ON -DUSE_INTERNAL_LINALG=no -DPKG_FEP=ON -DPKG_GPU=OFF -DPKG_GRANULAR=ON -DPKG_H5MD=ON -DPKG_KIM=ON -DPKG_KSPACE=ON -DPKG_LATBOLTZ=ON -DPKG_MANIFOLD=ON -DPKG_MANYBODY=ON -DPKG_MC=ON -DPKG_MEAM=ON -DPKG_MGPT=ON -DPKG_MISC=ON -DPKG_MOFFF=ON -DPKG_MOLFILE=ON -DPKG_MPIIO=ON -DPKG_MOLECULE=ON -DPKG_NETCDF=ON -DPKG_OPENMP==ON -DPKG_OPT=ON -DPKG_ORIENT=ON -DPKG_PERI=ON -DPKG_PHONON=ON -DPKG_POEMS=ON -DPKG_PYTHON=ON -DPKG_QEQ=ON -DPKG_QTB=ON -DPKG_REAXFF=OFF -DPKG_REPLICA=ON -DPKG_RIGID=ON -DPKG_SHOCK=ON -DPKG_SMTBQ=ON -DPKG_SNAP=ON -DPKG_SPH=ON -DPKG_SRD=ON -DPKG_TALLY=ON -DPKG_UEF=ON -DPKG_VTK=ON -DPKG_VORONOI=ON ../../cmake -- The CXX compiler identification is GNU 14.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Found Git: /usr/bin/git (found version "2.45.2") -- Running check for auto-generated files from make-based build system -- Found MPI_CXX: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") -- Looking for C++ include omp.h -- Looking for C++ include omp.h - found -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") found components: CXX -- The C compiler identification is GNU 14.2.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Looking for sgemm_ -- Looking for sgemm_ - not found -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Looking for sgemm_ -- Looking for sgemm_ - found -- Found BLAS: /usr/lib/x86_64-linux-gnu/libblas.so -- Looking for cheev_ -- Looking for cheev_ - not found -- Looking for cheev_ -- Looking for cheev_ - found -- Found LAPACK: /usr/lib/x86_64-linux-gnu/liblapack.so;/usr/lib/x86_64-linux-gnu/libblas.so -- Found JPEG: /usr/lib/x86_64-linux-gnu/libjpeg.so (found version "62") -- Found PNG: /usr/lib/x86_64-linux-gnu/libpng.so (found version "1.6.44") -- Found ZLIB: /usr/lib/x86_64-linux-gnu/libz.so (found version "1.3.1") -- Found GZIP: /usr/bin/gzip -- Could NOT find FFMPEG (missing: FFMPEG_EXECUTABLE) -- Found PkgConfig: /usr/bin/pkg-config (found version "1.8.1") -- Checking for module 'fftw3' -- Found fftw3, version 3.3.10 -- Found FFTW3: /usr/lib/x86_64-linux-gnu/libfftw3.so -- Found Python: /usr/bin/python3 (found version "3.12.8") found components: Interpreter -- Found Python: /usr/bin/python3 (found version "3.12.8") found components: Interpreter Development Development.Module Development.Embed -- Found VORO: /usr/lib/x86_64-linux-gnu/libvoro++.so -- Found NetCDF: /usr/lib/x86_64-linux-gnu/libnetcdf.so -- Found PNetCDF: /usr/lib/x86_64-linux-gnu/libpnetcdf.so -- Found Python3: /usr/bin/python3 (found suitable version "3.12.8", minimum required is "3.12") found components: Interpreter Development.Module Development.Embed -- Found GLEW: /usr/lib/x86_64-linux-gnu/libGLEW.so -- Found OpenGL: /usr/lib/x86_64-linux-gnu/libOpenGL.so found components: OpenGL GLX -- Found MPI_C: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so (found version "3.1") -- Found MPI: TRUE (found version "3.1") found components: C -- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libcrypto.so;/usr/lib/x86_64-linux-gnu/libcurl.so;/usr/lib/x86_64-linux-gnu/libpthread.a;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.a;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.14.5") found components: C HL -- Found NetCDF: /usr/include (found version "4.9.2") -- Found OGG: /usr/lib/x86_64-linux-gnu/libogg.so -- Found THEORA: /usr/lib/x86_64-linux-gnu/libtheora.so -- Found LibPROJ: /usr/lib/x86_64-linux-gnu/libproj.so (found version "9.5.1") -- Found JsonCpp: /usr/lib/x86_64-linux-gnu/libjsoncpp.so (found suitable version "1.9.6", minimum required is "0.7.0") -- Found LibXml2: /usr/lib/x86_64-linux-gnu/libxml2.so (found version "2.9.14") -- Found GL2PS: /usr/lib/x86_64-linux-gnu/libgl2ps.so (found suitable version "1.4.2", minimum required is "1.4.2") -- Found SQLite3: /usr/include (found version "3.46.1") -- Found Eigen3: /usr/include/eigen3 (found version "3.4.0") -- Found X11: /usr/include -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so -- Looking for XOpenDisplay in /usr/lib/x86_64-linux-gnu/libX11.so;/usr/lib/x86_64-linux-gnu/libXext.so - found -- Looking for gethostbyname -- Looking for gethostbyname - found -- Looking for connect -- Looking for connect - found -- Looking for remove -- Looking for remove - found -- Looking for shmat -- Looking for shmat - found -- Looking for IceConnectionNumber in ICE -- Looking for IceConnectionNumber in ICE - found -- Found EXPAT: /usr/lib/x86_64-linux-gnu/libexpat.so (found version "2.6.4") -- Found double-conversion: /usr/lib/x86_64-linux-gnu/libdouble-conversion.so -- Found LZ4: /usr/lib/x86_64-linux-gnu/liblz4.so (found version "1.9.4") -- Found LZMA: /usr/lib/x86_64-linux-gnu/liblzma.so (found version "5.6.3") -- Found TIFF: /usr/lib/x86_64-linux-gnu/libtiff.so (found version "4.5.1") -- Could NOT find freetype (missing: freetype_DIR) -- Found Freetype: /usr/lib/x86_64-linux-gnu/libfreetype.so (found version "2.13.3") -- Found utf8cpp: /usr/include/utf8cpp -- Found CURL: /usr/lib/x86_64-linux-gnu/libcurl.so (found version "8.11.1") -- Found KIM-API: /usr/lib/x86_64-linux-gnu/libkim-api.so.2.3.0 -- Checking for module 'libzstd>=1.4' -- Found libzstd, version 1.5.6 -- Looking for C++ include cmath -- Looking for C++ include cmath - found -- Found HDF5: /usr/lib/x86_64-linux-gnu/hdf5/serial/libhdf5.so;/usr/lib/x86_64-linux-gnu/libcrypto.so;/usr/lib/x86_64-linux-gnu/libcurl.so;/usr/lib/x86_64-linux-gnu/libpthread.a;/usr/lib/x86_64-linux-gnu/libsz.so;/usr/lib/x86_64-linux-gnu/libz.so;/usr/lib/x86_64-linux-gnu/libdl.a;/usr/lib/x86_64-linux-gnu/libm.so (found version "1.14.5") -- Generating style headers... -- Generating package headers... -- Generating lmpinstalledpkgs.h... -- Found Python: /usr/bin/python3 (found version "3.12.8") found components: Interpreter -- Found Python3: /usr/bin/python3 (found version "3.12.8") found components: Interpreter -- Could NOT find ClangFormat (missing: ClangFormat_EXECUTABLE) (Required is at least version "8.0") -- The following tools and libraries have been found and configured: * Git * OpenMP * LAPACK * BLAS * FFTW3 * VORO * PNetCDF * Qt5Core (required version >= 5.15.15) * Qt5Gui (required version >= 5.15.15) * GLEW * OpenGL * MPI * NetCDF * THEORA * OGG * LibPROJ * JsonCpp (required version >= 0.7.0) * LibXml2 * GL2PS (required version >= 1.4.2) * PNG * SQLite3 * Qt5OpenGL * Qt5Widgets * Qt5 (required version >= 5.15) * Eigen3 * X11 * EXPAT * double-conversion * LZ4 * LZMA * JPEG * TIFF * freetype * Freetype * TBB * Threads * utf8cpp * VTK * CURL * KIM-API (required version >= 2.2.0) * ZLIB * HDF5 * Python * Python3 -- <<< Build configuration >>> LAMMPS Version: 20240207 Operating System: Linux Debian CMake Version: 3.31.2 Build type: None Install path: /usr Generator: Unix Makefiles using /usr/bin/gmake -- Enabled packages: ASPHERE;ATC;AWPMD;BOCS;BODY;CG-DNA;CG-SPICA;CLASS2;COLLOID;COMPRESS;CORESHELL;DIELECTRIC;DIFFRACTION;DIPOLE;DPD-BASIC;DRUDE;EFF;ELECTRODE;EXTRA-PAIR;FEP;GRANULAR;H5MD;KIM;KSPACE;LATBOLTZ;MANIFOLD;MANYBODY;MC;MEAM;MGPT;MISC;MOFFF;MOLECULE;MOLFILE;NETCDF;OPENMP;OPT;ORIENT;PERI;PHONON;POEMS;PYTHON;QEQ;QTB;REPLICA;RIGID;SHOCK;SMTBQ;SPH;SRD;TALLY;UEF;VORONOI;VTK -- <<< Compilers and Flags: >>> -- C++ Compiler: /usr/bin/c++ Type: GNU Version: 14.2.0 C++ Flags: -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 Defines: LAMMPS_SMALLBIG;LAMMPS_MEMALIGN=64;LAMMPS_OMP_COMPAT=4;LAMMPS_JPEG;LAMMPS_PNG;LAMMPS_GZIP;FFT_FFTW3;FFT_FFTW_THREADS;LMP_PYTHON;LMP_HAS_NETCDF;LMP_HAS_PNETCDF;NC_64BIT_DATA=0x0020;LAMMPS_VTK;LMP_KIM_CURL;LAMMPS_ZSTD;LMP_OPENMP -- C compiler: /usr/bin/cc Type: GNU Version: 14.2.0 C Flags: -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -- <<< Linker flags: >>> -- Executable name: lmp -- Executable linker flags: -Wl,-z,relro -- Shared library flags: -Wl,-z,relro -- <<< MPI flags >>> -- MPI_defines: MPICH_SKIP_MPICXX;OMPI_SKIP_MPICXX;_MPICC_H -- MPI includes: /usr/lib/x86_64-linux-gnu/openmpi/include;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -- MPI libraries: /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so; -- <<< FFT settings >>> -- Primary FFT lib: FFTW3 -- Using double precision FFTs -- Using threaded FFTs -- Using builtin distributed FFT algorithms -- Configuring done (9.6s) -- Generating done (0.3s) -- Build files have been written to: /build/reproducible-path/lammps-20240207+dfsg/debian/build make[1]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg' 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/usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_TransferPartitionOfUnity.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_TransferPartitionOfUnity.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_TransferPartitionOfUnity.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_TransferPartitionOfUnity.cpp [ 2%] Building CXX object CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/colmatrix.cpp.o /usr/bin/c++ -I/build/reproducible-path/lammps-20240207+dfsg/lib/poems -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/colmatrix.cpp.o -MF CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/colmatrix.cpp.o.d -o CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/colmatrix.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/poems/colmatrix.cpp [ 2%] Building CXX object CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/eulerparameters.cpp.o /usr/bin/c++ -I/build/reproducible-path/lammps-20240207+dfsg/lib/poems -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD 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CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/fastmatrixops.cpp.o.d -o CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/fastmatrixops.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/poems/fastmatrixops.cpp In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_TypeDefs.h:17, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_Method.h:5, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_Coupling.h:10, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_CouplingEnergy.h:5, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_CouplingEnergy.cpp:2: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_TypeDefs.h:17, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_Method.h:5, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_Coupling.h:10, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_CouplingMomentum.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_CouplingMomentum.cpp:2: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_TypeDefs.h:17, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_Method.h:5, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_Coupling.h:10, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_CouplingMomentumEnergy.h:5, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_CouplingMomentumEnergy.cpp:2: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_TypeDefs.h:17, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_Method.h:5, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_Coupling.h:10, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_Coupling.cpp:2: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ [ 2%] Building CXX object CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/fixedpoint.cpp.o /usr/bin/c++ -I/build/reproducible-path/lammps-20240207+dfsg/lib/poems -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection 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CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/AtomToMoleculeTransfer.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/AtomToMoleculeTransfer.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/AtomToMoleculeTransfer.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/AtomToMoleculeTransfer.cpp [ 3%] Building CXX object CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/inertialframe.cpp.o /usr/bin/c++ -I/build/reproducible-path/lammps-20240207+dfsg/lib/poems -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/inertialframe.cpp.o -MF 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~~~~~~~~~^~~ make -f CMakeFiles/fix.h.dir/build.make CMakeFiles/fix.h.dir/depend make[3]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' cd /build/reproducible-path/lammps-20240207+dfsg/debian/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/lammps-20240207+dfsg/cmake /build/reproducible-path/lammps-20240207+dfsg/cmake /build/reproducible-path/lammps-20240207+dfsg/debian/build /build/reproducible-path/lammps-20240207+dfsg/debian/build /build/reproducible-path/lammps-20240207+dfsg/debian/build/CMakeFiles/fix.h.dir/DependInfo.cmake "--color=" [ 3%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/AtomicRegulator.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/AtomicRegulator.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/AtomicRegulator.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/AtomicRegulator.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/AtomicRegulator.cpp make[3]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' make -f CMakeFiles/fix.h.dir/build.make CMakeFiles/fix.h.dir/build make[3]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' [ 3%] Generating includes/lammps/fix.h /usr/bin/cmake -E copy_if_different 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'/build/reproducible-path/lammps-20240207+dfsg/debian/build' [ 5%] Built target kspace.h [ 5%] Building CXX object CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/mat4x4.cpp.o /usr/bin/c++ -I/build/reproducible-path/lammps-20240207+dfsg/lib/poems -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/mat4x4.cpp.o -MF CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/mat4x4.cpp.o.d -o CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/mat4x4.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/poems/mat4x4.cpp [ 5%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/CBLattice.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG 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-I/build/reproducible-path/lammps-20240207+dfsg/lib/poems -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/mat6x6.cpp.o -MF CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/mat6x6.cpp.o.d -o CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/mat6x6.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/poems/mat6x6.cpp [ 5%] Building CXX object CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/matrix.cpp.o /usr/bin/c++ -I/build/reproducible-path/lammps-20240207+dfsg/lib/poems -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/matrix.cpp.o -MF CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/matrix.cpp.o.d -o CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/matrix.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/poems/matrix.cpp make -f CMakeFiles/lammps.h.dir/build.make CMakeFiles/lammps.h.dir/depend make[3]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' cd /build/reproducible-path/lammps-20240207+dfsg/debian/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/lammps-20240207+dfsg/cmake /build/reproducible-path/lammps-20240207+dfsg/cmake /build/reproducible-path/lammps-20240207+dfsg/debian/build /build/reproducible-path/lammps-20240207+dfsg/debian/build 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CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/onbody.cpp.o -MF CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/onbody.cpp.o.d -o CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/onbody.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/poems/onbody.cpp In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CauchyBorn.h:4, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CauchyBorn.cpp:1: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ [ 5%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ConcentrationRegulator.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ConcentrationRegulator.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ConcentrationRegulator.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ConcentrationRegulator.cpp.o -c 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CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/poemstreenode.cpp.o -MF CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/poemstreenode.cpp.o.d -o CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/poemstreenode.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/poems/poemstreenode.cpp [ 6%] Linking CXX static library liblammps_awpmd.a /usr/bin/cmake -P CMakeFiles/awpmd.dir/cmake_clean_target.cmake /usr/bin/cmake -E cmake_link_script CMakeFiles/awpmd.dir/link.txt --verbose=1 [ 6%] Building CXX object CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/point.cpp.o /usr/bin/c++ -I/build/reproducible-path/lammps-20240207+dfsg/lib/poems -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT 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-I/build/reproducible-path/lammps-20240207+dfsg/lib/poems -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/prismaticjoint.cpp.o -MF CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/prismaticjoint.cpp.o.d -o CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/prismaticjoint.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/poems/prismaticjoint.cpp [ 6%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ElectronHeatCapacity.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ElectronHeatCapacity.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ElectronHeatCapacity.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ElectronHeatCapacity.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ElectronHeatCapacity.cpp [ 6%] Building CXX object CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/revolutejoint.cpp.o /usr/bin/c++ -I/build/reproducible-path/lammps-20240207+dfsg/lib/poems -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. 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-ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ElectronHeatFlux.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ElectronHeatFlux.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ElectronHeatFlux.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ElectronHeatFlux.cpp make -f CMakeFiles/memory.h.dir/build.make CMakeFiles/memory.h.dir/depend make[3]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' cd /build/reproducible-path/lammps-20240207+dfsg/debian/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/lammps-20240207+dfsg/cmake /build/reproducible-path/lammps-20240207+dfsg/cmake 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-DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ElectronPhononExchange.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ElectronPhononExchange.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ElectronPhononExchange.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ElectronPhononExchange.cpp [ 6%] Building CXX object CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/rigidbody.cpp.o /usr/bin/c++ -I/build/reproducible-path/lammps-20240207+dfsg/lib/poems -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/rigidbody.cpp.o -MF CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/rigidbody.cpp.o.d -o CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/rigidbody.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/poems/rigidbody.cpp In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_TypeDefs.h:17, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ElectronFlux.h:6, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ElectronFlux.cpp:1: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ [ 6%] Building CXX object CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/rowmatrix.cpp.o /usr/bin/c++ -I/build/reproducible-path/lammps-20240207+dfsg/lib/poems -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/rowmatrix.cpp.o -MF CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/rowmatrix.cpp.o.d -o 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CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/FE_Element.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/FE_Element.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/FE_Element.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/FE_Element.cpp [ 7%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ExtrinsicModelTwoTemperature.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ExtrinsicModelTwoTemperature.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ExtrinsicModelTwoTemperature.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ExtrinsicModelTwoTemperature.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ExtrinsicModelTwoTemperature.cpp make -f CMakeFiles/neigh_list.h.dir/build.make CMakeFiles/neigh_list.h.dir/depend make[3]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' cd /build/reproducible-path/lammps-20240207+dfsg/debian/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/lammps-20240207+dfsg/cmake /build/reproducible-path/lammps-20240207+dfsg/cmake /build/reproducible-path/lammps-20240207+dfsg/debian/build /build/reproducible-path/lammps-20240207+dfsg/debian/build 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-MF CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/vect4.cpp.o.d -o CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/vect4.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/poems/vect4.cpp [ 9%] Building CXX object CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/vect6.cpp.o /usr/bin/c++ -I/build/reproducible-path/lammps-20240207+dfsg/lib/poems -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/vect6.cpp.o -MF CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/vect6.cpp.o.d -o CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/vect6.cpp.o -c 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-ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/virtualrowmatrix.cpp.o -MF CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/virtualrowmatrix.cpp.o.d -o CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/virtualrowmatrix.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/poems/virtualrowmatrix.cpp [ 9%] Building CXX object CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/virtualmatrix.cpp.o /usr/bin/c++ -I/build/reproducible-path/lammps-20240207+dfsg/lib/poems -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/virtualmatrix.cpp.o -MF CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/virtualmatrix.cpp.o.d -o CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/virtualmatrix.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/poems/virtualmatrix.cpp make -f CMakeFiles/region.h.dir/build.make CMakeFiles/region.h.dir/depend make[3]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' cd /build/reproducible-path/lammps-20240207+dfsg/debian/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/lammps-20240207+dfsg/cmake /build/reproducible-path/lammps-20240207+dfsg/cmake /build/reproducible-path/lammps-20240207+dfsg/debian/build /build/reproducible-path/lammps-20240207+dfsg/debian/build 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/build/reproducible-path/lammps-20240207+dfsg/cmake /build/reproducible-path/lammps-20240207+dfsg/debian/build /build/reproducible-path/lammps-20240207+dfsg/debian/build /build/reproducible-path/lammps-20240207+dfsg/debian/build/CMakeFiles/timer.h.dir/DependInfo.cmake "--color=" [ 9%] Built target region.h make[3]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' make -f CMakeFiles/timer.h.dir/build.make CMakeFiles/timer.h.dir/build make[3]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' [ 9%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/FieldEulerIntegrator.cpp.o [ 9%] Generating includes/lammps/timer.h /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/FieldEulerIntegrator.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/FieldEulerIntegrator.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/FieldEulerIntegrator.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/FieldEulerIntegrator.cpp /usr/bin/cmake -E copy_if_different /build/reproducible-path/lammps-20240207+dfsg/src/timer.h /build/reproducible-path/lammps-20240207+dfsg/debian/build/includes/lammps/timer.h make[3]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' [ 9%] Built target timer.h In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/FE_Mesh.h:6, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/FE_Element.cpp:3: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ [ 9%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/FieldManager.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/FieldManager.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/FieldManager.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/FieldManager.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/FieldManager.cpp [ 9%] Building CXX object CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/workspace.cpp.o /usr/bin/c++ -I/build/reproducible-path/lammps-20240207+dfsg/lib/poems -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/workspace.cpp.o -MF CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/workspace.cpp.o.d -o CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/workspace.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/poems/workspace.cpp [ 9%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Function.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Function.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Function.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Function.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/Function.cpp In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/FE_Element.h:8, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/FE_Interpolate.cpp:3: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_TypeDefs.h:17, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ExtrinsicModel.h:8, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ExtrinsicModelTwoTemperature.h:6, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ExtrinsicModelTwoTemperature.cpp:2: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ [ 9%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/FundamentalAtomicQuantity.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/FundamentalAtomicQuantity.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/FundamentalAtomicQuantity.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/FundamentalAtomicQuantity.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/FundamentalAtomicQuantity.cpp make -f CMakeFiles/universe.h.dir/build.make CMakeFiles/universe.h.dir/depend make[3]: Entering directory 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Leaving directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' [ 9%] Built target universe.h [ 10%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/GhostManager.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/GhostManager.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/GhostManager.cpp.o.d -o 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"CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/virtualrowmatrix.cpp.o" "CMakeFiles/poems.dir/build/reproducible-path/lammps-20240207+dfsg/lib/poems/workspace.cpp.o" /usr/bin/ranlib liblammps_poems.a make[3]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' [ 10%] Built target poems make -f CMakeFiles/update.h.dir/build.make CMakeFiles/update.h.dir/depend make[3]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' cd /build/reproducible-path/lammps-20240207+dfsg/debian/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/lammps-20240207+dfsg/cmake /build/reproducible-path/lammps-20240207+dfsg/cmake /build/reproducible-path/lammps-20240207+dfsg/debian/build /build/reproducible-path/lammps-20240207+dfsg/debian/build /build/reproducible-path/lammps-20240207+dfsg/debian/build/CMakeFiles/update.h.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' make -f CMakeFiles/update.h.dir/build.make CMakeFiles/update.h.dir/build make[3]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' [ 10%] Generating includes/lammps/update.h /usr/bin/cmake -E copy_if_different /build/reproducible-path/lammps-20240207+dfsg/src/update.h /build/reproducible-path/lammps-20240207+dfsg/debian/build/includes/lammps/update.h make[3]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' [ 10%] Built target update.h [ 10%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ImplicitSolveOperator.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ImplicitSolveOperator.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ImplicitSolveOperator.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ImplicitSolveOperator.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ImplicitSolveOperator.cpp In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_TypeDefs.h:17, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ExtrinsicModel.h:8, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ExtrinsicModelElectrostatic.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ExtrinsicModelElectrostatic.cpp:2: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_TypeDefs.h:17, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ExtrinsicModel.h:8, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ExtrinsicModelTwoTemperature.h:6, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ExtrinsicModelDriftDiffusion.h:8, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ExtrinsicModelDriftDiffusion.cpp:2: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/FE_Element.h:8, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/FE_Mesh.cpp:2: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_TypeDefs.h:17, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/FE_Engine.h:9, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/FE_Engine.cpp:1: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/FieldEulerIntegrator.h:6, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/FieldEulerIntegrator.cpp:1: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ make -f CMakeFiles/utils.h.dir/build.make CMakeFiles/utils.h.dir/depend make[3]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' cd /build/reproducible-path/lammps-20240207+dfsg/debian/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/lammps-20240207+dfsg/cmake /build/reproducible-path/lammps-20240207+dfsg/cmake /build/reproducible-path/lammps-20240207+dfsg/debian/build /build/reproducible-path/lammps-20240207+dfsg/debian/build /build/reproducible-path/lammps-20240207+dfsg/debian/build/CMakeFiles/utils.h.dir/DependInfo.cmake "--color=" [ 10%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/InterscaleOperators.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H 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Entering directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' [ 10%] Generating includes/lammps/utils.h /usr/bin/cmake -E copy_if_different /build/reproducible-path/lammps-20240207+dfsg/src/utils.h /build/reproducible-path/lammps-20240207+dfsg/debian/build/includes/lammps/utils.h make[3]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' [ 10%] Built target utils.h make -f CMakeFiles/variable.h.dir/build.make CMakeFiles/variable.h.dir/depend make[3]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' cd /build/reproducible-path/lammps-20240207+dfsg/debian/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/lammps-20240207+dfsg/cmake /build/reproducible-path/lammps-20240207+dfsg/cmake /build/reproducible-path/lammps-20240207+dfsg/debian/build /build/reproducible-path/lammps-20240207+dfsg/debian/build /build/reproducible-path/lammps-20240207+dfsg/debian/build/CMakeFiles/variable.h.dir/DependInfo.cmake "--color=" make[3]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' make -f CMakeFiles/variable.h.dir/build.make CMakeFiles/variable.h.dir/build make[3]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' [ 11%] Generating includes/lammps/variable.h /usr/bin/cmake -E copy_if_different /build/reproducible-path/lammps-20240207+dfsg/src/variable.h /build/reproducible-path/lammps-20240207+dfsg/debian/build/includes/lammps/variable.h make[3]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' [ 11%] Built target variable.h [ 11%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/KD_Tree.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/KD_Tree.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/KD_Tree.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/KD_Tree.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/KD_Tree.cpp [ 11%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/KernelFunction.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/KernelFunction.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/KernelFunction.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/KernelFunction.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/KernelFunction.cpp In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ImplicitSolveOperator.h:6, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ImplicitSolveOperator.cpp:2: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ make -f CMakeFiles/fmt_core.h.dir/build.make CMakeFiles/fmt_core.h.dir/depend make[3]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' cd /build/reproducible-path/lammps-20240207+dfsg/debian/build && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/lammps-20240207+dfsg/cmake /build/reproducible-path/lammps-20240207+dfsg/cmake /build/reproducible-path/lammps-20240207+dfsg/debian/build /build/reproducible-path/lammps-20240207+dfsg/debian/build 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-I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/KinetoThermostat.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/KinetoThermostat.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/KinetoThermostat.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/KinetoThermostat.cpp [ 11%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Kinetostat.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Kinetostat.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Kinetostat.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Kinetostat.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/Kinetostat.cpp [ 11%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/LammpsInterface.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H 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-DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/MPI_Wrappers.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/MPI_Wrappers.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/MPI_Wrappers.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MPI_Wrappers.cpp [ 11%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Material.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG 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-DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Matrix.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Matrix.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Matrix.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/Matrix.cpp [ 11%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/MeshReader.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/MeshReader.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/MeshReader.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/MeshReader.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MeshReader.cpp In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_TypeDefs.h:17, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/AtomicRegulator.h:6, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/KinetoThermostat.h:4, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/KinetoThermostat.cpp:1: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ [ 12%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/MoleculeSet.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/MoleculeSet.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/MoleculeSet.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/MoleculeSet.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MoleculeSet.cpp [ 12%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/NonLinearSolver.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/NonLinearSolver.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/NonLinearSolver.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/NonLinearSolver.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/NonLinearSolver.cpp In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_TypeDefs.h:17, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/LammpsInterface.h:25, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/LammpsInterface.cpp:2: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ [ 12%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/OutputManager.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/OutputManager.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/OutputManager.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/OutputManager.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/OutputManager.cpp [ 12%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/PaqAtcUtility.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/PaqAtcUtility.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/PaqAtcUtility.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/PaqAtcUtility.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/PaqAtcUtility.cpp [ 12%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ParDiagonalMatrix.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ParDiagonalMatrix.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ParDiagonalMatrix.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ParDiagonalMatrix.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ParDiagonalMatrix.cpp In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/Material.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/Material.cpp:1: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ [ 12%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ParSparseMatrix.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ParSparseMatrix.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ParSparseMatrix.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ParSparseMatrix.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ParSparseMatrix.cpp [ 12%] 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CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/PhysicsModel.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/PhysicsModel.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/PhysicsModel.cpp [ 12%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/PoissonSolver.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/PoissonSolver.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/PoissonSolver.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/PoissonSolver.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/PoissonSolver.cpp [ 12%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/PolynomialSolver.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/PolynomialSolver.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/PolynomialSolver.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/PolynomialSolver.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/PolynomialSolver.cpp [ 12%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/PrescribedDataManager.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/PrescribedDataManager.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/PrescribedDataManager.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/PrescribedDataManager.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/PrescribedDataManager.cpp [ 12%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Quadrature.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Quadrature.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Quadrature.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Quadrature.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/Quadrature.cpp [ 13%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/SchrodingerSolver.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/SchrodingerSolver.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/SchrodingerSolver.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/SchrodingerSolver.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/SchrodingerSolver.cpp [ 13%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/SpeciesTimeIntegrator.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/SpeciesTimeIntegrator.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/SpeciesTimeIntegrator.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/SpeciesTimeIntegrator.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/SpeciesTimeIntegrator.cpp [ 13%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Stress.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Stress.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Stress.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Stress.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/Stress.cpp [ 13%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ThermalTimeIntegrator.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ThermalTimeIntegrator.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ThermalTimeIntegrator.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ThermalTimeIntegrator.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ThermalTimeIntegrator.cpp [ 13%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Thermostat.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Thermostat.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Thermostat.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Thermostat.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/Thermostat.cpp In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/PhysicsModel.h:8, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/PhysicsModel.cpp:1: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ [ 13%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/TimeFilter.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/TimeFilter.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/TimeFilter.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/TimeFilter.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/TimeFilter.cpp In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_TypeDefs.h:17, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/LammpsInterface.h:25, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/PerAtomQuantity.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/PerAtomQuantityLibrary.h:6, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/PerAtomQuantityLibrary.cpp:2: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_TypeDefs.h:17, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/LinearSolver.h:5, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/PoissonSolver.h:6, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/PoissonSolver.cpp:1: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/Stress.h:8, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/Stress.cpp:1: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ [ 13%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/TimeIntegrator.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/TimeIntegrator.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/TimeIntegrator.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/TimeIntegrator.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/TimeIntegrator.cpp [ 13%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/TransferLibrary.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/TransferLibrary.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/TransferLibrary.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/TransferLibrary.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/TransferLibrary.cpp In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_TypeDefs.h:17, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/AtomicRegulator.h:6, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/Thermostat.h:4, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/Thermostat.cpp:1: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ [ 13%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/TransferOperator.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/TransferOperator.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/TransferOperator.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/TransferOperator.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/TransferOperator.cpp [ 13%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/Vector.cpp.o [ 13%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ViscousStress.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong 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CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ViscousStress.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ViscousStress.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/ViscousStress.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ViscousStress.cpp [ 13%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationChargeDiffusion.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 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-Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationDiffusion.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationDiffusion.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationDiffusion.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationDiffusion.cpp [ 14%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationElectronContinuity.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. 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/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationElectronMomentum.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationElectronMomentum.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationElectronMomentum.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationElectronMomentum.cpp [ 14%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationElectronTemperature.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationElectronTemperature.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationElectronTemperature.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationElectronTemperature.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationElectronTemperature.cpp In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ViscousStress.h:8, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ViscousStress.cpp:1: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ [ 14%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationMassDiffusion.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationMassDiffusion.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationMassDiffusion.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationMassDiffusion.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationMassDiffusion.cpp In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_TypeDefs.h:17, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquation.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationElectronMomentum.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationElectronMomentum.cpp:1: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ [ 14%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationMomentum.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationMomentum.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationMomentum.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationMomentum.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationMomentum.cpp [ 14%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationPhononTemperature.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationPhononTemperature.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationPhononTemperature.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationPhononTemperature.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationPhononTemperature.cpp [ 14%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationPoisson.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationPoisson.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationPoisson.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationPoisson.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationPoisson.cpp In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_TypeDefs.h:17, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/LammpsInterface.h:25, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/PerAtomQuantity.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/PerAtomQuantityLibrary.h:6, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/TransferOperator.h:6, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/TransferLibrary.h:11, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/TransferLibrary.cpp:2: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ [ 14%] Building CXX object CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationSchrodinger.cpp.o /usr/bin/c++ -DLAMMPS_SMALLBIG -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX -D_MPICC_H -I/build/reproducible-path/lammps-20240207+dfsg/lib/atc -I/build/reproducible-path/lammps-20240207+dfsg/src -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -g -O2 -ffile-prefix-map=/build/reproducible-path/lammps-20240207+dfsg=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -std=c++11 -fPIC -MD -MT CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationSchrodinger.cpp.o -MF CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationSchrodinger.cpp.o.d -o CMakeFiles/atc.dir/build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationSchrodinger.cpp.o -c /build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationSchrodinger.cpp In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_TypeDefs.h:17, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/LammpsInterface.h:25, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/PerAtomQuantity.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/PerAtomQuantityLibrary.h:6, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/TransferOperator.h:6, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/TransferOperator.cpp:2: /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h: In member function 'T& ATC_matrix::CloneVector::operator[](ATC_matrix::INDEX) [with T = double]': /build/reproducible-path/lammps-20240207+dfsg/lib/atc/CloneVector.h:117:19: warning: 'this' pointer is null [-Wnonnull] 117 | return (*_baseV)(i); | ~~~~~~~~~^~~ In file included from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/MatrixLibrary.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/ATC_TypeDefs.h:17, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquation.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationMomentum.h:7, from /build/reproducible-path/lammps-20240207+dfsg/lib/atc/WeakEquationMomentum.cpp:1: 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/build/reproducible-path/lammps-20240207+dfsg/src/MGPT/mgpt_readpot.cpp: In member function 'void potdata::readpot(const char*, const char*, double)': /build/reproducible-path/lammps-20240207+dfsg/src/MGPT/mgpt_readpot.cpp:188:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 188 | fgets(line,sizeof(line),in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/lammps-20240207+dfsg/src/MGPT/mgpt_readpot.cpp:204:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 204 | fgets(line,sizeof(line),in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/lammps-20240207+dfsg/src/MGPT/mgpt_readpot.cpp:247:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 247 | fgets(line,sizeof(line),in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/lammps-20240207+dfsg/src/MGPT/mgpt_readpot.cpp:307:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 307 | fgets(line,sizeof(line),in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/lammps-20240207+dfsg/src/MGPT/mgpt_readpot.cpp:330:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 330 | fgets(line,sizeof(line),in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/lammps-20240207+dfsg/src/MGPT/mgpt_readpot.cpp:332:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 332 | fgets(line,sizeof(line),in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/lammps-20240207+dfsg/src/MGPT/mgpt_readpot.cpp:335:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 335 | fgets(line,sizeof(line),in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/lammps-20240207+dfsg/src/MGPT/mgpt_readpot.cpp:344:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 344 | fgets(line,sizeof(line),in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/lammps-20240207+dfsg/src/MGPT/mgpt_readpot.cpp:346:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 346 | fgets(line,sizeof(line),in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/lammps-20240207+dfsg/src/MGPT/mgpt_readpot.cpp:359:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 359 | fgets(line,sizeof(line),in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/lammps-20240207+dfsg/src/MGPT/mgpt_readpot.cpp: In function 'void getparmindata(const char*, int*, double*, double*, double*)': /build/reproducible-path/lammps-20240207+dfsg/src/MGPT/mgpt_readpot.cpp:110:10: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 110 | fgets(line,sizeof(line),in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/lammps-20240207+dfsg/src/MGPT/mgpt_readpot.cpp:120:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 120 | fgets(line,sizeof(line),in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/lammps-20240207+dfsg/src/MGPT/mgpt_readpot.cpp:124:12: warning: ignoring return value of 'char* fgets(char*, int, FILE*)' declared with attribute 'warn_unused_result' [-Wunused-result] 124 | fgets(line,sizeof(line),in); | ~~~~~^~~~~~~~~~~~~~~~~~~~~~ [ 70%] Building CXX 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Parsing file /build/reproducible-path/lammps-20240207+dfsg/src/text_file_reader.cpp... Reading /build/reproducible-path/lammps-20240207+dfsg/src/text_file_reader.h... Parsing file /build/reproducible-path/lammps-20240207+dfsg/src/text_file_reader.h... Reading /build/reproducible-path/lammps-20240207+dfsg/src/potential_file_reader.cpp... Parsing file /build/reproducible-path/lammps-20240207+dfsg/src/potential_file_reader.cpp... Reading /build/reproducible-path/lammps-20240207+dfsg/src/potential_file_reader.h... Parsing file /build/reproducible-path/lammps-20240207+dfsg/src/potential_file_reader.h... Reading /build/reproducible-path/lammps-20240207+dfsg/src/my_page.cpp... Parsing file /build/reproducible-path/lammps-20240207+dfsg/src/my_page.cpp... Reading /build/reproducible-path/lammps-20240207+dfsg/src/my_page.h... Parsing file /build/reproducible-path/lammps-20240207+dfsg/src/my_page.h... Reading /build/reproducible-path/lammps-20240207+dfsg/src/my_pool_chunk.cpp... Parsing file /build/reproducible-path/lammps-20240207+dfsg/src/my_pool_chunk.cpp... Reading /build/reproducible-path/lammps-20240207+dfsg/src/my_pool_chunk.h... Parsing file /build/reproducible-path/lammps-20240207+dfsg/src/my_pool_chunk.h... Reading /build/reproducible-path/lammps-20240207+dfsg/src/math_eigen.h... Parsing file /build/reproducible-path/lammps-20240207+dfsg/src/math_eigen.h... Reading /build/reproducible-path/lammps-20240207+dfsg/src/platform.h... Parsing file /build/reproducible-path/lammps-20240207+dfsg/src/platform.h... Reading /build/reproducible-path/lammps-20240207+dfsg/src/platform.cpp... Parsing file /build/reproducible-path/lammps-20240207+dfsg/src/platform.cpp... Reading /build/reproducible-path/lammps-20240207+dfsg/src/math_special.h... Parsing file /build/reproducible-path/lammps-20240207+dfsg/src/math_special.h... Reading /build/reproducible-path/lammps-20240207+dfsg/src/math_special.cpp... Parsing file /build/reproducible-path/lammps-20240207+dfsg/src/math_special.cpp... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Building concept list... Computing nesting relations for classes... Associating documentation with classes... Associating documentation with concepts... Associating documentation with modules... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Search for main page... Computing page relations... Determining the scope of groups... Computing module relations... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating example documentation... Generating file sources... Generating code for file arg_info.h... Generating code for file atom.h... Generating code for file input.h... Generating code for file lammps.h... Generating code for file library.h... Generating code for file lmptype.h... Generating code for file math_eigen.h... Generating code for file math_special.h... Generating code for file my_page.h... Generating code for file my_pool_chunk.h... Generating code for file platform.h... Generating code for file pointers.h... Generating code for file potential_file_reader.h... Generating code for file text_file_reader.h... Generating code for file tokenizer.h... Generating code for file utils.h... Generating file documentation... Generating page documentation... Generating group documentation... Generating class documentation... Generating docs for compound compress_info... Generating concept documentation... Generating module documentation... Generating namespace documentation... Generating docs for compound LAMMPS_NS::Atom... Generating docs for compound LAMMPS_NS::Input... Generating docs for compound LAMMPS_NS::InvalidFloatException... Generating docs for compound LAMMPS_NS::InvalidIntegerException... Generating docs for compound LAMMPS_NS::LAMMPS... Generating docs for compound LAMMPS_NS::multitype... Generating docs for compound LAMMPS_NS::MyPage... Generating docs for compound LAMMPS_NS::MyPoolChunk... Generating docs for compound LAMMPS_NS::Pointers... Generating docs for compound LAMMPS_NS::TokenizerException... Generating docs for compound LAMMPS_NS::ubuf... Generating graph info page... Generating directory documentation... finalizing index lists... writing tag file... Generating XML output... Generating XML output for class LAMMPS_NS::ArgInfo Generating XML output for class LAMMPS_NS::Atom Generating XML output for class compress_info Generating XML output for class LAMMPS_NS::EOFException Generating XML output for class LAMMPS_NS::FileReaderException Generating XML output for class LAMMPS_NS::Atom::HashElem Generating XML output for class LAMMPS_NS::HyperOneCoeff Generating XML output for class LAMMPS_NS::Input Generating XML output for class LAMMPS_NS::InvalidFloatException Generating XML output for class LAMMPS_NS::InvalidIntegerException Generating XML output for class LAMMPS_NS::LAMMPS Generating XML output for class LAMMPS_NS::multitype Generating XML output for class LAMMPS_NS::MyPage Generating XML output for class LAMMPS_NS::MyPoolChunk Generating XML output for class LAMMPS_NS::package_styles_lists Generating XML output for class LAMMPS_NS::Atom::PerAtom Generating XML output for class LAMMPS_NS::Pointers Generating XML output for class LAMMPS_NS::PotentialFileReader Generating XML output for class regex_context_t Generating XML output for class regex_t Generating XML output for class LAMMPS_NS::TextFileReader Generating XML output for class LAMMPS_NS::Tokenizer Generating XML output for class LAMMPS_NS::TokenizerException Generating XML output for class LAMMPS_NS::ubuf Generating XML output for class udi_t Generating XML output for class LAMMPS_NS::ValueTokenizer Generating XML output for namespace LAMMPS_NS Generating XML output for namespace LAMMPS_NS::MathSpecial Generating XML output for namespace LAMMPS_NS::platform Generating XML output for namespace LAMMPS_NS::utils Generating XML output for namespace MathConst Generating XML output for namespace MathEigen Generating XML output for namespace std Generating XML output for file arg_info.cpp Generating XML output for file arg_info.h Generating XML output for file atom.cpp Generating XML output for file atom.h Generating XML output for file input.cpp Generating XML output for file input.h Generating XML output for file lammps.cpp Generating XML output for file lammps.h Generating XML output for file library.cpp Generating XML output for file library.h Generating XML output for file lmptype.h Generating XML output for file math_eigen.h Generating XML output for file math_special.cpp Generating XML output for file math_special.h Generating XML output for file my_page.cpp Generating XML output for file my_page.h Generating XML output for file my_pool_chunk.cpp Generating XML output for file my_pool_chunk.h Generating XML output for file platform.cpp Generating XML output for file platform.h Generating XML output for file pointers.h Generating XML output for file potential_file_reader.cpp Generating XML output for file potential_file_reader.h Generating XML output for file text_file_reader.cpp Generating XML output for file text_file_reader.h Generating XML output for file tokenizer.cpp Generating XML output for file tokenizer.h Generating XML output for file utils.cpp Generating XML output for file utils.h Generate XML output for dir /build/reproducible-path/lammps-20240207+dfsg/src/ Running plantuml with JAVA... Running dot... type lookup cache used 7693/262144 hits=62872 misses=7925 symbol lookup cache used 5303/262144 hits=49970 misses=5303 finished... sed -e 's,@DOXYGEN_XML_DIR@,/build/reproducible-path/lammps-20240207+dfsg/doc/doxygen/xml,g' \ -e 's,@LAMMPS_SOURCE_DIR@,/build/reproducible-path/lammps-20240207+dfsg/doc/../src,g' \ -e 's,@LAMMPS_PYTHON_DIR@,/build/reproducible-path/lammps-20240207+dfsg/doc/../python,g' \ -e 's,@LAMMPS_DOC_DIR@,/build/reproducible-path/lammps-20240207+dfsg/doc,g' /build/reproducible-path/lammps-20240207+dfsg/doc/utils/sphinx-config/conf.py.in > /build/reproducible-path/lammps-20240207+dfsg/doc/utils/sphinx-config/conf.py WARNING: The directory '/nonexistent/first-build/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag. Obtaining file:///build/reproducible-path/lammps-20240207%2Bdfsg/doc/utils/converters Installing build dependencies: started Installing build dependencies: finished with status 'error' error: subprocess-exited-with-error × pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> [8 lines of output] WARNING: The directory '/nonexistent/first-build/.cache/pip' or its parent directory is not owned or is not writable by the current user. The cache has been disabled. Check the permissions and owner of that directory. If executing pip with sudo, you should use sudo's -H flag. WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))': /simple/setuptools/ WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))': /simple/setuptools/ WARNING: Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))': /simple/setuptools/ WARNING: Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))': /simple/setuptools/ WARNING: Retrying (Retry(total=0, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ProxyError('Cannot connect to proxy.', NewConnectionError(': Failed to establish a new connection: [Errno 111] Connection refused'))': /simple/setuptools/ ERROR: Could not find a version that satisfies the requirement setuptools>=40.8.0 (from versions: none) ERROR: No matching distribution found for setuptools>=40.8.0 [end of output] note: This error originates from a subprocess, and is likely not a problem with pip. error: subprocess-exited-with-error × pip subprocess to install build dependencies did not run successfully. │ exit code: 1 ╰─> See above for output. note: This error originates from a subprocess, and is likely not a problem with pip. make[3]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg/doc/graphviz' make[3]: Nothing to be done for 'all'. make[3]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg/doc/graphviz' Running Sphinx v8.1.3 loading translations [en]... done Initializing Spelling Checker 7.7.0 making output directory... done Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 987 source files that are out of date updating environment: [new config] 987 added, 0 changed, 0 removed reading sources... [ 3%] Bibliography .. Commands_parse reading sources... [ 6%] Commands_removed .. Errors_common reading sources... [ 8%] Errors_debug .. Howto_lammps_gui reading sources... [ 11%] Howto_library .. Install reading sources... [ 14%] Install_conda .. Manual_version reading sources... [ 17%] Modify .. Python_examples reading sources... [ 19%] Python_execute .. Speed_opt reading sources... [ 22%] Speed_packages .. angle_spica reading sources... [ 25%] angle_style .. atc_hardy_fields reading sources... [ 28%] atc_hardy_gradients .. atc_output_nodeset reading sources... [ 31%] atc_output_volume_integral .. bond_coeff reading sources... [ 33%] bond_fene .. comm_style reading sources... [ 36%] commands_list .. compute_dihedral_local reading sources... [ 39%] compute_dilatation_atom .. compute_improper reading sources... [ 42%] compute_improper_local .. compute_property_grid reading sources... [ 44%] compute_property_local .. compute_smd_ulsph_num_neighs reading sources... [ 47%] compute_smd_ulsph_strain .. compute_temp_ramp reading sources... [ 50%] compute_temp_region .. dihedral_lepton reading sources... [ 53%] dihedral_multi_harmonic .. fix_accelerate_cos reading sources... [ 56%] fix_acks2_reaxff .. fix_box_relax reading sources... [ 58%] fix_brownian .. fix_freeze reading sources... [ 61%] fix_gcmc .. fix_mol_swap reading sources... [ 64%] fix_momentum .. fix_nve_dotc_langevin reading sources... [ 67%] fix_nve_eff .. fix_precession_spin reading sources... [ 69%] fix_press_berendsen .. fix_smd_adjust_dt reading sources... [ 72%] fix_smd_integrate_tlsph .. fix_viscous reading sources... [ 75%] fix_viscous_sphere .. improper_hybrid reading sources... [ 78%] improper_inversion_harmonic .. neb_spin reading sources... [ 81%] neigh_modify .. pair_colloid reading sources... [ 83%] pair_comb .. pair_gromacs reading sources... [ 86%] pair_gw .. pair_lj_switch3_coulgauss_long reading sources... [ 89%] pair_local_density .. pair_python reading sources... [ 92%] pair_quip .. pair_style reading sources... [ 94%] pair_sw .. quit reading sources... [ 97%] read_data .. unfix reading sources... [100%] units .. write_restart WARNING: unknown directive or role name: f:mod /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1: ERROR: Unknown interpreted text role "f:mod". [docutils] WARNING: unknown directive or role name: f:mod /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:4: ERROR: Unknown interpreted text role "f:mod". [docutils] WARNING: unknown directive or role name: f:mod /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:43: ERROR: Unknown interpreted text role "f:mod". [docutils] WARNING: unknown directive or role name: f:func /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:64: ERROR: Unknown interpreted text role "f:func". [docutils] WARNING: unknown directive or role name: f:func /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:64: ERROR: Unknown interpreted text role "f:func". [docutils] WARNING: unknown directive or role name: f:func /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:133: ERROR: Unknown interpreted text role "f:func". [docutils] WARNING: unknown directive or role name: f:func /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:133: ERROR: Unknown interpreted text role "f:func". [docutils] WARNING: unknown directive or role name: f:func /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:133: ERROR: Unknown interpreted text role "f:func". [docutils] WARNING: unknown directive or role name: f:func /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:133: ERROR: Unknown interpreted text role "f:func". [docutils] WARNING: unknown directive or role name: f:mod /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:254: ERROR: Unknown interpreted text role "f:mod". [docutils] WARNING: unknown directive or role name: f:module /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:257: ERROR: Unknown directive type "f:module". .. f:module:: LIBLAMMPS [docutils] WARNING: unknown directive or role name: f:mod /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:259: ERROR: Unknown interpreted text role "f:mod". [docutils] WARNING: unknown directive or role name: f:currentmodule /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:262: ERROR: Unknown directive type "f:currentmodule". .. f:currentmodule:: None [docutils] WARNING: unknown directive or role name: f:type /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:264: ERROR: Unknown directive type "f:type". .. f:type:: lammps Derived type that is the general class of the Fortran interface. It holds a reference to the :cpp:class:`LAMMPS ` class instance to which any of the included calls are forwarded. :f handle: reference to the LAMMPS class :ftype handle: c_ptr :f style: derived type to access lammps style constants :ftype style: type(lammps_style) :f type: derived type to access lammps type constants :ftype type: type(lammps_type) :f dtype: derived type to access lammps data type constants :ftype dtype: type(lammps_dtype) :f close: :f:subr:`close` :ftype close: subroutine :f subroutine error: :f:subr:`error` :ftype error: subroutine :f file: :f:subr:`file` :ftype file: subroutine :f command: :f:subr:`command` :ftype command: subroutine :f commands_list: :f:subr:`commands_list` :ftype commands_list: subroutine :f commands_string: :f:subr:`commands_string` :ftype commands_string: subroutine :f get_natoms: :f:func:`get_natoms` :ftype get_natoms: function :f get_thermo: :f:func:`get_thermo` :ftype get_thermo: function :f last_thermo: :f:func:`last_thermo` :ftype last_thermo: function :f extract_box: :f:subr:`extract_box` :ftype extract_box: subroutine :f reset_box: :f:subr:`reset_box` :ftype reset_box: subroutine :f memory_usage: :f:subr:`memory_usage` :ftype memory_usage: subroutine :f get_mpi_comm: :f:func:`get_mpi_comm` :ftype get_mpi_comm: function :f extract_setting: :f:func:`extract_setting` :ftype extract_setting: function :f extract_global: :f:func:`extract_global` :ftype extract_global: function :f extract_atom: :f:func:`extract_atom` :ftype extract_atom: function :f extract_compute: :f:func:`extract_compute` :ftype extract_compute: function :f extract_fix: :f:func:`extract_fix` :ftype extract_fix: function :f extract_variable: :f:func:`extract_variable` :ftype extract_variable: function :f set_variable: :f:subr:`set_variable` :ftype set_variable: subroutine :f set_string_variable: :f:subr:`set_set_string_variable` :ftype set_string_variable: subroutine :f set_internal_variable: :f:subr:`set_internal_variable` :ftype set_internal_variable: subroutine :f gather_atoms: :f:subr:`gather_atoms` :ftype gather_atoms: subroutine :f gather_atoms_concat: :f:subr:`gather_atoms_concat` :ftype gather_atoms_concat: subroutine :f gather_atoms_subset: :f:subr:`gather_atoms_subset` :ftype gather_atoms_subset: subroutine :f scatter_atoms: :f:subr:`scatter_atoms` :ftype scatter_atoms: subroutine :f scatter_atoms_subset: :f:subr:`scatter_atoms_subset` :ftype scatter_atoms_subset: subroutine :f gather_bonds: :f:subr:`gather_bonds` :ftype gather_bonds: subroutine :f gather_angles: :f:subr:`gather_angles` :ftype gather_angles: subroutine :f gather_dihedrals: :f:subr:`gather_dihedrals` :ftype gather_dihedrals: subroutine :f gather_impropers: :f:subr:`gather_impropers` :ftype gather_impropers: subroutine :f gather: :f:subr:`gather` :ftype gather: subroutine :f gather_concat: :f:subr:`gather_concat` :ftype gather_concat: subroutine :f gather_subset: :f:subr:`gather_subset` :ftype gather_subset: subroutine :f scatter: :f:subr:`scatter` :ftype scatter: subroutine :f scatter_subset: :f:subr:`scatter_subset` :ftype scatter_subset: subroutine :f create_atoms: :f:subr:`create_atoms` :ftype create_atoms: subroutine :f find_pair_neighlist: :f:func:`find_pair_neighlist` :ftype find_pair_neighlist: function :f find_fix_neighlist: :f:func:`find_fix_neighlist` :ftype find_fix_neighlist: function :f find_compute_neighlist: :f:func:`find_compute_neighlist` :ftype find_compute_neighlist: function :f neighlist_num_elements: :f:func:`neighlist_num_elements` :ftype neighlist_num_elements: function :f neighlist_element_neighbors: :f:subr:`neighlist_element_neighbors` :ftype neighlist_element_neighbors: subroutine :f version: :f:func:`version` :ftype version: function :f get_os_info: :f:subr:`get_os_info` :ftype get_os_info: subroutine :f config_has_mpi_support: :f:func:`config_has_mpi_support` :ftype config_has_mpi_support: function :f config_has_gzip_support: :f:func:`config_has_gzip_support` :ftype config_has_gzip_support: function :f config_has_png_support: :f:func:`config_has_png_support` :ftype config_has_png_support: function :f config_has_jpeg_support: :f:func:`config_has_jpeg_support` :ftype config_has_jpeg_support: function :f config_has_ffmpeg_support: :f:func:`config_has_ffmpeg_support` :ftype config_has_ffmpeg_support: function :f config_has_exceptions: :f:func:`config_has_exceptions` :ftype config_has_exceptions: function :f config_has_package: :f:func:`config_has_package` :ftype config_has_package: function :f config_package_count: :f:func:`config_package_count` :ftype config_package_count: function :f config_package_name: :f:func:`config_package_name` :ftype config_package_name: function :f installed_packages: :f:subr:`installed_packages` :ftype installed_packages: subroutine :f config_accelerator: :f:func:`config_accelerator` :ftype config_accelerator: function :f has_gpu_device: :f:func:`has_gpu_device` :ftype has_gpu_device: function :f get_gpu_device_info: :f:subr:`get_gpu_device_info` :ftype get_gpu_device_info: subroutine :f has_style: :f:func:`has_style` :ftype has_style: function :f style_count: :f:func:`style_count` :ftype style_count: function :f style_name: :f:func:`style_name` :ftype style_name: function :f has_id: :f:func:`has_id` :ftype has_id: function :f id_count: :f:func:`id_count` :ftype id_count: function :f id_name: :f:subr:`id_name` :ftype id_name: subroutine :f plugin_count: :f:func:`plugin_count` :ftype plugin_count: function :f plugin_name: :f:subr:`plugin_name` :ftype plugin_count: subroutine :f encode_image_flags: :f:func:`encode_image_flags` :ftype encode_image_flags: function :f decode_image_flags: :f:subr:`decode_image_flags` :ftype decode_image_flags: subroutine :f set_fix_external_callback: :f:subr:`set_fix_external_callback` :ftype set_fix_external_callback: subroutine :f fix_external_get_force: :f:func:`fix_external_get_force` :ftype fix_external_get_force: function :f fix_external_set_energy_global: :f:subr:`fix_external_set_energy_global` :ftype fix_external_set_energy_global: subroutine :f fix_external_set_virial_global: :f:subr:`fix_external_set_virial_global` :ftype fix_external_set_virial_global: subroutine :f fix_external_set_energy_peratom: :f:subr:`fix_external_set_energy_peratom` :ftype fix_external_set_energy_peratom: subroutine :f fix_external_set_virial_peratom: :f:subr:`fix_external_set_virial_peratom` :ftype fix_external_set_virial_peratom: subroutine :f fix_external_set_vector_length: :f:subr:`fix_external_set_vector_length` :ftype fix_external_set_vector_length: subroutine :f fix_external_set_vector: :f:subr:`fix_external_set_vector` :ftype fix_external_set_vector: subroutine :f flush_buffers: :f:subr:`flush_buffers` :ftype flush_buffers: subroutine :f is_running: :f:func:`is_running` :ftype is_running: function :f force_timeout: :f:subr:`force_timeout` :ftype force_timeout: subroutine :f has_error: :f:func:`has_error` :ftype has_error: function :f get_last_error_message: :f:subr:`get_last_error_message` :ftype get_last_error_message: subroutine [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:441: ERROR: Unknown directive type "f:function". .. f:function:: lammps([args][,comm]) This is the constructor for the Fortran class and will forward the arguments to a call to either :cpp:func:`lammps_open_fortran` or :cpp:func:`lammps_open_no_mpi`. If the LAMMPS library has been compiled with MPI support, it will also initialize MPI, if it has not already been initialized before. The *args* argument with the list of command line parameters is optional and so it the *comm* argument with the MPI communicator. If *comm* is not provided, ``MPI_COMM_WORLD`` is assumed. For more details please see the documentation of :cpp:func:`lammps_open`. :o args: arguments as list of strings :otype args: character(len=\*),dimension(:),optional :o comm: MPI communicator :otype comm: integer,optional :to: :cpp:func:`lammps_open_fortran` :to: :cpp:func:`lammps_open_no_mpi` :r lammps: an instance of the :f:type:`lammps` derived type .. note:: The :f:mod:`MPI_F08` module, which defines Fortran 2008 bindings for MPI, is not directly supported by this interface due to the complexities of supporting both the :f:mod:`MPI_F08` and :f:mod:`MPI` modules at the same time. However, you should be able to use the ``MPI_VAL`` member of the ``MPI_comm`` derived type to access the integer value of the communicator, such as in .. code-block:: fortran PROGRAM testmpi USE LIBLAMMPS USE MPI_F08 TYPE(lammps) :: lmp lmp = lammps(comm=MPI_COMM_SELF%MPI_VAL) END PROGRAM testmpi [docutils] WARNING: unknown directive or role name: f:type /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:480: ERROR: Unknown directive type "f:type". .. f:type:: lammps_style This derived type is there to provide a convenient interface for the style constants used with :f:func:`extract_compute`, :f:func:`extract_fix`, and :f:func:`extract_variable`. Assuming your LAMMPS instance is called ``lmp``, these constants will be ``lmp%style%global``, ``lmp%style%atom``, and ``lmp%style%local``. These values are identical to the values described in :cpp:enum:`_LMP_STYLE_CONST` for the C library interface. :f integer(c_int) global: used to request global data :f integer(c_int) atom: used to request per-atom data :f integer(c_int) local: used to request local data [docutils] WARNING: unknown directive or role name: f:type /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:493: ERROR: Unknown directive type "f:type". .. f:type:: lammps_type This derived type is there to provide a convenient interface for the type constants used with :f:func:`extract_compute`, :f:func:`extract_fix`, and :f:func:`extract_variable`. Assuming your LAMMPS instance is called ``lmp``, these constants will be ``lmp%type%scalar``, ``lmp%type%vector``, and ``lmp%type%array``. These values are identical to the values described in :cpp:enum:`_LMP_TYPE_CONST` for the C library interface. :f integer(c_int) scalar: used to request scalars :f integer(c_int) vector: used to request vectors :f integer(c_int) array: used to request arrays (matrices) [docutils] WARNING: unknown directive or role name: f:type /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:506: ERROR: Unknown interpreted text role "f:type". [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:509: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: close([finalize]) This method will close down the LAMMPS instance through calling :cpp:func:`lammps_close`. If the *finalize* argument is present and has a value of ``.TRUE.``, then this subroutine also calls :cpp:func:`lammps_kokkos_finalize` and :cpp:func:`lammps_mpi_finalize`. :o finalize: shut down the MPI environment of the LAMMPS library if ``.TRUE.``. :otype finalize: logical,optional :to: :cpp:func:`lammps_close` :to: :cpp:func:`lammps_mpi_finalize` :to: :cpp:func:`lammps_kokkos_finalize` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:526: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: error(error_type, error_text) This method is a wrapper around the :cpp:func:`lammps_error` function and will dispatch an error through the LAMMPS Error class. .. versionadded:: 3Nov2022 :p error_type: constant to select which Error class function to call :ptype error_type: integer(c_int) :p character(len=\*) error_text: error message :to: :cpp:func:`lammps_error` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:540: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: file(filename) This method will call :cpp:func:`lammps_file` to have LAMMPS read and process commands from a file. :p character(len=\*) filename: name of file with LAMMPS commands :to: :cpp:func:`lammps_file` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:550: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: command(cmd) This method will call :cpp:func:`lammps_command` to have LAMMPS execute a single command. :p character(len=\*) cmd: single LAMMPS command :to: :cpp:func:`lammps_command` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:560: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: commands_list(cmds) This method will call :cpp:func:`lammps_commands_list` to have LAMMPS execute a list of input lines. :p character(len=\*) cmd [dimension(:)]: list of LAMMPS input lines :to: :cpp:func:`lammps_commands_list` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:570: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: commands_string(str) This method will call :cpp:func:`lammps_commands_string` to have LAMMPS execute a block of commands from a string. :p character(len=\*) str: LAMMPS input in string :to: :cpp:func:`lammps_commands_string` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:580: ERROR: Unknown directive type "f:function". .. f:function:: get_natoms() This function will call :cpp:func:`lammps_get_natoms` and return the number of atoms in the system. :to: :cpp:func:`lammps_get_natoms` :r real(c_double) natoms: number of atoms .. note:: If you would prefer to get the number of atoms in its native format (i.e., as a 32- or 64-bit integer, depending on how LAMMPS was compiled), this can be extracted with :f:func:`extract_global`. [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:596: ERROR: Unknown directive type "f:function". .. f:function:: get_thermo(name) This function will call :cpp:func:`lammps_get_thermo` and return the value of the corresponding thermodynamic keyword. .. versionadded:: 3Nov2022 :p character(len=\*) name: string with the name of the thermo keyword :to: :cpp:func:`lammps_get_thermo` :r value [real(c_double)]: value of the requested thermo property or `0.0_c_double` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:609: ERROR: Unknown directive type "f:function". .. f:function:: last_thermo(what, index) This function will call :cpp:func:`lammps_last_thermo` and returns either a string or a pointer to a cached copy of LAMMPS last thermodynamic output, depending on the data requested through *what*. Note that *index* uses 1-based indexing to access thermo output columns. .. versionadded:: 15Jun2023 Note that this function actually does not return a value, but rather associates the pointer on the left side of the assignment to point to internal LAMMPS data (with the exception of string data, which are copied and returned as ordinary Fortran strings). Pointers must be of the correct data type to point to said data (typically ``INTEGER(c_int)``, ``INTEGER(c_int64_t)``, or ``REAL(c_double)``). The pointer being associated with LAMMPS data is type-checked at run-time via an overloaded assignment operator. The pointers returned by this function point to temporary, read-only data that may be overwritten at any time, so their target values need to be copied to local storage if they are supposed to persist. For example, .. code-block:: fortran PROGRAM thermo USE LIBLAMMPS USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int64_t, c_int TYPE(lammps) :: lmp INTEGER(KIND=c_int64_t), POINTER :: ntimestep, bval REAL(KIND=c_double), POINTER :: dval INTEGER(KIND=c_int), POINTER :: nfield, typ, ival INTEGER(KIND=c_int) :: i CHARACTER(LEN=11) :: key lmp = lammps() CALL lmp%file('in.sysinit') ntimestep = lmp%last_thermo('step', 0) nfield = lmp%last_thermo('num', 0) PRINT*, 'Last thermo output on step: ', ntimestep, ' Number of fields: ', nfield DO i=1, nfield key = lmp%last_thermo('keyword',i) typ = lmp%last_thermo('type',i) IF (typ == lmp%dtype%i32) THEN ival = lmp%last_thermo('data',i) PRINT*, key, ':', ival ELSE IF (typ == lmp%dtype%i64) THEN bval = lmp%last_thermo('data',i) PRINT*, key, ':', bval ELSE IF (typ == lmp%dtype%r64) THEN dval = lmp%last_thermo('data',i) PRINT*, key, ':', dval END IF END DO CALL lmp%close(.TRUE.) END PROGRAM thermo would extract the last timestep where thermo output was done and the number of columns it printed. Then it loops over the columns to print out column header keywords and the corresponding data. .. note:: If :f:func:`last_thermo` returns a string, the string must have a length greater than or equal to the length of the string (not including the terminal ``NULL`` character) that LAMMPS returns. If the variable's length is too short, the string will be truncated. As usual in Fortran, strings are padded with spaces at the end. If you use an allocatable string, the string **must be allocated** prior to calling this function. :p character(len=\*) what: string with the name of the thermo keyword :p integer(c_int) index: 1-based column index :to: :cpp:func:`lammps_last_thermo` :r pointer [polymorphic]: pointer to LAMMPS data. The left-hand side of the assignment should be either a string (if expecting string data) or a C-compatible pointer (e.g., ``INTEGER(c_int), POINTER :: nlocal``) to the extracted property. .. warning:: Modifying the data in the location pointed to by the returned pointer may lead to inconsistent internal data and thus may cause failures, crashes, or bogus simulations. In general, it is much better to use a LAMMPS input command that sets or changes these parameters. Using an input command will take care of all side effects and necessary updates of settings derived from such settings. [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:699: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: extract_box([boxlo][, boxhi][, xy][, yz][, xz][, pflags][, boxflag]) This subroutine will call :cpp:func:`lammps_extract_box`. All parameters are optional, though obviously at least one should be present. The parameters *pflags* and *boxflag* are stored in LAMMPS as integers, but should be declared as ``LOGICAL`` variables when calling from Fortran. .. versionadded:: 3Nov2022 :o real(c_double) boxlo [dimension(3),optional]: vector in which to store lower-bounds of simulation box :o real(c_double) boxhi [dimension(3),optional]: vector in which to store upper-bounds of simulation box :o real(c_double) xy [optional]: variable in which to store *xy* tilt factor :o real(c_double) yz [optional]: variable in which to store *yz* tilt factor :o real(c_double) xz [optional]: variable in which to store *xz* tilt factor :o pflags: vector in which to store periodicity flags (``.TRUE.`` means periodic in that dimension) :otype pflags: logical,dimension(3),optional :o boxflag: variable in which to store boolean denoting whether the box will change during a simulation (``.TRUE.`` means box will change) :otype boxflag: logical,optional :to: :cpp:func:`lammps_extract_box` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:741: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: reset_box(boxlo, boxhi, xy, yz, xz) This subroutine will call :cpp:func:`lammps_reset_box`. All parameters are required. .. versionadded:: 3Nov2022 :p real(c_double) boxlo [dimension(3)]: vector of three doubles containing the lower box boundary :p real(c_double) boxhi [dimension(3)]: vector of three doubles containing the upper box boundary :p real(c_double) xy: *x--y* tilt factor :p real(c_double) yz: *y--z* tilt factor :p real(c_double) xz: *x--z* tilt factor :to: :cpp:func:`lammps_reset_box` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:759: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: memory_usage(meminfo) This subroutine will call :cpp:func:`lammps_memory_usage` and store the result in the three-element array *meminfo*. .. versionadded:: 3Nov2022 :p real(c_double) meminfo [dimension(3)]: vector of three doubles in which to store memory usage data :to: :cpp:func:`lammps_memory_usage` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:772: ERROR: Unknown directive type "f:function". .. f:function:: get_mpi_comm() This function returns a Fortran representation of the LAMMPS "world" communicator. .. versionadded:: 3Nov2022 :to: :cpp:func:`lammps_get_mpi_comm` :r comm: Fortran integer equivalent to the MPI communicator LAMMPS is using :rtype comm: integer .. note:: The C library interface currently returns type ``int`` instead of type ``MPI_Fint``, which is the C type corresponding to Fortran ``INTEGER`` types of the default kind. On most compilers, these are the same anyway, but this interface exchanges values this way to avoid warning messages. .. note:: The :f:mod:`MPI_F08` module, which defines Fortran 2008 bindings for MPI, is not directly supported by this function. However, you should be able to convert between the two using the `MPI_VAL` member of the communicator. For example, .. code-block:: fortran USE MPI_F08 USE LIBLAMMPS TYPE(lammps) :: lmp TYPE(MPI_Comm) :: comm ! ... [commands to set up LAMMPS/etc.] comm%MPI_VAL = lmp%get_mpi_comm() should assign an :f:mod:`MPI_F08` communicator properly. [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:812: ERROR: Unknown directive type "f:function". .. f:function:: extract_setting(keyword) Query LAMMPS about global settings. See the documentation for the :cpp:func:`lammps_extract_setting` function from the C library. .. versionadded:: 3Nov2022 :p character(len=\*) keyword: string containing the name of the thermo keyword :to: :cpp:func:`lammps_extract_setting` :r integer(c_int) setting: value of the queried setting or :math:`-1` if unknown [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:826: ERROR: Unknown directive type "f:function". .. f:function:: extract_global(name) This function calls :cpp:func:`lammps_extract_global` and returns either a string or a pointer to internal global LAMMPS data, depending on the data requested through *name*. .. versionadded:: 3Nov2022 Note that this function actually does not return a value, but rather associates the pointer on the left side of the assignment to point to internal LAMMPS data (with the exception of string data, which are copied and returned as ordinary Fortran strings). Pointers must be of the correct data type to point to said data (typically ``INTEGER(c_int)``, ``INTEGER(c_int64_t)``, or ``REAL(c_double)``) and have compatible kind and rank. The pointer being associated with LAMMPS data is type-, kind-, and rank-checked at run-time via an overloaded assignment operator. The pointers returned by this function are generally persistent; therefore it is not necessary to call the function again unless a :doc:`clear` command has been issued, which wipes out and recreates the contents of the :cpp:class:`LAMMPS ` class. For example, .. code-block:: fortran PROGRAM demo USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int64_t, c_int, c_double USE LIBLAMMPS TYPE(lammps) :: lmp INTEGER(c_int), POINTER :: nlocal => NULL() INTEGER(c_int64_t), POINTER :: ntimestep => NULL() REAL(c_double), POINTER :: dt => NULL() CHARACTER(LEN=10) :: units lmp = lammps() ! other commands nlocal = lmp%extract_global('nlocal') ntimestep = lmp%extract_global('ntimestep') dt = lmp%extract_global('dt') units = lmp%extract_global('units') ! more commands lmp.close(.TRUE.) END PROGRAM demo would extract the number of atoms on this processor, the current time step, the size of the current time step, and the units being used into the variables *nlocal*, *ntimestep*, *dt*, and *units*, respectively. .. note:: If :f:func:`extract_global` returns a string, the string must have a length greater than or equal to the length of the string (not including the terminal ``NULL`` character) that LAMMPS returns. If the variable's length is too short, the string will be truncated. As usual in Fortran, strings are padded with spaces at the end. If you use an allocatable string, the string **must be allocated** prior to calling this function, but you can automatically reallocate it to the correct length after the function returns, viz., .. code-block :: fortran PROGRAM test USE LIBLAMMPS TYPE(lammps) :: lmp CHARACTER(LEN=:), ALLOCATABLE :: str lmp = lammps() CALL lmp%command('units metal') ALLOCATE(CHARACTER(LEN=80) :: str) str = lmp%extract_global('units') str = TRIM(str) ! re-allocates to length len_trim(str) here PRINT*, LEN(str), LEN_TRIM(str) END PROGRAM test will print the number 5 (the length of the word "metal") twice. :p character(len=\*) name: string with the name of the property to extract :to: :cpp:func:`lammps_extract_global` :r pointer [polymorphic]: pointer to LAMMPS data. The left-hand side of the assignment should be either a string (if expecting string data) or a C-compatible pointer (e.g., ``INTEGER(c_int), POINTER :: nlocal``) to the extracted property. If expecting vector data, the pointer should have dimension ":". .. warning:: Modifying the data in the location pointed to by the returned pointer may lead to inconsistent internal data and thus may cause failures, crashes, or bogus simulations. In general, it is much better to use a LAMMPS input command that sets or changes these parameters. Using an input command will take care of all side effects and necessary updates of settings derived from such settings. [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:921: ERROR: Unknown directive type "f:function". .. f:function:: extract_atom(name) This function calls :cpp:func:`lammps_extract_atom` and returns a pointer to LAMMPS data tied to the :cpp:class:`Atom` class, depending on the data requested through *name*. .. versionadded:: 3Nov2022 Note that this function actually does not return a pointer, but rather associates the pointer on the left side of the assignment to point to internal LAMMPS data. Pointers must be of the correct type, kind, and rank (e.g., ``INTEGER(c_int), DIMENSION(:)`` for "type", "mask", or "id"; ``INTEGER(c_int64_t), DIMENSION(:)`` for "id" if LAMMPS was compiled with the ``-DLAMMPS_BIGBIG`` flag; ``REAL(c_double), DIMENSION(:,:)`` for "x", "v", or "f"; and so forth). The pointer being associated with LAMMPS data is type-, kind-, and rank-checked at run-time. :p character(len=\*) name: string with the name of the property to extract :to: :cpp:func:`lammps_extract_atom` :r pointer: pointer to LAMMPS data. The left-hand side of the assignment should be a C-interoperable pointer of appropriate kind and rank (e.g., ``INTEGER(c_int), POINTER :: mask(:)``) to the extracted property. If expecting vector data, the pointer should have dimension ":"; if expecting matrix data, the pointer should have dimension ":,:". :rtype pointer: polymorphic .. warning:: Pointers returned by this function are generally not persistent, as per-atom data may be redistributed, reallocated, and reordered at every re-neighboring operation. It is advisable to re-bind pointers using :f:func:`extract_atom` between runs. .. admonition:: Array index order Two-dimensional arrays returned from :f:func:`extract_atom` will be **transposed** from equivalent arrays in C, and they will be indexed from 1 instead of 0. For example, in C, .. code-block:: c void *lmp; double **x; /* more code to setup, etc. */ x = lammps_extract_atom(lmp, "x"); printf("%f\n", x[5][1]); will print the *y*-coordinate of the sixth atom on this processor. Conversely, .. code-block:: fortran TYPE(lammps) :: lmp REAL(c_double), DIMENSION(:,:), POINTER :: x => NULL() ! more code to setup, etc. x = lmp%extract_atom("x") PRINT '(f0.6)', x(2,6) will print the *y*-coordinate of the sixth atom on this processor (note the transposition of the two indices). This is not a choice, but rather a consequence of the different conventions adopted by the Fortran and C standards decades ago: in C, the block of data .. parsed-literal:: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 interpreted as a :math:`4\times4` matrix would be .. math:: \begin{bmatrix} 1 & 2 & 3 & 4 \\ 5 & 6 & 7 & 8 \\ 9 & 10 & 11 & 12 \\ 13 & 14 & 15 & 16 \end{bmatrix}, that is, in row-major order. In Fortran, the same block of data is interpreted in column-major order, namely, .. math:: \begin{bmatrix} 1 & 5 & 9 & 13 \\ 2 & 6 & 10 & 14 \\ 3 & 7 & 11 & 15 \\ 4 & 8 & 12 & 16 \end{bmatrix}. This difference in interpretation of the same block of data by the two languages means, in effect, that matrices from C or C++ will be transposed when interpreted in Fortran. .. note:: If you would like the indices to start at 0 instead of 1 (which follows typical notation in C and C++, but not Fortran), you can create another pointer and associate it thus: .. code-block:: fortran REAL(c_double), DIMENSION(:,:), POINTER :: x, x0 x = lmp%extract_atom("x") x0(0:,0:) => x The above would cause the dimensions of *x* to be (1:3, 1:nmax) and those of *x0* to be (0:2, 0:nmax\ :math:`-`\ 1). [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1032: ERROR: Unknown directive type "f:function". .. f:function:: extract_compute(id, style, type) This function calls :cpp:func:`lammps_extract_compute` and returns a pointer to LAMMPS data tied to the :cpp:class:`Compute` class, specifically data provided by the compute identified by *id*. Computes may provide global, per-atom, or local data, and those data may be a scalar, a vector, or an array. Since computes may provide multiple kinds of data, the user is required to specify which set of data is to be returned through the *style* and *type* variables. .. versionadded:: 3Nov2022 Note that this function actually does not return a value, but rather associates the pointer on the left side of the assignment to point to internal LAMMPS data. Pointers must be of the correct data type to point to said data (i.e., ``REAL(c_double)``) and have compatible rank. The pointer being associated with LAMMPS data is type-, kind-, and rank-checked at run-time via an overloaded assignment operator. For example, .. code-block:: fortran TYPE(lammps) :: lmp REAL(c_double), DIMENSION(:), POINTER :: COM ! code to setup, create atoms, etc. CALL lmp%command('compute COM all com') COM = lmp%extract_compute('COM', lmp%style%global, lmp%style%type) will bind the variable *COM* to the center of mass of the atoms created in your simulation. The vector in this case has length 3; the length (or, in the case of array data, the number of rows and columns) is determined for you based on data from the :cpp:class:`Compute` class. .. admonition:: Array index order Two-dimensional arrays returned from :f:func:`extract_compute` will be **transposed** from equivalent arrays in C, and they will be indexed from 1 instead of 0. See the note at :f:func:`extract_atom` for further details. The following combinations are possible (assuming ``lmp`` is the name of your LAMMPS instance): .. list-table:: :header-rows: 1 :widths: auto * - Style - Type - Type to assign to - Returned data * - ``lmp%style%global`` - ``lmp%type%scalar`` - ``REAL(c_double), POINTER`` - Global scalar * - ``lmp%style%global`` - ``lmp%type%vector`` - ``REAL(c_double), DIMENSION(:), POINTER`` - Global vector * - ``lmp%style%global`` - ``lmp%type%array`` - ``REAL(c_double), DIMENSION(:,:), POINTER`` - Global array * - ``lmp%style%atom`` - ``lmp%type%vector`` - ``REAL(c_double), DIMENSION(:), POINTER`` - Per-atom vector * - ``lmp%style%atom`` - ``lmp%type%array`` - ``REAL(c_double), DIMENSION(:,:), POINTER`` - Per-atom array * - ``lmp%style%local`` - ``lmp%type%vector`` - ``REAL(c_double), DIMENSION(:), POINTER`` - Local vector * - ``lmp%style%local`` - ``lmp%type%array`` - ``REAL(c_double), DIMENSION(:,:), POINTER`` - Local array :p character(len=\*) id: compute ID from which to extract data :p integer(c_int) style: value indicating the style of data to extract (global, per-atom, or local) :p integer(c_int) type: value indicating the type of data to extract (scalar, vector, or array) :to: :cpp:func:`lammps_extract_compute` :r pointer: pointer to LAMMPS data. The left-hand side of the assignment should be a C-compatible pointer (e.g., ``REAL(c_double), POINTER :: x``) to the extracted property. If expecting vector data, the pointer should have dimension ":"; if expecting array (matrix) data, the pointer should have dimension ":,:". :rtype pointer: polymorphic .. note:: If the compute's data are not already computed for the current step, the compute will be invoked. LAMMPS cannot easily check at that time if it is valid to invoke a compute, so it may fail with an error. The caller has to check to avoid such an error. .. warning:: The pointers returned by this function are generally not persistent, since the computed data may be re-distributed, re-allocated, and re-ordered at every invocation. It is advisable to re-invoke this function before the data are accessed or make a copy if the data are to be used after other LAMMPS commands have been issued. Do **not** modify the data returned by this function. [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1144: ERROR: Unknown directive type "f:function". .. f:function:: extract_fix(id, style, type[, nrow][, ncol]) This function calls :cpp:func:`lammps_extract_fix` and returns a pointer to LAMMPS data tied to the :cpp:class:`Fix` class, specifically data provided by the fix identified by *id*. Fixes may provide global, per-atom, or local data, and those data may be a scalar, a vector, or an array. Since many fixes provide multiple kinds of data, the user is required to specify which set of data is to be returned through the *style* and *type* variables. .. versionadded:: 3Nov2022 Global data are calculated at the time they are requested and are only available element-by-element. As such, the user is expected to provide the *nrow* variable to specify which element of a global vector or the *nrow* and *ncol* variables to specify which element of a global array the user wishes LAMMPS to return. The *ncol* variable is optional for global scalar or vector data, and both *nrow* and *ncol* are optional when a global scalar is requested, as well as when per-atom or local data are requested. The following combinations are possible (assuming ``lmp`` is the name of your LAMMPS instance): .. list-table:: :header-rows: 1 :widths: auto * - Style - Type - nrow - ncol - Type to assign to - Returned data * - ``lmp%style%global`` - ``lmp%type%scalar`` - Ignored - Ignored - ``REAL(c_double)`` - Global scalar * - ``lmp%style%global`` - ``lmp%type%vector`` - Required - Ignored - ``REAL(c_double)`` - Element of global vector * - ``lmp%style%global`` - ``lmp%type%array`` - Required - Required - ``REAL(c_double)`` - Element of global array * - ``lmp%style%atom`` - ``lmp%type%scalar`` - - - - (not allowed) * - ``lmp%style%atom`` - ``lmp%type%vector`` - Ignored - Ignored - ``REAL(c_double), DIMENSION(:), POINTER`` - Per-atom vector * - ``lmp%style%atom`` - ``lmp%type%array`` - Ignored - Ignored - ``REAL(c_double), DIMENSION(:,:), POINTER`` - Per-atom array * - ``lmp%style%local`` - ``lmp%type%scalar`` - - - - (not allowed) * - ``lmp%style%local`` - ``lmp%type%vector`` - Ignored - Ignored - ``REAL(c_double), DIMENSION(:), POINTER`` - Per-atom vector * - ``lmp%style%local`` - ``lmp%type%array`` - Ignored - Ignored - ``REAL(c_double), DIMENSION(:,:), POINTER`` - Per-atom array In the case of global data, this function returns a value of type ``REAL(c_double)``. For per-atom or local data, this function does not return a value but instead associates the pointer on the left side of the assignment to point to internal LAMMPS data. Pointers must be of the correct type and kind to point to said data (i.e., ``REAL(c_double)``) and have compatible rank. The pointer being associated with LAMMPS data is type-, kind-, and rank-checked at run-time via an overloaded assignment operator. For example, .. code-block:: fortran TYPE(lammps) :: lmp REAL(c_double) :: dr, dx, dy, dz ! more code to set up, etc. lmp%command('fix george all recenter 2 2 2') ! more code dr = lmp%extract_fix("george", lmp%style%global, lmp%style%scalar) dx = lmp%extract_fix("george", lmp%style%global, lmp%style%vector, 1) dy = lmp%extract_fix("george", lmp%style%global, lmp%style%vector, 2) dz = lmp%extract_fix("george", lmp%style%global, lmp%style%vector, 3) will extract the global scalar calculated by :doc:`fix recenter ` into the variable *dr* and the three elements of the global vector calculated by fix recenter into the variables *dx*, *dy*, and *dz*, respectively. If asked for per-atom or local data, :f:func:`extract_compute` returns a pointer to actual LAMMPS data. The pointer so returned will have the appropriate size to match the internal data, and will be type/kind/rank-checked at the time of the assignment. For example, .. code-block:: fortran TYPE(lammps) :: lmp REAL(c_double), DIMENSION(:), POINTER :: r ! more code to set up, etc. lmp%command('fix state all store/state 0 x y z') ! more code r = lmp%extract_fix('state', lmp%style%atom, lmp%type%array) will bind the pointer *r* to internal LAMMPS data representing the per-atom array computed by :doc:`fix store/state ` when three inputs are specified. Similarly, .. code-block:: fortran TYPE(lammps) :: lmp REAL(c_double), DIMENSION(:), POINTER :: x ! more code to set up, etc. lmp%command('fix state all store/state 0 x') ! more code x = lmp%extract_fix('state', lmp%style%atom, lmp%type%vector) will associate the pointer *x* with internal LAMMPS data corresponding to the per-atom vector computed by :doc:`fix store/state ` when only one input is specified. Similar examples with ``lmp%style%atom`` replaced by ``lmp%style%local`` will extract local data from fixes that define local vectors and/or arrays. .. warning:: The pointers returned by this function for per-atom or local data are generally not persistent, since the computed data may be redistributed, reallocated, and reordered at every invocation of the fix. It is thus advisable to re-invoke this function before the data are accessed or to make a copy if the data are to be used after other LAMMPS commands have been issued. .. note:: LAMMPS cannot easily check if it is valid to access the data, so it may fail with an error. The caller has to avoid such an error. :p character(len=\*) id: string with the name of the fix from which to extract data :p integer(c_int) style: value indicating the style of data to extract (global, per-atom, or local) :p integer(c_int) type: value indicating the type of data to extract (scalar, vector, or array) :p integer(c_int) nrow: row index (used only for global vectors and arrays) :p integer(c_int) ncol: column index (only used for global arrays) :to: :cpp:func:`lammps_extract_fix` :r data: LAMMPS data (for global data) or a pointer to LAMMPS data (for per-atom or local data). The left-hand side of the assignment should be of type ``REAL(c_double)`` and have appropriate rank (i.e., ``DIMENSION(:)`` if expecting per-atom or local vector data and ``DIMENSION(:,:)`` if expecting per-atom or local array data). If expecting local or per-atom data, it should have the ``POINTER`` attribute, but if expecting global data, it should be an ordinary (non-``POINTER``) variable. :rtype data: polymorphic .. admonition:: Array index order Two-dimensional global, per-atom, or local array data from :f:func:`extract_fix` will be **transposed** from equivalent arrays in C (or in the ordinary LAMMPS interface accessed through thermodynamic output), and they will be indexed from 1, not 0. This is true even for global data, which are returned as scalars---this is done primarily so the interface is consistent, as there is no choice but to transpose the indices for per-atom or local array data. See the similar note under :f:func:`extract_atom` for further details. [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1337: ERROR: Unknown directive type "f:function". .. f:function:: extract_variable(name[,group]) This function calls :cpp:func:`lammps_extract_variable` and returns a scalar, vector, or string containing the value of the variable identified by *name*. When the variable is an *equal*-style variable (or one compatible with that style such as *internal*), the variable is evaluated and the corresponding value returned. When the variable is an *atom*-style variable, the variable is evaluated and a vector of values is returned. With all other variables, a string is returned. The *group* argument is only used for *atom* style variables and is ignored otherwise. If *group* is absent for *atom*-style variables, the group is assumed to be "all". .. versionadded:: 3Nov2022 This function returns the values of the variables, not pointers to them. Vectors pointing to *atom*-style variables should be of type ``REAL(c_double)``, be of rank 1 (i.e., ``DIMENSION(:)``), and have the ``ALLOCATABLE`` attribute. .. note:: Unlike the C library interface, the Fortran interface does not require you to deallocate memory when you are through; this is done for you, behind the scenes. For example, .. code-block:: fortran TYPE(lammps) :: lmp REAL(c_double) :: area ! more code to set up, etc. lmp%command('variable A equal lx*ly') ! more code area = lmp%extract_variable("A") will extract the *x*\ --*y* cross-sectional area of the simulation into the variable *area*. :p character(len=\*) name: variable name to evaluate :o character(len=\*) group [optional]: group for which to extract per-atom data (if absent, use "all") :to: :cpp:func:`lammps_extract_variable` :r data: scalar of type ``REAL(c_double)`` (for *equal*-style variables and others that are *equal*-compatible), vector of type ``REAL(c_double), DIMENSION(:), ALLOCATABLE`` for *atom*- or *vector*-style variables, or ``CHARACTER(LEN=*)`` for *string*-style and compatible variables. Strings whose length is too short to hold the result will be truncated. Allocatable strings must be allocated before this function is called; see note at :f:func:`extract_global` regarding allocatable strings. Allocatable arrays (for *atom*- and *vector*-style data) will be reallocated on assignment. :rtype data: polymorphic [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1401: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: set_variable(name, str) Set the value of a string-style variable. .. deprecated:: 7Feb2024 This function assigns a new value from the string *str* to the string-style variable *name*\ . If *name* does not exist or is not a string-style variable, an error is generated. .. warning:: This subroutine is deprecated and :f:subr:`set_string_variable` should be used instead. :p character(len=*) name: name of the variable :p character(len=*) str: new value to assign to the variable :to: :cpp:func:`lammps_set_variable` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1422: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: set_string_variable(name, str) Set the value of a string-style variable. .. versionadded:: 7Feb2024 This function assigns a new value from the string *str* to the string-style variable *name*\ . If *name* does not exist or is not a string-style variable, an error is generated. :p character(len=*) name: name of the variable :p character(len=*) str: new value to assign to the variable :to: :cpp:func:`lammps_set_string_variable` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1438: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: set_internal_variable(name, val) Set the value of a internal-style variable. .. versionadded:: 7Feb2024 This function assigns a new value from the floating-point number *val* to the internal-style variable *name*\ . If *name* does not exist or is not an internal-style variable, an error is generated. :p character(len=*) name: name of the variable :p read(c_double) val: new value to assign to the variable :to: :cpp:func:`lammps_set_internal_variable` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1454: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: gather_atoms(name, count, data) This function calls :cpp:func:`lammps_gather_atoms` to gather the named atom-based entity for all atoms on all processors and return it in the vector *data*. The vector *data* will be ordered by atom ID, which requires consecutive atom IDs (1 to *natoms*). .. versionadded:: 3Nov2022 If you need a similar array but have non-consecutive atom IDs, see :f:func:`gather_atoms_concat`; for a similar array but for a subset of atoms, see :f:func:`gather_atoms_subset`. The *data* array will be ordered in groups of *count* values, sorted by atom ID (e.g., if *name* is *x* and *count* = 3, then *data* = [*x*\ (1,1), *x*\ (2,1), *x*\ (3,1), *x*\ (1,2), *x*\ (2,2), *x*\ (3,2), *x*\ (1,3), :math:`\dots`]); *data* must be ``ALLOCATABLE`` and will be allocated to length (*count* :math:`\times` *natoms*), as queried by :f:func:`get_natoms`. This function is not compatible with ``-DLAMMPS_BIGBIG``. :p character(len=\*) name: desired quantity (e.g., *x* or *mask*) :p integer(c_int) count: number of per-atom values you expect per atom (e.g., 1 for *type*, *mask*, or *charge*; 3 for *x*, *v*, or *f*). Use *count* = 3 with *image* if you want a single image flag unpacked into *x*/*y*/*z* components. :p data: array into which to store the data. Array *must* have the ``ALLOCATABLE`` attribute and be of rank 1 (i.e., ``DIMENSION(:)``). If this array is already allocated, it will be reallocated to fit the length of the incoming data. It should have type ``INTEGER(c_int)`` if expecting integer data and ``REAL(c_double)`` if expecting floating-point data. :ptype data: polymorphic,dimension(:),allocatable :to: :cpp:func:`lammps_gather_atoms` .. note:: If you want data from this function to be accessible as a two-dimensional array, you can declare a rank-2 pointer and reassign it, like so: .. code-block:: fortran USE, INTRINSIC :: ISO_C_BINDING USE LIBLAMMPS TYPE(lammps) :: lmp REAL(c_double), DIMENSION(:), ALLOCATABLE, TARGET :: xdata REAL(c_double), DIMENSION(:,:), POINTER :: x ! other code to set up, etc. CALL lmp%gather_atoms('x',3,xdata) x(1:3,1:size(xdata)/3) => xdata You can then access the *y*\ -component of atom 3 with ``x(2,3)``. See the note about array index order at :f:func:`extract_atom`. [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1511: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: gather_atoms_concat(name, count, data) This function calls :cpp:func:`lammps_gather_atoms_concat` to gather the named atom-based entity for all atoms on all processors and return it in the vector *data*. .. versionadded:: 3Nov2022 The vector *data* will not be ordered by atom ID, and there is no restriction on the IDs being consecutive. If you need the IDs, you can do another :f:func:`gather_atoms_concat` with *name* set to ``id``. If you need a similar array but have consecutive atom IDs, see :f:func:`gather_atoms`; for a similar array but for a subset of atoms, see :f:func:`gather_atoms_subset`. This function is not compatible with ``-DLAMMPS_BIGBIG``. :p character(len=\*) name: desired quantity (e.g., *x* or *mask*) :p integer(c_int) count: number of per-atom values you expect per atom (e.g., 1 for *type*, *mask*, or *charge*; 3 for *x*, *v*, or *f*). Use *count* = 3 with *image* if you want a single image flag unpacked into *x*/*y*/*z* components. :p data: array into which to store the data. Array *must* have the ``ALLOCATABLE`` attribute and be of rank 1 (i.e., ``DIMENSION(:)``). If this array is already allocated, it will be reallocated to fit the length of the incoming data. It should have type ``INTEGER(c_int)`` if expecting integer data and ``REAL(c_double)`` if expecting floating-point data. :ptype data: polymorphic,dimension(:),allocatable :to: :cpp:func:`lammps_gather_atoms_concat` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1545: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: gather_atoms_subset(name, count, ids, data) This function calls :cpp:func:`lammps_gather_atoms_subset` to gather the named atom-based entity for the atoms in the array *ids* from all processors and return it in the vector *data*. .. versionadded:: 3Nov2022 This subroutine gathers data for the requested atom IDs and stores them in a one-dimensional allocatable array. The data will be ordered by atom ID, but there is no requirement that the IDs be consecutive. If you wish to return a similar array for *all* the atoms, use :f:func:`gather_atoms` or :f:func:`gather_atoms_concat`. The *data* array will be in groups of *count* values, sorted by atom ID in the same order as the array *ids* (e.g., if *name* is *x*, *count* = 3, and *ids* is [100, 57, 210], then *data* might look like [*x*\ (1,100), *x*\ (2,100), *x*\ (3,100), *x*\ (1,57), *x*\ (2,57), *x*\ (3,57), *x*\ (1,210), :math:`\dots`]; *ids* must be provided by the user, and *data* must be of rank 1 (i.e., ``DIMENSION(:)``) and have the ``ALLOCATABLE`` attribute. This function is not compatible with ``-DLAMMPS_BIGBIG``. :p character(len=\*) name: desired quantity (e.g., *x* or *mask*) :p integer(c_int) count: number of per-atom values you expect per atom (e.g., 1 for *type*, *mask*, or *charge*; 3 for *x*, *v*, or *f*). Use *count* = 3 with *image* if you want a single image flag unpacked into *x*/*y*/*z* components. :p integer(c_int) ids [dimension(:)]: atom IDs corresponding to the atoms to be gathered :p data: array into which to store the data. Array *must* have the ``ALLOCATABLE`` attribute and be of rank 1 (i.e., ``DIMENSION(:)``). If this array is already allocated, it will be reallocated to fit the length of the incoming data. It should have type ``INTEGER(c_int)`` if expecting integer data and ``REAL(c_double)`` if expecting floating-point data. :ptype data: polymorphic,dimension(:),allocatable :to: :cpp:func:`lammps_gather_atoms_subset` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1587: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: scatter_atoms(name, data) This function calls :cpp:func:`lammps_scatter_atoms` to scatter the named atom-based entities in *data* to all processors. .. versionadded:: 3Nov2022 This subroutine takes data stored in a one-dimensional array supplied by the user and scatters them to all atoms on all processors. The data must be ordered by atom ID, with the requirement that the IDs be consecutive. Use :f:func:`scatter_atoms_subset` to scatter data for some (or all) atoms, in any order. The *data* array needs to be ordered in groups of *count* values, sorted by atom ID (e.g., if *name* is *x* and *count* = 3, then *data* = [*x*\ (1,1), *x*\ (2,1), *x*\ (3,1), *x*\ (1,2), *x*\ (2,2), *x*\ (3,2), *x*\ (1,3), :math:`\dots`]); *data* must be of length *natoms* or 3\*\ *natoms*. :p character(len=\*) name: quantity to be scattered (e.g., *x* or *charge*) :p data: per-atom values packed in a one-dimensional array containing the data to be scattered. This array must have length *natoms* (e.g., for *type* or *charge*) or length *natoms*\ :math:`{}\times 3` (e.g., for *x* or *f*). The array *data* must be rank 1 (i.e., ``DIMENSION(:)``) and be of type ``INTEGER(c_int)`` (e.g., for *mask* or *type*) or of type ``REAL(c_double)`` (e.g., for *x* or *charge* or *f*). :ptype data: polymorphic,dimension(:) :to: :cpp:func:`lammps_scatter_atoms` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1618: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: scatter_atoms_subset(name, ids, data) This function calls :cpp:func:`lammps_scatter_atoms_subset` to scatter the named atom-based entities in *data* to all processors. .. versionadded:: 3Nov2022 This subroutine takes data stored in a one-dimensional array supplied by the user and scatters them to a subset of atoms on all processors. The array *data* contains data associated with atom IDs, but there is no requirement that the IDs be consecutive, as they are provided in a separate array, *ids*. Use :f:func:`scatter_atoms` to scatter data for all atoms, in order. The *data* array needs to be organized in groups of 1 or 3 values, depending on which quantity is being scattered, with the groups in the same order as the array *ids*. For example, if you want *data* to be the array [*x*\ (1,1), *x*\ (2,1), *x*\ (3,1), *x*\ (1,100), *x*\ (2,100), *x*\ (3,100), *x*\ (1,57), *x*\ (2,57), *x*\ (3,57)], then *ids* would be [1, 100, 57] and *name* would be *x*. :p character(len=\*) name: quantity to be scattered (e.g., *x* or *charge*) :p integer(c_int) ids [dimension(:)]: atom IDs corresponding to the atoms being scattered :p data: per-atom values packed into a one-dimensional array containing the data to be scattered. This array must have either the same length as *ids* (for *mask*, *type*, etc.) or three times its length (for *x*, *f*, etc.); the array must be rank 1 and be of type ``INTEGER(c_int)`` (e.g., for *mask* or *type*) or of type ``REAL(c_double)`` (e.g., for *charge*, *x*, or *f*). :ptype data: polymorphic,dimension(:) :to: :cpp:func:`lammps_scatter_atoms_subset` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1652: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: gather_bonds(data) Gather type and constituent atom information for all bonds. .. versionadded:: 3Nov2022 This function copies the list of all bonds into an allocatable array. The array will be filled with (bond type, bond atom 1, bond atom 2) for each bond. The array is allocated to the right length (i.e., three times the number of bonds). The array *data* must be of the same type as the LAMMPS ``tagint`` type, which is equivalent to either ``INTEGER(c_int)`` or ``INTEGER(c_int64_t)``, depending on whether ``-DLAMMPS_BIGBIG`` was used when LAMMPS was built. If the supplied array does not match, an error will result at run-time. An example of how to use this routine is below: .. code-block:: fortran PROGRAM bonds USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT USE LIBLAMMPS IMPLICIT NONE INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET :: bonds INTEGER(c_int), DIMENSION(:,:), POINTER :: bonds_array TYPE(lammps) :: lmp INTEGER :: i ! other commands to initialize LAMMPS, create bonds, etc. CALL lmp%gather_bonds(bonds) bonds_array(1:3, 1:SIZE(bonds)/3) => bonds DO i = 1, SIZE(bonds)/3 WRITE(OUTPUT_UNIT,'(A,1X,I4,A,I4,1X,I4)') 'bond', bonds_array(1,i), & '; type = ', bonds_array(2,i), bonds_array(3,i) END DO END PROGRAM bonds :p data: array into which to copy the result. \*The ``KIND`` parameter is either ``c_int`` or, if LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, kind ``c_int64_t``. :ptype data: integer(kind=\*),allocatable :to: :cpp:func:`lammps_gather_bonds` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1697: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: gather_angles(data) Gather type and constituent atom information for all angles. .. versionadded:: 8Feb2023 This function copies the list of all angles into an allocatable array. The array will be filled with (angle type, angle atom 1, angle atom 2, angle atom 3) for each angle. The array is allocated to the right length (i.e., four times the number of angles). The array *data* must be of the same type as the LAMMPS ``tagint`` type, which is equivalent to either ``INTEGER(c_int)`` or ``INTEGER(c_int64_t)``, depending on whether ``-DLAMMPS_BIGBIG`` was used when LAMMPS was built. If the supplied array does not match, an error will result at run-time. An example of how to use this routine is below: .. code-block:: fortran PROGRAM angles USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT USE LIBLAMMPS IMPLICIT NONE INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET :: angles INTEGER(c_int), DIMENSION(:,:), POINTER :: angles_array TYPE(lammps) :: lmp INTEGER :: i ! other commands to initialize LAMMPS, create angles, etc. CALL lmp%gather_angles(angles) angles_array(1:4, 1:SIZE(angles)/4) => angles DO i = 1, SIZE(angles)/4 WRITE(OUTPUT_UNIT,'(A,1X,I4,A,I4,1X,I4,1X,I4)') 'angle', angles_array(1,i), & '; type = ', angles_array(2,i), angles_array(3,i), angles_array(4,i) END DO END PROGRAM angles :p data: array into which to copy the result. \*The ``KIND`` parameter is either ``c_int`` or, if LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, kind ``c_int64_t``. :ptype data: integer(kind=\*),allocatable :to: :cpp:func:`lammps_gather_angles` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1742: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: gather(self, name, count, data) Gather the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entities from all processes, in order by atom ID. .. versionadded:: 22Dec2022 This subroutine gathers data from all processes and stores them in a one-dimensional allocatable array. The array *data* will be ordered by atom ID, which requires consecutive IDs (1 to *natoms*\ ). If you need a similar array but for non-consecutive atom IDs, see :cpp:func:`lammps_gather_concat`; for a similar array but for a subset of atoms, see :cpp:func:`lammps_gather_subset`. The *data* array will be ordered in groups of *count* values, sorted by atom ID (e.g., if *name* is *x*, then *data* is [x(1,1), x(2,1), x(3,1), x(1,2), x(2,2), x(3,2), x(1,3), :math:`\dots`]); *data* must be ``ALLOCATABLE`` and will be allocated to length (*count*\ :math:`{}\times{}`\ *natoms*), as queried by :f:func:`get_natoms`. This function will return an error if fix or compute data are requested and the fix or compute ID given does not have per-atom data. See the note about re-interpreting the vector as a matrix at :f:subr:`gather_atoms`. This function is not compatible with ``-DLAMMPS_BIGBIG``. :p character(len=\*) name: desired quantity (e.g., "x" or "mask" for atom properties, "f_id" for per-atom fix data, "c_id" for per-atom compute data, "d_name" or "i_name" for fix property/atom vectors with *count* = 1, "d2_name" or "i2_name" for fix property/atom vectors with *count*\ :math:`{}> 1`) :p integer(c_int) count: number of per-atom values (e.g., 1 for *type* or *charge*, 3 for *x* or *f*); use *count* = 3 with *image* if you want the image flags unpacked into (*x*,\ *y*,\ *z*) components. :p real(c_double) data [dimension(:),allocatable]: array into which to store the data. Array *must* have the ``ALLOCATABLE`` attribute and be of rank 1 (i.e., ``DIMENSION(:)``). If this array is already allocated, it will be reallocated to fit the length of the incoming data. :to: :cpp:func:`lammps_gather` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1784: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: gather_dihedrals(data) Gather type and constituent atom information for all dihedrals. .. versionadded:: 8Feb2023 This function copies the list of all dihedrals into an allocatable array. The array will be filled with (dihedral type, dihedral atom 1, dihedral atom 2, dihedral atom 3, dihedral atom 4) for each dihedral. The array is allocated to the right length (i.e., five times the number of dihedrals). The array *data* must be of the same type as the LAMMPS ``tagint`` type, which is equivalent to either ``INTEGER(c_int)`` or ``INTEGER(c_int64_t)``, depending on whether ``-DLAMMPS_BIGBIG`` was used when LAMMPS was built. If the supplied array does not match, an error will result at run-time. An example of how to use this routine is below: .. code-block:: fortran PROGRAM dihedrals USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT USE LIBLAMMPS IMPLICIT NONE INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET :: dihedrals INTEGER(c_int), DIMENSION(:,:), POINTER :: dihedrals_array TYPE(lammps) :: lmp INTEGER :: i ! other commands to initialize LAMMPS, create dihedrals, etc. CALL lmp%gather_dihedrals(dihedrals) dihedrals_array(1:5, 1:SIZE(dihedrals)/5) => dihedrals DO i = 1, SIZE(dihedrals)/5 WRITE(OUTPUT_UNIT,'(A,1X,I4,A,I4,1X,I4,1X,I4,1X,I4)') 'dihedral', dihedrals_array(1,i), & '; type = ', dihedrals_array(2,i), dihedrals_array(3,i), dihedrals_array(4,i), dihedrals_array(5,i) END DO END PROGRAM dihedrals :p data: array into which to copy the result. \*The ``KIND`` parameter is either ``c_int`` or, if LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, kind ``c_int64_t``. :ptype data: integer(kind=\*),allocatable :to: :cpp:func:`lammps_gather_dihedrals` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1830: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: gather_impropers(data) Gather type and constituent atom information for all impropers. .. versionadded:: 8Feb2023 This function copies the list of all impropers into an allocatable array. The array will be filled with (improper type, improper atom 1, improper atom 2, improper atom 3, improper atom 4) for each improper. The array is allocated to the right length (i.e., five times the number of impropers). The array *data* must be of the same type as the LAMMPS ``tagint`` type, which is equivalent to either ``INTEGER(c_int)`` or ``INTEGER(c_int64_t)``, depending on whether ``-DLAMMPS_BIGBIG`` was used when LAMMPS was built. If the supplied array does not match, an error will result at run-time. An example of how to use this routine is below: .. code-block:: fortran PROGRAM impropers USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT USE LIBLAMMPS IMPLICIT NONE INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET :: impropers INTEGER(c_int), DIMENSION(:,:), POINTER :: impropers_array TYPE(lammps) :: lmp INTEGER :: i ! other commands to initialize LAMMPS, create impropers, etc. CALL lmp%gather_impropers(impropers) impropers_array(1:5, 1:SIZE(impropers)/5) => impropers DO i = 1, SIZE(impropers)/5 WRITE(OUTPUT_UNIT,'(A,1X,I4,A,I4,1X,I4,1X,I4,1X,I4)') 'improper', impropers_array(1,i), & '; type = ', impropers_array(2,i), impropers_array(3,i), impropers_array(4,i), impropers_array(5,i) END DO END PROGRAM impropers :p data: array into which to copy the result. \*The ``KIND`` parameter is either ``c_int`` or, if LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, kind ``c_int64_t``. :ptype data: integer(kind=\*),allocatable :to: :cpp:func:`lammps_gather_impropers` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1876: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: gather_concat(self, name, count, data) Gather the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entities from all processes, unordered. .. versionadded:: 22Dec2022 This subroutine gathers data for all atoms and stores them in a one-dimensional allocatable array. The data will be a concatenation of chunks from each processor's owned atoms, in whatever order the atoms are in on each processor. This process has no requirement that the atom IDs be consecutive. If you need the ID of each atom, you can do another call to either :f:subr:`gather_atoms_concat` or :f:subr:`gather_concat` with *name* set to ``id``. If you have consecutive IDs and want the data to be in order, use :f:subr:`gather`; for a similar array but for a subset of atoms, use :f:subr:`gather_subset`. The *data* array will be in groups of *count* values, with *natoms* groups total, but not in order by atom ID (e.g., if *name* is *x* and *count* is 3, then *data* might be something like [x(1,11), x(2,11), x(3,11), x(1,3), x(2,3), x(3,3), x(1,5), :math:`\dots`]); *data* must be ``ALLOCATABLE`` and will be allocated to length (*count* :math:`\times` *natoms*), as queried by :f:func:`get_natoms`. This function is not compatible with ``-DLAMMPS_BIGBIG``. :p character(len=\*) name: desired quantity (e.g., "x" or "mask" for atom properties, "f_id" for per-atom fix data, "c_id" for per-atom compute data, "d_name" or "i_name" for fix property/atom vectors with *count* = 1, "d2_name" or "i2_name" for fix property/atom vectors with *count*\ :math:`{}> 1`) :p integer(c_int) count: number of per-atom values you expect per atom (e.g., 1 for *type*, *mask*, or *charge*; 3 for *x*, *v*, or *f*). Use *count* = 3 with *image* if you want a single image flag unpacked into *x*/*y*/*z* components. :p data: array into which to store the data. Array *must* have the ``ALLOCATABLE`` attribute and be of rank 1 (i.e., ``DIMENSION(:)``). If this array is already allocated, it will be reallocated to fit the length of the incoming data. It should have type ``INTEGER(c_int)`` if expecting integer data and ``REAL(c_double)`` if expecting floating-point data. :ptype data: polymorphic,dimension(:),allocatable :to: :cpp:func:`lammps_gather_concat` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1922: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: gather_subset(name, count, ids, data) Gather the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entities from all processes for a subset of atoms. .. versionadded:: 22Dec2022 This subroutine gathers data for the requested atom IDs and stores them in a one-dimensional allocatable array. The data will be ordered by atom ID, but there is no requirement that the IDs be consecutive. If you wish to return a similar array for *all* the atoms, use :f:subr:`gather` or :f:subr:`gather_concat`. The *data* array will be in groups of *count* values, sorted by atom ID in the same order as the array *ids* (e.g., if *name* is *x*, *count* = 3, and *ids* is [100, 57, 210], then *data* might look like [*x*\ (1,100), *x*\ (2,100), *x*\ (3,100), *x*\ (1,57), *x*\ (2,57), *x*\ (3,57), *x*\ (1,210), :math:`\dots`]); *ids* must be provided by the user, and *data* must have the ``ALLOCATABLE`` attribute and be of rank 1 (i.e., ``DIMENSION(:)``). If *data* is already allocated, it will be reallocated to fit the length of the incoming data. This function is not compatible with ``-DLAMMPS_BIGBIG``. :p character(len=\*) name: quantity to be scattered :p integer(c_int) ids [dimension(:)]: atom IDs corresponding to the atoms being scattered (e.g., "x" or "f" for atom properties, "f_id" for per-atom fix data, "c_id" for per-atom compute data, "d_name" or "i_name" for fix property/atom vectors with *count* = 1, "d2_name" or "i2_name" for fix property/atom vectors with *count*\ :math:`{} > 1`) :p integer(c_int) count: number of per-atom values you expect per atom (e.g., 1 for *type*, *mask*, or *charge*; 3 for *x*, *v*, or *f*). Use *count* = 3 with *image* if you want a single image flag unpacked into *x*/*y*/*z* components. :p data: per-atom values packed into a one-dimensional array containing the data to be scattered. This array must have the ``ALLOCATABLE`` attribute and will be allocated either to the same length as *ids* (for *mask*, *type*, etc.) or to three times its length (for *x*, *f*, etc.); the array must be rank 1 and be of type ``INTEGER(c_int)`` (e.g., for *mask* or *type*) or of type ``REAL(c_double)`` (e.g., for *charge*, *x*, or *f*). :ptype data: polymorphic,dimension(:),allocatable :to: :cpp:func:`lammps_gather_subset` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1969: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: scatter(name, data) This function calls :cpp:func:`lammps_scatter` to scatter the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entity in *data* to all processes. .. versionadded:: 22Dec2022 This subroutine takes data stored in a one-dimensional array supplied by the user and scatters them to all atoms on all processes. The data must be ordered by atom ID, with the requirement that the IDs be consecutive. Use :f:subr:`scatter_subset` to scatter data for some (or all) atoms, unordered. The *data* array needs to be ordered in groups of *count* values, sorted by atom ID (e.g., if *name* is *x* and *count* = 3, then *data* = [*x*\ (1,1), *x*\ (2,1), *x*\ (3,1), *x*\ (1,2), *x*\ (2,2), *x*\ (3,2), *x*\ (1,3), :math:`\dots`]); *data* must be of length (*count* :math:`\times` *natoms*). This function is not compatible with ``-DLAMMPS_BIGBIG``. :p character(len=*) name: desired quantity (e.g., "x" or "f" for atom properties, "f_id" for per-atom fix data, "c_id" for per-atom compute data, "d_name" or "i_name" for fix property/atom vectors with *count* = 1, "d2_name" or "i2_name" for fix property/atom vectors with *count*\ :math:`{} > 1`) :p data: per-atom values packed in a one-dimensional array; *data* should be of type ``INTEGER(c_int)`` or ``REAL(c_double)``, depending on the type of data being scattered, and be of rank 1 (i.e., ``DIMENSION(:)``). :ptype data: polymorphic,dimension(:) :to: :cpp:func:`lammps_scatter` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2002: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: scatter_subset(name, ids, data) This function calls :cpp:func:`lammps_scatter_subset` to scatter the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entities in *data* from a subset of atoms to all processes. .. versionadded:: 22Dec2022 This subroutine takes data stored in a one-dimensional array supplied by the user and scatters them to a subset of atoms on all processes. The array *data* contains data associated with atom IDs, but there is no requirement that the IDs be consecutive, as they are provided in a separate array. Use :f:subr:`scatter` to scatter data for all atoms, in order. The *data* array needs to be organized in groups of *count* values, with the groups in the same order as the array *ids*. For example, if you want *data* to be the array [x(1,1), x(2,1), x(3,1), x(1,100), x(2,100), x(3,100), x(1,57), x(2,57), x(3,57)], then *count* = 3 and *ids* = [1, 100, 57]. This function is not compatible with ``-DLAMMPS_BIGBIG``. :p character(len=\*) name: desired quantity (e.g., "x" or "mask" for atom properties, "f_id" for per-atom fix data, "c_id" for per-atom compute data, "d_name" or "i_name" for fix property/atom vectors with *count* = 1, "d2_name" or "i2_name" for fix property/atom vectors with *count*\ :math:`{}> 1`) :p integer(c_int) ids: list of atom IDs to scatter data for :p polymorphic data [dimension(:)]: per-atom values packed in a one-dimensional array of length *size(ids)* \* *count*. :to: :cpp:func:`lammps_scatter_subset` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2035: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: create_atoms([id,] type, x, [v,] [image,] [bexpand]) This method calls :cpp:func:`lammps_create_atoms` to create additional atoms from a given list of coordinates and a list of atom types. Additionally, the atom IDs, velocities, and image flags may be provided. .. versionadded:: 3Nov2022 :p integer(c_int) type [dimension(N)]: vector of :math:`N` atom types (required/see note below) :p real(c_double) x [dimension(3N)]: vector of :math:`3N\ x/y/z` positions of the new atoms, arranged as :math:`[x_1,y_1,z_1,x_2,y_2,\dotsc]` (required/see note below) :o integer(kind=\*) id [dimension(N),optional]: vector of :math:`N` atom IDs; if absent, LAMMPS will generate them for you. \*The ``KIND`` parameter should be ``c_int`` unless LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, in which case it should be ``c_int64_t``. :o real(c_double) v [dimension(3N),optional]: vector of :math:`3N` *x*\ /*y*\ /*z* velocities of the new atoms, arranged as :math:`[v_{1,x},v_{1,y},v_{1,z},v_{2,x}, \dotsc]`; if absent, they will be set to zero :o integer(kind=\*) image [dimension(N),optional]: vector of :math:`N` image flags; if absent, they are set to zero. \*The ``KIND`` parameter should be ``c_int`` unless LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, in which case it should be ``c_int64_t``. See note below. :o bexpand: if ``.TRUE.``, atoms outside of shrink-wrap boundaries will be created, not dropped, and the box dimensions will be extended. Default is ``.FALSE.`` :otype bexpand: logical,optional :to: :cpp:func:`lammps_create_atoms` .. note:: The *type* and *x* arguments are required, but they are declared ``OPTIONAL`` in the module because making them mandatory would require *id* to be present as well. To have LAMMPS generate the ids for you, use a call something like .. code-block:: fortran lmp%create_atoms(type=new_types, x=new_xs) .. note:: When LAMMPS has been compiled with ``-DLAMMPS_BIGBIG``, it is not possible to include the *image* parameter but omit the *id* parameter. Either *id* must be present, or both *id* and *image* must be absent. This is required because having all arguments be optional in both generic functions creates an ambiguous interface. This limitation does not exist if LAMMPS was not compiled with ``-DLAMMPS_BIGBIG``. [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2088: ERROR: Unknown directive type "f:function". .. f:function:: find_pair_neighlist(style[, exact][, nsub][, reqid]) Find index of a neighbor list requested by a pair style. .. versionadded:: 3Nov2022 This function determines which of the available neighbor lists for pair styles matches the given conditions. It first matches the style name. If *exact* is ``.TRUE.``, the name must match exactly; if ``.FALSE.``, a regular expression or sub-string match is done. If the pair style is *hybrid* or *hybrid/overlay*, the style is matched against the sub-styles instead. If the same pair style is used multiple times as a sub-style, the *nsub* argument must be :math:`> 0`; this argument represents the *n*\ th instance of the sub-style (same as for the :doc:`pair_coeff ` command, for example). In that case, *nsub*\ :math:`{} = 0` will not produce a match, and the function will return :math:`-1`. The final condition to be checked is the request ID (\ *reqid*\ ). This will usually be zero, but some pair styles request multiple neighbor lists and set the request ID to a value greater than zero. :p character(len=\*) style: String used to search for pair style instance. :o exact: Flag to control whether style should match exactly or only a regular expression/sub-string match is applied. Default: ``.TRUE.``. :otype exact: logical,optional :o integer(c_int) nsub [optional]: Match *nsub*\ th hybrid sub-style instance of the same style. Default: 0. :o integer(c_int) reqid [optional]: Request ID to identify the neighbor list in case there are multiple requests from the same pair style instance. Default: 0. :to: :cpp:func:`lammps_find_pair_neighlist` :r integer(c_int) index: Neighbor list index if found, otherwise :math:`-1`. [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2124: ERROR: Unknown directive type "f:function". .. f:function:: find_fix_neighlist(id[, reqid]) Find index of a neighbor list requested by a fix. .. versionadded:: 3Nov2022 The neighbor list request from a fix is identified by the fix ID and the request ID. The request ID is typically zero, but will be :math:`>0` for fixes with multiple neighbor list requests. :p character(len=\*) id: Identifier of fix instance :o integer(c_int) reqid [optional]: request ID to identify the neighbor list in cases in which there are multiple requests from the same fix. Default: 0. :to: :cpp:func:`lammps_find_fix_neighlist` :r index: neighbor list index if found, otherwise :math:`-1` :rtype index: integer(c_int) [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2144: ERROR: Unknown directive type "f:function". .. f:function:: find_compute_neighlist(id[, reqid]) Find index of a neighbor list requested by a compute. .. versionadded:: 3Nov2022 The neighbor list request from a compute is identified by the compute ID and the request ID. The request ID is typically zero, but will be :math:`> 0` in case a compute has multiple neighbor list requests. :p character(len=\*) id: Identifier of compute instance. :o integer(c_int) reqid [optional]: request ID to identify the neighbor list in cases in which there are multiple requests from the same compute. Default: 0. :to: :cpp:func:`lammps_find_compute_neighlist` :r index: neighbor list index if found, otherwise :math:`-1`. :rtype index: integer(c_int) [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2164: ERROR: Unknown directive type "f:function". .. f:function:: neighlist_num_elements(idx) Return the number of entries in the neighbor list with the given index. .. versionadded:: 3Nov2022 :p integer(c_int) idx: neighbor list index :to: :cpp:func:`lammps_neighlist_num_elements` :r inum: number of entries in neighbor list, or :math:`-1` if *idx* is not a valid index. :rtype inum: integer(c_int) :to: :cpp:func:`lammps_neighlist_num_elements` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2179: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: neighlist_element_neighbors(idx, element, iatom, neighbors) Return atom local index, number of neighbors, and array of neighbor local atom indices of a neighbor list entry. .. versionadded:: 3Nov2022 :p integer(c_int) idx: index of this neighbor list in the list of all neighbor lists :p integer(c_int) element: index of this neighbor list entry :p integer(c_int) iatom: local atom index (i.e., in the range [1,nlocal+nghost]; -1 if invalid or element value :p integer(c_int) neighbors [dimension(:),pointer]: pointer to an array of neighboring atom local indices :to: :cpp:func:`lammps_neighlist_element_neighbors` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2197: ERROR: Unknown directive type "f:function". .. f:function:: version() This method returns the numeric LAMMPS version like :cpp:func:`lammps_version` does. :to: :cpp:func:`lammps_version` :r version: LAMMPS version :rtype version: integer [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2208: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: get_os_info(buffer) This function can be used to retrieve detailed information about the hosting operating system and compiler/runtime environment. .. versionadded:: 3Nov2022 A suitable buffer has to be provided. The assembled text will be truncated so as not to overflow this buffer. The string is typically a few hundred bytes long. :p character(len=\*) buffer: string that will house the information. :to: :cpp:func:`lammps_get_os_info` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2225: ERROR: Unknown directive type "f:function". .. f:function:: config_has_mpi_support() This function is used to query whether LAMMPS was compiled with a real MPI library or in serial. .. versionadded:: 3Nov2022 :to: :cpp:func:`lammps_config_has_mpi_support` :r has_mpi: ``.FALSE.`` when compiled with STUBS, ``.TRUE.`` if complied with MPI. :rtype has_mpi: logical [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2239: ERROR: Unknown directive type "f:function". .. f:function:: config_has_gzip_support() Check if the LAMMPS library supports reading or writing compressed files via a pipe to gzip or similar compression programs. .. versionadded:: 3Nov2022 Several LAMMPS commands (e.g., :doc:`read_data`, :doc:`write_data`, :doc:`dump styles atom, custom, and xyz `) support reading and writing compressed files via creating a pipe to the ``gzip`` program. This function checks whether this feature was :ref:`enabled at compile time `. It does **not** check whether ``gzip`` or any other supported compression programs themselves are installed and usable. :to: :cpp:func:`lammps_config_has_gzip_support` :r has_gzip: :rtype has_gzip: logical [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2259: ERROR: Unknown directive type "f:function". .. f:function:: config_has_png_support() Check if the LAMMPS library supports writing PNG format images. .. versionadded:: 3Nov2022 The LAMMPS :doc:`dump style image ` supports writing multiple image file formats. Most of them, however, need support from an external library, and using that has to be :ref:`enabled at compile time `. This function checks whether support for the `PNG image file format `_ is available in the current LAMMPS library. :to: :cpp:func:`lammps_config_has_png_support` :r has_png: :rtype has_png: logical [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2278: ERROR: Unknown directive type "f:function". .. f:function:: config_has_jpeg_support() Check if the LAMMPS library supports writing JPEG format images. .. versionadded:: 3Nov2022 The LAMMPS :doc:`dump style image ` supports writing multiple image file formats. Most of them, however, need support from an external library, and using that has to be :ref:`enabled at compile time `. This function checks whether support for the `JPEG image file format `_ is available in the current LAMMPS library. :to: :cpp:func:`lammps_config_has_jpeg_support` :r has_jpeg: :rtype has_jpeg: logical [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2296: ERROR: Unknown directive type "f:function". .. f:function:: config_has_ffmpeg_support() Check if the LAMMPS library supports creating movie files via a pipe to ffmpeg. .. versionadded:: 3Nov2022 The LAMMPS :doc:`dump style movie ` supports generating movies from images on-the-fly via creating a pipe to the `ffmpeg `_ program. This function checks whether this feature was :ref:`enabled at compile time `. It does **not** check whether the ``ffmpeg`` itself is installed and usable. :to: :cpp:func:`lammps_config_has_ffmpeg_support` :r has_ffmpeg: :rtype has_ffmpeg: logical [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2316: ERROR: Unknown directive type "f:function". .. f:function:: config_has_exceptions() Check whether LAMMPS errors will throw C++ exceptions. .. versionadded:: 3Nov2022 When using the library interface, the library interface functions will "catch" exceptions, and then the error status can be checked by calling :f:func:`has_error`. The most recent error message can be retrieved via :f:func:`get_last_error_message`. This allows to restart a calculation or delete and recreate the LAMMPS instance when a C++ exception occurs. One application of using exceptions this way is the :ref:`lammps_shell`. :to: :cpp:func:`lammps_config_has_exceptions` :r has_exceptions: :rtype has_exceptions: logical [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2336: ERROR: Unknown directive type "f:function". .. f:function:: config_has_package(name) Check whether a specific package has been included in LAMMPS .. versionadded:: 3Nov2022 This function checks whether the LAMMPS library in use includes the specific :doc:`LAMMPS package ` provided as argument. :to: :cpp:func:`lammps_config_has_package` :r has_package: :rtype has_package: logical [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2351: ERROR: Unknown directive type "f:function". .. f:function:: config_package_count() Count the number of installed packages in the LAMMPS library. .. versionadded:: 3Nov2022 This function counts how many :doc:`LAMMPS packages ` are included in the LAMMPS library in use. It directly calls the C library function :cpp:func:`lammps_config_package_count`. :to: :cpp:func:`lammps_config_package_count` :r integer(c_int) npackages: number of packages installed [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2366: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: config_package_name(idx, buffer) Get the name of a package in the list of installed packages in the LAMMPS library. .. versionadded:: 3Nov2022 This subroutine copies the name of the package with the index *idx* into the provided string *buffer*. If the name of the package exceeds the length of the buffer, it will be truncated accordingly. If the index is out of range, *buffer* is set to an empty string. :p integer(c_int) idx: index of the package in the list of included packages :math:`(0 \le idx < \text{package count})` :p character(len=\*) buffer: string to hold the name of the package :to: :cpp:func:`lammps_config_package_name` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2385: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: installed_packages(package[, length]) Obtain a list of the names of enabled packages in the LAMMPS shared library and store it in *package*. .. versionadded:: 3Nov2022 This function is analogous to the :py:meth:`installed_packages ` function in the Python API. The optional argument *length* sets the length of each string in the vector *package* (default: 31). :p character(len=:) package [dimension(:),allocatable]: list of packages; *must* have the ``ALLOCATABLE`` attribute and be of rank 1 (i.e., ``DIMENSION(:)``) with allocatable length. :o length: length of each string in the list. Default: 31. :otype length: integer,optional :to: :cpp:func:`lammps_config_package_count` :to: :cpp:func:`lammps_config_package_name` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2407: ERROR: Unknown directive type "f:function". .. f:function:: config_accelerator(package, category, setting) This function calls :cpp:func:`lammps_config_accelerator` to check the availability of compile time settings of included :doc:`accelerator packages ` in LAMMPS. .. versionadded:: 3Nov2022 Supported packages names are "GPU", "KOKKOS", "INTEL", and "OPENMP". Supported categories are "api" with possible settings "cuda", "hip", "phi", "pthreads", "opencl", "openmp", and "serial"; and "precision" with possible settings "double", "mixed", and "single". :p character(len=\*) package: string with the name of the accelerator package :p character(len=\*) category: string with the name of the setting :p character(len=\*) setting: string with the name of the specific setting :to: :cpp:func:`lammps_config_accelerator` :r available: ``.TRUE.`` if the combination of package, category, and setting is available, otherwise ``.FALSE.``. :rtype available: logical [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2432: ERROR: Unknown directive type "f:function". .. f:function:: has_gpu_device() Checks for the presence of a viable GPU package device. .. versionadded:: 3Nov2022 This function calls :cpp:func:`lammps_has_gpu_device`, which checks at runtime whether an accelerator device is present that can be used with the :doc:`GPU package `. More detailed information about the available device or devices can be obtained by calling the :f:subr:`get_gpu_device_info` subroutine. :to: :cpp:func:`lammps_has_gpu_device` :r available: ``.TRUE.`` if a viable device is available, ``.FALSE.`` if not. :rtype available: logical [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2452: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: get_gpu_device_info(buffer) Get GPU package device information. .. versionadded:: 3Nov2022 Calls :cpp:func:`lammps_get_gpu_device_info` to retrieve detailed information about any accelerator devices that are viable for use with the :doc:`GPU package `. It will fill *buffer* with a string that is equivalent to the output of the ``nvc_get_device`` or ``ocl_get_device`` or ``hip_get_device`` tools that are compiled alongside LAMMPS if the GPU package is enabled. A suitable-length Fortran string has to be provided. The assembled text will be truncated so as not to overflow this buffer. This string can be several kilobytes long if multiple devices are present. :p character(len=\*) buffer: string into which to copy the information. :to: :cpp:func:`lammps_get_gpu_device_info` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2474: ERROR: Unknown directive type "f:function". .. f:function:: has_style(category, name) Check whether a specific style has been included in LAMMPS. .. versionadded:: 3Nov2022 This function calls :cpp:func:`lammps_has_style` to check whether the LAMMPS library in use includes the specific style *name* associated with a specific *category* provided as arguments. Please see :cpp:func:`lammps_has_style` for a list of valid categories. :p character(len=\*) category: category of the style :p character(len=\*) name: name of the style :to: :cpp:func:`lammps_has_style` :r has_style: ``.TRUE.`` if included, ``.FALSE.`` if not. :rtype has_style: logical [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2493: ERROR: Unknown directive type "f:function". .. f:function:: style_count(category) Count the number of styles of *category* in the LAMMPS library. .. versionadded:: 3Nov2022 This function counts how many styles in the provided *category* are included in the LAMMPS library currently in use. Please see :cpp:func:`lammps_has_style` for a list of valid categories. :p character(len=\*) category: category of styles to count :to: :cpp:func:`lammps_style_count` :r integer(c_int) count: number of styles in *category* [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2509: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: style_name(category, idx, buffer) Look up the name of a style by index in the list of styles of a given category in the LAMMPS library. .. versionadded:: 3Nov2022 This function calls :cpp:func:`lammps_style_name` and copies the name of the *category* style with index *idx* into the provided string *buffer*. The length of *buffer* must be long enough to contain the name of the style; if it is too short, the name will be truncated accordingly. If *idx* is out of range, *buffer* will be the empty string and a warning will be issued. :p character(len=\*) category: category of styles :p integer(c_int) idx: index of the style in the list of *category* styles :math:`(1 \leq idx \leq \text{style count})` :p character(len\*) buffer: string buffer to copy the name of the style into :to: :cpp:func:`lammps_style_name` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2532: ERROR: Unknown directive type "f:function". .. f:function:: has_id(category, name) This function checks if the current LAMMPS instance a *category* ID of the given *name* exists. Valid categories are: *compute*\ , *dump*\ , *fix*\ , *group*\ , *molecule*\ , *region*\ , and *variable*\ . .. versionadded:: 3Nov2022 :p character(len=\*) category: category of the ID :p character(len=\*) name: name of the ID :to: :cpp:func:`lammps_has_id` :r has_id: ``.TRUE.`` if *category* style *name* exists, ``.FALSE.`` if not. :rtype has_id: logical [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2548: ERROR: Unknown directive type "f:function". .. f:function:: id_count(category) This function counts how many IDs in the provided *category* are defined in the current LAMMPS instance. Please see :f:func:`has_id` for a list of valid categories. .. versionadded:: 3Nov2022 :p character(len=\*) category: category of the ID :to: :cpp:func:`lammps_id_count` :r count: number of IDs in *category* :rtype count: integer(c_int) [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2563: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: id_name(category, idx, buffer) Look up the name of an ID by index in the list of IDs of a given category. .. versionadded:: 3Nov2022 This function copies the name of the *category* ID with the index *idx* into the provided string *buffer*\ . The length of the buffer must be long enough to hold the string; if the name of the style exceeds the length of the buffer, it will be truncated accordingly. If *buffer* is ``ALLOCATABLE``, it must be allocated *before* the function is called. If *idx* is out of range, *buffer* is set to an empty string and a warning is issued. :p character(len=\*) category: category of IDs :p integer(c_int) idx: index of the ID in the list of *category* styles (:math:`0 \leq idx < count`) :p character(len=\*) buffer: string into which to copy the name of the style :to: :cpp:func:`lammps_id_name` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2586: ERROR: Unknown directive type "f:function". .. f:function:: plugin_count() This function counts the number of loaded plugins. .. versionadded:: 3Nov2022 :to: :cpp:func:`lammps_plugin_count` :r n: number of loaded plugins :rtype n: integer(c_int) [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2598: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: plugin_name(idx, stylebuf, namebuf) Look up the style and name of a plugin by its index in the list of plugins. .. versionadded:: 3Nov2022 This function copies the name of the *style* plugin with the index *idx* into the provided C-style string buffer. The length of the buffer must be provided as *buf_size* argument. If the name of the style exceeds the length of the buffer, it will be truncated accordingly. If the index is out of range, both strings are set to the empty string and a warning is printed. :p integer(c_int) idx: index of the plugin in the list all or *style* plugins :p character(len=\*) stylebuf: string into which to copy the style of the plugin :p character(len=\*) namebuf: string into which to copy the style of the plugin :to: :cpp:func:`lammps_plugin_name` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2621: ERROR: Unknown directive type "f:function". .. f:function:: encode_image_flags(ix, iy, iz) Encodes three integer image flags into a single imageint. .. versionadded:: 3Nov2022 This function performs the bit-shift, addition, and bit-wise OR operations necessary to combine the values of three integers representing the image flags in the :math:`x`-, :math:`y`-, and :math:`z`-directions. Unless LAMMPS is compiled with ``-DLAMMPS_BIGBIG``, those integers are limited to 10-bit signed integers :math:`[-512,512)`. If ``-DLAMMPS_BIGBIG`` was used when compiling, then the return value is of kind ``c_int64_t`` instead of kind ``c_int``, and the valid range for the individual image flags becomes :math:`[-1048576,1048575)` (i.e., the range of a 21-bit signed integer). There is no check on whether the arguments conform to these requirements; values out of range will simply be wrapped back into the interval. :p integer(c_int) ix: image flag in :math:`x`-direction :p integer(c_int) iy: image flag in :math:`y`-direction :p integer(c_int) iz: image flag in :math:`z`-direction :r integer(kind=\*) imageint: encoded image flag. \*The ``KIND`` parameter is ``c_int`` unless LAMMPS was built with ``-DLAMMPS_BIGBIG``, in which case it is ``c_int64_t``. .. note:: The fact that the programmer does not know the ``KIND`` parameter of the return value until compile time means that it is impossible to define an interface that works for both sizes of ``imageint``. One side effect of this is that you must assign the return value of this function to a variable; it cannot be used as the argument to another function or as part of an array constructor. For example, .. code-block:: fortran my_images = [lmp%encode_image_flags(0,0,0), lmp%encode_image_flags(1,0,0)] will *not* work; instead, do something like .. code-block:: fortran my_images(1) = lmp%encode_image_flags(0,0,0) my_images(2) = lmp%encode_image_flags(1,0,0) [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2667: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: decode_image_flags(image, flags) This function does the reverse operation of :f:func:`encode_image_flags`: it takes the image flag and performs the bit-shift and bit-masking operations to decode it and stores the resulting three integers into the array *flags*. .. versionadded:: 3Nov2022 :p integer(kind=\*) image: encoded image flag. \*The ``KIND`` parameter is either ``c_int`` or, if LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, ``c_int64_t``. Kind compatibility is checked at run-time. :p integer(c_int) flags [dimension(3)]: three-element vector where the decoded image flags will be stored. [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2684: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: set_fix_external_callback(id, callback, caller) Set the callback function for a :doc:`fix external ` instance with the given ID. .. versionadded:: 22Dec2022 Fix :doc:`external ` allows programs that are running LAMMPS through its library interface to modify certain LAMMPS properties on specific time steps, similar to the way other fixes do. This subroutine sets the callback function for use with the "pf/callback" mode. The function should have Fortran language bindings with the following interface, which depends on how LAMMPS was compiled: .. code-block:: fortran ABSTRACT INTERFACE SUBROUTINE external_callback(caller, timestep, ids, x, fexternal) USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double, c_int64_t CLASS(*), INTENT(INOUT) :: caller INTEGER(c_bigint), INTENT(IN) :: timestep INTEGER(c_tagint), DIMENSION(:), INTENT(IN) :: ids REAL(c_double), DIMENSION(:,:), INTENT(IN) :: x REAL(c_double), DIMENSION(:,:), INTENT(OUT) :: fexternal END SUBROUTINE external_callback END INTERFACE where ``c_bigint`` is ``c_int`` if ``-DLAMMPS_SMALLSMALL`` was used and ``c_int64_t`` otherwise; and ``c_tagint`` is ``c_int64_t`` if ``-DLAMMPS_BIGBIG`` was used and ``c_int`` otherwise. The argument *caller* to :f:subr:`set_fix_external_callback` is unlimited polymorphic (i.e., it can be any Fortran object you want to pass to the calling function) and will be available as the first argument to the callback function. It can be your LAMMPS instance, which you might need if the callback function needs access to the library interface. The argument must be a scalar; to pass non-scalar data, wrap those data in a derived type and pass an instance of the derived type to *caller*. The array *ids* is an array of length *nlocal* (as accessed from the :cpp:class:`Atom` class or through :f:func:`extract_global`). The arrays *x* and *fexternal* are :math:`3 \times {}`\ *nlocal* arrays; these are transposed from what they would look like in C (see note about array index order at :f:func:`extract_atom`). The callback mechanism is one of two ways that forces can be applied to a simulation with the help of :doc:`fix external `. The alternative is *array* mode, where one calls :f:func:`fix_external_get_force`. Please see the documentation for :doc:`fix external ` for more information about how to use the fix and couple it with external programs. :p character(len=*) id: ID of :doc:`fix external ` instance :p callback: subroutine :doc:`fix external ` should call :ptype callback: external :p class(*) caller [optional]: object you wish to pass to the callback procedure (must be a scalar; see note) :to: :cpp:func:`lammps_set_fix_external_callback` .. note:: The interface for your callback function must match types precisely with the abstract interface block given above. **The compiler probably will not be able to check this for you.** In particular, the first argument ("caller") must be of type ``CLASS(*)`` or you will probably get a segmentation fault or at least a misinterpretation of whatever is in memory there. You can resolve the object using the ``SELECT TYPE`` construct. An example callback function (assuming LAMMPS was compiled with ``-DLAMMPS_SMALLBIG``) that applies something akin to Hooke's Law (with each atom having a different *k* value) is shown below. .. code-block:: fortran MODULE stuff USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double, c_int64_t USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : error_unit IMPLICIT NONE TYPE shield REAL(c_double), DIMENSION(:,:), ALLOCATABLE :: k ! assume k gets allocated to dimension(3,nlocal) at some point ! and assigned values END TYPE shield SUBROUTINE my_callback(caller, timestep, ids, x, fexternal) CLASS(*), INTENT(INOUT) :: caller INTEGER(c_int), INTENT(IN) :: timestep INTEGER(c_int64_t), INTENT(IN) :: ids REAL(c_double), INTENT(IN) :: x(:,:) REAL(c_double), INTENT(OUT) :: fexternal(:,:) SELECT TYPE (caller) TYPE IS (shield) fexternal = - caller%k * x CLASS DEFAULT WRITE(error_unit,*) 'UH OH...' END SELECT END SUBROUTINE my_callback END MODULE stuff ! then, when assigning the callback function, do this: PROGRAM example USE LIBLAMMPS USE stuff TYPE(lammps) :: lmp TYPE(shield) :: my_shield lmp = lammps() CALL lmp%command('fix ext all external pf/callback 1 1') CALL lmp%set_fix_external_callback('ext', my_callback, my_shield) END PROGRAM example [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2800: ERROR: Unknown directive type "f:function". .. f:function:: fix_external_get_force(id) Get pointer to the force array storage in a fix external instance with the given ID. .. versionadded:: 22Dec2022 Fix :doc:`external ` allows programs that are running LAMMPS through its library interfaces to add or modify certain LAMMPS properties on specific time steps, similar to the way other fixes do. This function provides access to the per-atom force storage in a fix external instance with the given fix-ID to be added to the individual atoms when using the "pf/array" mode. The *fexternal* array can be accessed like other "native" per-atom arrays accessible via the :f:func:`extract_atom` function. Please note that the array stores the forces for *local* atoms for each MPI rank, in the order determined by the neighbor list build. Because the underlying data structures can change as well as the order of atom as they migrate between MPI processes because of the domain decomposition parallelization, this function should be always called immediately before the forces are going to be set to get an up-to-date pointer. You can use, for example, :f:func:`extract_setting` to obtain the number of local atoms `nlocal` and then assume the dimensions of the returned force array as ``REAL(c_double) :: force(3,nlocal)``. This function is an alternative to the callback mechanism in fix external set up by :f:subr:`set_fix_external_callback`. The main difference is that this mechanism can be used when forces are to be pre-computed and the control alternates between LAMMPS and the external driver, while the callback mechanism can call an external subroutine to compute the force when the fix is triggered and needs them. Please see the documentation for :doc:`fix external ` for more information about how to use the fix and how to couple it with an external program. :p character(len=*) id: ID of :doc:`fix external ` instance :to: :cpp:func:`lammps_fix_external_get_force` :r fexternal: pointer to the per-atom force array allocated by the fix :rtype fexternal: real(c_double),dimension(3,nlocal) [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2844: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: fix_external_set_energy_global(id, eng) Set the global energy contribution for a :doc:`fix external ` instance with the given ID. .. versionadded:: 22Dec2022 This is a companion function to :f:func:`set_fix_external_callback` and :f:func:`fix_external_get_force` that also sets the contribution to the global energy from the external program. The value of the *eng* argument will be stored in the fix and applied on the current and all following time steps until changed by another call to this function. The energy is in energy units as determined by the current :doc:`units ` settings and is the **total** energy of the contribution. Thus, when running in parallel, all MPI processes have to call this function with the **same** value, and this will be returned as a scalar property of the fix external instance when accessed in LAMMPS input commands or from variables. Please see the documentation for :doc:`fix external ` for more information about how to use the fix and how to couple it with an external program. :p character(len=*) id: fix ID of fix external instance :p real(c_double) eng: total energy to be added to the global energy :to: :cpp:func:`lammps_fix_external_set_energy_global` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2872: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: fix_external_set_virial_global(id, virial) Set the global virial contribution for a fix external instance with the given ID. .. versionadded:: 22Dec2022 This is a companion function to :f:subr:`set_fix_external_callback` and :f:func:`fix_external_get_force` to set the contribution to the global virial from an external program. The six values of the *virial* array will be stored in the fix and applied on the current and all following time steps until changed by another call to this function. The components of the virial need to be stored in the following order: *xx*, *yy*, *zz*, *xy*, *xz*, *yz*. In LAMMPS, the virial is stored internally as `stress*volume` in units of `pressure*volume` as determined by the current :doc:`units ` settings and is the **total** contribution. Thus, when running in parallel, all MPI processes have to call this function with the **same** value, and this will then be added by fix external. Please see the documentation for :doc:`fix external ` for more information about how to use the fix and how to couple it with an external code. :p character(len=*) id: fix ID of fix external instance :p real(c_double) virial [dimension(6)]: the six global stress tensor components to be added to the global virial :to: :cpp:func:`lammps_fix_external_set_virial_global` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2904: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: fix_external_set_energy_peratom(id, eng) Set the per-atom energy contribution for a fix external instance with the given ID. .. versionadded:: 22Dec2022 This is a companion function to :f:subr:`set_fix_external_callback` to set the per-atom energy contribution due to the fix from the external program as part of the callback function. For this to work, the LAMMPS object must be passed as part of the *caller* argument when registering the callback function, or the callback function must otherwise have access to the LAMMPS object, such as through a module-based pointer. .. note:: This function is fully independent from :f:subr:`fix_external_set_energy_global` and will **NOT** add any contributions to the global energy tally and will **NOT** check whether the sum of the contributions added here are consistent with the global added energy. Please see the documentation for :doc:`fix external ` for more information about how to use the fix and how to couple it with an external code. :p character(len=*) id: fix ID of the fix external instance :p real(c_double) eng [dimension(:)]: array of length *nlocal* containing the energy to add to the per-atom energy :to: :cpp:func:`lammps_fix_external_set_energy_peratom` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2937: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: set_fix_external_set_virial_peratom(id, virial) This is a companion function to :f:subr:`set_fix_external_callback` to set the per-atom virial contribution due to the fix from the external program as part of the callback function. For this to work, the LAMMPS object must be passed as the *caller* argument when registering the callback function. .. versionadded:: 22Dec2022 .. note:: This function is fully independent from :f:subr:`fix_external_set_virial_global` and will **NOT** add any contributions to the global virial tally and **NOT** check whether the sum of the contributions added here are consistent with the global added virial. The order and units of the per-atom stress tensor elements are the same as for the global virial. The type and dimensions of the per-atom virial array must be ``REAL(c_double), DIMENSION(6,nlocal)``. Please see the documentation for :doc:`fix external ` for more information about how to use the fix and how to couple it with an external program. :p character(len=*) id: fix ID of fix external instance :p real(c_double) virial [dimension(:,:)]: an array of :math:`6 \times{}`\ *nlocal* components to be added to the per-atom virial :to: :cpp:func:`lammps_set_virial_peratom` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2969: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: fix_external_set_vector_length(id, length) Set the vector length for a global vector stored with fix external for analysis. .. versionadded:: 22Dec2022 This is a companion function to :f:subr:`set_fix_external_callback` and :f:func:`fix_external_get_force` to set the length of a global vector of properties that will be stored with the fix via :f:subr:`fix_external_set_vector`. This function needs to be called **before** a call to :f:subr:`fix_external_set_vector` and **before** a run or minimize command. When running in parallel, it must be called from **all** MPI processes with the same length argument. Please see the documentation for :doc:`fix external ` for more information about how to use the fix and how to couple it with an external program. :p character(len=*) id: fix ID of fix external instance :p integer(c_int) length: length of the global vector to be stored with the fix :to: :cpp:func:`lammps_fix_external_set_vector_length` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2997: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: fix_external_set_vector(id, idx, val) Store a global vector value for a fix external instance with the given ID. .. versionadded:: 22Dec2022 This is a companion function to :f:subr:`set_fix_external_callback` and :f:func:`fix_external_get_force` to set the values of a global vector of properties that will be stored with the fix and can be accessed from within LAMMPS input commands (e.g., fix ave/time or variables) when used in a vector context. This function needs to be called **after** a call to :f:subr:`fix_external_set_vector_length` and **before** a run or minimize command. When running in parallel, it must be called from **all** MPI processes with the **same** *idx* and *val* parameters. The variable *val* is assumed to be extensive. .. note:: The index in the *idx* parameter is 1-based (i.e., the first element is set with *idx*\ :math:`{} = 1`, and the last element of the vector with *idx*\ :math:`{} = N`, where :math:`N` is the value of the *length* parameter of the call to :f:subr:`fix_external_set_vector_length`). Please see the documentation for :doc:`fix external ` for more information about how to use the fix and how to couple it with an external code. :p character(len=*) id: ID of fix external instance :p integer(c_int) idx: 1-based index in global vector :p integer(c_int) val: value to be stored in global vector at index *idx* :to: :cpp:func:`lammps_fix_external_set_vector` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:3033: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: flush_buffers() This function calls :cpp:func:`lammps_flush_buffers`, which flushes buffered output to be written to screen and logfile. This can simplify capturing output from LAMMPS library calls. .. versionadded:: 3Nov2022 :to: :cpp:func:`lammps_flush_buffers` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:3045: ERROR: Unknown directive type "f:function". .. f:function:: is_running() Check if LAMMPS is currently inside a run or minimization. .. versionadded:: 3Nov2022 This function can be used from signal handlers or multi-threaded applications to determine if the LAMMPS instance is currently active. :to: :cpp:func:`lammps_is_running` :r is_running: ``.FALSE.`` if idle or ``.TRUE.`` if active :rtype is_running: logical [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:3060: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: force_timeout() Force a timeout to stop an ongoing run cleanly. .. versionadded:: 3Nov2022 This function can be used from signal handlers or multi-threaded applications to terminate an ongoing run cleanly. :to: :cpp:func:`lammps_force_timeout` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:3073: ERROR: Unknown directive type "f:function". .. f:function:: has_error() Check if there is a (new) error message available. .. versionadded:: 3Nov2022 This function can be used to query if an error inside of LAMMPS has thrown a :ref:`C++ exception `. :to: :cpp:func:`lammps_has_error` :r has_error: ``.TRUE.`` if there is an error. :rtype has_error: logical [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:3088: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: get_last_error_message(buffer[,status]) Copy the last error message into the provided buffer. .. versionadded:: 3Nov2022 This function can be used to retrieve the error message that was set in the event of an error inside of LAMMPS that resulted in a :ref:`C++ exception `. A suitable buffer for a string has to be provided. If the internally-stored error message is longer than the string, it will be truncated accordingly. The optional argument *status* indicates the kind of error: a "1" indicates an error that occurred on all MPI ranks and is often recoverable, while a "2" indicates an abort that would happen only in a single MPI rank and thus may not be recoverable, as other MPI ranks may be waiting on the failing MPI rank(s) to send messages. :p character(len=\*) buffer: string buffer to copy the error message into :o integer(c_int) status [optional]: 1 when all ranks had the error, 2 on a single-rank error. :to: :cpp:func:`lammps_get_last_error_message` [docutils] WARNING: unknown directive or role name: f:func /build/reproducible-path/lammps-20240207+dfsg/doc/src/Classes_lammps.rst:4: ERROR: Unknown interpreted text role "f:func". [docutils] WARNING: unknown directive or role name: f:func :4: ERROR: Unknown interpreted text role "f:func". [docutils] looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/lammps-20240207+dfsg/doc/src/angle_coeff.rst: document is referenced in multiple toctrees: ['angles', 'commands_list'], selecting: commands_list <- angle_coeff /build/reproducible-path/lammps-20240207+dfsg/doc/src/angle_style.rst: document is referenced in multiple toctrees: ['angles', 'commands_list'], selecting: commands_list <- angle_style /build/reproducible-path/lammps-20240207+dfsg/doc/src/angle_write.rst: document is referenced in multiple toctrees: ['angles', 'commands_list'], selecting: commands_list <- angle_write /build/reproducible-path/lammps-20240207+dfsg/doc/src/bond_coeff.rst: document is referenced in multiple toctrees: ['bonds', 'commands_list'], selecting: commands_list <- bond_coeff /build/reproducible-path/lammps-20240207+dfsg/doc/src/bond_style.rst: document is referenced in multiple toctrees: ['bonds', 'commands_list'], selecting: commands_list <- bond_style /build/reproducible-path/lammps-20240207+dfsg/doc/src/bond_write.rst: document is referenced in multiple toctrees: ['bonds', 'commands_list'], selecting: commands_list <- bond_write /build/reproducible-path/lammps-20240207+dfsg/doc/src/compute_modify.rst: document is referenced in multiple toctrees: ['computes', 'commands_list'], selecting: computes <- compute_modify /build/reproducible-path/lammps-20240207+dfsg/doc/src/dihedral_coeff.rst: document is referenced in multiple toctrees: ['dihedrals', 'commands_list'], selecting: dihedrals <- dihedral_coeff /build/reproducible-path/lammps-20240207+dfsg/doc/src/dihedral_style.rst: document is referenced in multiple toctrees: ['dihedrals', 'commands_list'], selecting: dihedrals <- dihedral_style /build/reproducible-path/lammps-20240207+dfsg/doc/src/dihedral_write.rst: document is referenced in multiple toctrees: ['dihedrals', 'commands_list'], selecting: dihedrals <- dihedral_write /build/reproducible-path/lammps-20240207+dfsg/doc/src/dump.rst: document is referenced in multiple toctrees: ['dumps', 'commands_list'], selecting: dumps <- dump /build/reproducible-path/lammps-20240207+dfsg/doc/src/dump_adios.rst: document is referenced in multiple toctrees: ['dumps', 'commands_list'], selecting: dumps <- dump_adios /build/reproducible-path/lammps-20240207+dfsg/doc/src/dump_cfg_uef.rst: document is referenced in multiple toctrees: ['dumps', 'commands_list'], selecting: dumps <- dump_cfg_uef /build/reproducible-path/lammps-20240207+dfsg/doc/src/dump_h5md.rst: document is referenced in multiple toctrees: ['dumps', 'commands_list'], selecting: dumps <- dump_h5md /build/reproducible-path/lammps-20240207+dfsg/doc/src/dump_image.rst: document is referenced in multiple toctrees: ['dumps', 'commands_list'], selecting: dumps <- dump_image /build/reproducible-path/lammps-20240207+dfsg/doc/src/dump_modify.rst: document is referenced in multiple toctrees: ['dumps', 'commands_list'], selecting: dumps <- dump_modify /build/reproducible-path/lammps-20240207+dfsg/doc/src/dump_molfile.rst: document is referenced in multiple toctrees: ['dumps', 'commands_list'], selecting: dumps <- dump_molfile /build/reproducible-path/lammps-20240207+dfsg/doc/src/dump_netcdf.rst: document is referenced in multiple toctrees: ['dumps', 'commands_list'], selecting: dumps <- dump_netcdf /build/reproducible-path/lammps-20240207+dfsg/doc/src/dump_vtk.rst: document is referenced in multiple toctrees: ['dumps', 'commands_list'], selecting: dumps <- dump_vtk /build/reproducible-path/lammps-20240207+dfsg/doc/src/fix_modify.rst: document is referenced in multiple toctrees: ['fixes', 'commands_list'], selecting: fixes <- fix_modify /build/reproducible-path/lammps-20240207+dfsg/doc/src/fix_modify_atc_commands.rst: document is referenced in multiple toctrees: ['fixes', 'Manual'], selecting: fixes <- fix_modify_atc_commands /build/reproducible-path/lammps-20240207+dfsg/doc/src/improper_coeff.rst: document is referenced in multiple toctrees: ['impropers', 'commands_list'], selecting: impropers <- improper_coeff /build/reproducible-path/lammps-20240207+dfsg/doc/src/improper_style.rst: document is referenced in multiple toctrees: ['impropers', 'commands_list'], selecting: impropers <- improper_style /build/reproducible-path/lammps-20240207+dfsg/doc/src/pair_coeff.rst: document is referenced in multiple toctrees: ['pairs', 'commands_list'], selecting: pairs <- pair_coeff /build/reproducible-path/lammps-20240207+dfsg/doc/src/pair_modify.rst: document is referenced in multiple toctrees: ['pairs', 'commands_list'], selecting: pairs <- pair_modify /build/reproducible-path/lammps-20240207+dfsg/doc/src/pair_style.rst: document is referenced in multiple toctrees: ['pairs', 'commands_list'], selecting: pairs <- pair_style /build/reproducible-path/lammps-20240207+dfsg/doc/src/pair_write.rst: document is referenced in multiple toctrees: ['pairs', 'commands_list'], selecting: pairs <- pair_write done preparing documents... done copying assets... copying static files... 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Running Sphinx v8.1.3 loading translations [en]... done Initializing Spelling Checker 7.7.0 Converting `source_suffix = '.rst'` to `source_suffix = {'.rst': 'restructuredtext'}`. loading pickled environment... The configuration has changed (2 options: 'html_css_files', 'html_static_path') done building [mo]: targets for 0 po files that are out of date writing output... building [html]: targets for 1 source files that are out of date updating environment: 0 added, 1 changed, 0 removed reading sources... [100%] Fortran WARNING: unknown directive or role name: f:mod /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1: ERROR: Unknown interpreted text role "f:mod". [docutils] WARNING: unknown directive or role name: f:mod /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:4: ERROR: Unknown interpreted text role "f:mod". [docutils] WARNING: unknown directive or role name: f:mod /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:43: ERROR: Unknown interpreted text role "f:mod". [docutils] WARNING: unknown directive or role name: f:func /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:64: ERROR: Unknown interpreted text role "f:func". [docutils] WARNING: unknown directive or role name: f:func /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:64: ERROR: Unknown interpreted text role "f:func". [docutils] WARNING: unknown directive or role name: f:func /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:133: ERROR: Unknown interpreted text role "f:func". [docutils] WARNING: unknown directive or role name: f:func /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:133: ERROR: Unknown interpreted text role "f:func". [docutils] WARNING: unknown directive or role name: f:func /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:133: ERROR: Unknown interpreted text role "f:func". [docutils] WARNING: unknown directive or role name: f:func /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:133: ERROR: Unknown interpreted text role "f:func". [docutils] WARNING: unknown directive or role name: f:mod /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:254: ERROR: Unknown interpreted text role "f:mod". [docutils] WARNING: unknown directive or role name: f:module /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:257: ERROR: Unknown directive type "f:module". .. f:module:: LIBLAMMPS [docutils] WARNING: unknown directive or role name: f:mod /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:259: ERROR: Unknown interpreted text role "f:mod". [docutils] WARNING: unknown directive or role name: f:currentmodule /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:262: ERROR: Unknown directive type "f:currentmodule". .. f:currentmodule:: None [docutils] WARNING: unknown directive or role name: f:type /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:264: ERROR: Unknown directive type "f:type". .. f:type:: lammps Derived type that is the general class of the Fortran interface. It holds a reference to the :cpp:class:`LAMMPS ` class instance to which any of the included calls are forwarded. :f handle: reference to the LAMMPS class :ftype handle: c_ptr :f style: derived type to access lammps style constants :ftype style: type(lammps_style) :f type: derived type to access lammps type constants :ftype type: type(lammps_type) :f dtype: derived type to access lammps data type constants :ftype dtype: type(lammps_dtype) :f close: :f:subr:`close` :ftype close: subroutine :f subroutine error: :f:subr:`error` :ftype error: subroutine :f file: :f:subr:`file` :ftype file: subroutine :f command: :f:subr:`command` :ftype command: subroutine :f commands_list: :f:subr:`commands_list` :ftype commands_list: subroutine :f commands_string: :f:subr:`commands_string` :ftype commands_string: subroutine :f get_natoms: :f:func:`get_natoms` :ftype get_natoms: function :f get_thermo: :f:func:`get_thermo` :ftype get_thermo: function :f last_thermo: :f:func:`last_thermo` :ftype last_thermo: function :f extract_box: :f:subr:`extract_box` :ftype extract_box: subroutine :f reset_box: :f:subr:`reset_box` :ftype reset_box: subroutine :f memory_usage: :f:subr:`memory_usage` :ftype memory_usage: subroutine :f get_mpi_comm: :f:func:`get_mpi_comm` :ftype get_mpi_comm: function :f extract_setting: :f:func:`extract_setting` :ftype extract_setting: function :f extract_global: :f:func:`extract_global` :ftype extract_global: function :f extract_atom: :f:func:`extract_atom` :ftype extract_atom: function :f extract_compute: :f:func:`extract_compute` :ftype extract_compute: function :f extract_fix: :f:func:`extract_fix` :ftype extract_fix: function :f extract_variable: :f:func:`extract_variable` :ftype extract_variable: function :f set_variable: :f:subr:`set_variable` :ftype set_variable: subroutine :f set_string_variable: :f:subr:`set_set_string_variable` :ftype set_string_variable: subroutine :f set_internal_variable: :f:subr:`set_internal_variable` :ftype set_internal_variable: subroutine :f gather_atoms: :f:subr:`gather_atoms` :ftype gather_atoms: subroutine :f gather_atoms_concat: :f:subr:`gather_atoms_concat` :ftype gather_atoms_concat: subroutine :f gather_atoms_subset: :f:subr:`gather_atoms_subset` :ftype gather_atoms_subset: subroutine :f scatter_atoms: :f:subr:`scatter_atoms` :ftype scatter_atoms: subroutine :f scatter_atoms_subset: :f:subr:`scatter_atoms_subset` :ftype scatter_atoms_subset: subroutine :f gather_bonds: :f:subr:`gather_bonds` :ftype gather_bonds: subroutine :f gather_angles: :f:subr:`gather_angles` :ftype gather_angles: subroutine :f gather_dihedrals: :f:subr:`gather_dihedrals` :ftype gather_dihedrals: subroutine :f gather_impropers: :f:subr:`gather_impropers` :ftype gather_impropers: subroutine :f gather: :f:subr:`gather` :ftype gather: subroutine :f gather_concat: :f:subr:`gather_concat` :ftype gather_concat: subroutine :f gather_subset: :f:subr:`gather_subset` :ftype gather_subset: subroutine :f scatter: :f:subr:`scatter` :ftype scatter: subroutine :f scatter_subset: :f:subr:`scatter_subset` :ftype scatter_subset: subroutine :f create_atoms: :f:subr:`create_atoms` :ftype create_atoms: subroutine :f find_pair_neighlist: :f:func:`find_pair_neighlist` :ftype find_pair_neighlist: function :f find_fix_neighlist: :f:func:`find_fix_neighlist` :ftype find_fix_neighlist: function :f find_compute_neighlist: :f:func:`find_compute_neighlist` :ftype find_compute_neighlist: function :f neighlist_num_elements: :f:func:`neighlist_num_elements` :ftype neighlist_num_elements: function :f neighlist_element_neighbors: :f:subr:`neighlist_element_neighbors` :ftype neighlist_element_neighbors: subroutine :f version: :f:func:`version` :ftype version: function :f get_os_info: :f:subr:`get_os_info` :ftype get_os_info: subroutine :f config_has_mpi_support: :f:func:`config_has_mpi_support` :ftype config_has_mpi_support: function :f config_has_gzip_support: :f:func:`config_has_gzip_support` :ftype config_has_gzip_support: function :f config_has_png_support: :f:func:`config_has_png_support` :ftype config_has_png_support: function :f config_has_jpeg_support: :f:func:`config_has_jpeg_support` :ftype config_has_jpeg_support: function :f config_has_ffmpeg_support: :f:func:`config_has_ffmpeg_support` :ftype config_has_ffmpeg_support: function :f config_has_exceptions: :f:func:`config_has_exceptions` :ftype config_has_exceptions: function :f config_has_package: :f:func:`config_has_package` :ftype config_has_package: function :f config_package_count: :f:func:`config_package_count` :ftype config_package_count: function :f config_package_name: :f:func:`config_package_name` :ftype config_package_name: function :f installed_packages: :f:subr:`installed_packages` :ftype installed_packages: subroutine :f config_accelerator: :f:func:`config_accelerator` :ftype config_accelerator: function :f has_gpu_device: :f:func:`has_gpu_device` :ftype has_gpu_device: function :f get_gpu_device_info: :f:subr:`get_gpu_device_info` :ftype get_gpu_device_info: subroutine :f has_style: :f:func:`has_style` :ftype has_style: function :f style_count: :f:func:`style_count` :ftype style_count: function :f style_name: :f:func:`style_name` :ftype style_name: function :f has_id: :f:func:`has_id` :ftype has_id: function :f id_count: :f:func:`id_count` :ftype id_count: function :f id_name: :f:subr:`id_name` :ftype id_name: subroutine :f plugin_count: :f:func:`plugin_count` :ftype plugin_count: function :f plugin_name: :f:subr:`plugin_name` :ftype plugin_count: subroutine :f encode_image_flags: :f:func:`encode_image_flags` :ftype encode_image_flags: function :f decode_image_flags: :f:subr:`decode_image_flags` :ftype decode_image_flags: subroutine :f set_fix_external_callback: :f:subr:`set_fix_external_callback` :ftype set_fix_external_callback: subroutine :f fix_external_get_force: :f:func:`fix_external_get_force` :ftype fix_external_get_force: function :f fix_external_set_energy_global: :f:subr:`fix_external_set_energy_global` :ftype fix_external_set_energy_global: subroutine :f fix_external_set_virial_global: :f:subr:`fix_external_set_virial_global` :ftype fix_external_set_virial_global: subroutine :f fix_external_set_energy_peratom: :f:subr:`fix_external_set_energy_peratom` :ftype fix_external_set_energy_peratom: subroutine :f fix_external_set_virial_peratom: :f:subr:`fix_external_set_virial_peratom` :ftype fix_external_set_virial_peratom: subroutine :f fix_external_set_vector_length: :f:subr:`fix_external_set_vector_length` :ftype fix_external_set_vector_length: subroutine :f fix_external_set_vector: :f:subr:`fix_external_set_vector` :ftype fix_external_set_vector: subroutine :f flush_buffers: :f:subr:`flush_buffers` :ftype flush_buffers: subroutine :f is_running: :f:func:`is_running` :ftype is_running: function :f force_timeout: :f:subr:`force_timeout` :ftype force_timeout: subroutine :f has_error: :f:func:`has_error` :ftype has_error: function :f get_last_error_message: :f:subr:`get_last_error_message` :ftype get_last_error_message: subroutine [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:441: ERROR: Unknown directive type "f:function". .. f:function:: lammps([args][,comm]) This is the constructor for the Fortran class and will forward the arguments to a call to either :cpp:func:`lammps_open_fortran` or :cpp:func:`lammps_open_no_mpi`. If the LAMMPS library has been compiled with MPI support, it will also initialize MPI, if it has not already been initialized before. The *args* argument with the list of command line parameters is optional and so it the *comm* argument with the MPI communicator. If *comm* is not provided, ``MPI_COMM_WORLD`` is assumed. For more details please see the documentation of :cpp:func:`lammps_open`. :o args: arguments as list of strings :otype args: character(len=\*),dimension(:),optional :o comm: MPI communicator :otype comm: integer,optional :to: :cpp:func:`lammps_open_fortran` :to: :cpp:func:`lammps_open_no_mpi` :r lammps: an instance of the :f:type:`lammps` derived type .. note:: The :f:mod:`MPI_F08` module, which defines Fortran 2008 bindings for MPI, is not directly supported by this interface due to the complexities of supporting both the :f:mod:`MPI_F08` and :f:mod:`MPI` modules at the same time. However, you should be able to use the ``MPI_VAL`` member of the ``MPI_comm`` derived type to access the integer value of the communicator, such as in .. code-block:: fortran PROGRAM testmpi USE LIBLAMMPS USE MPI_F08 TYPE(lammps) :: lmp lmp = lammps(comm=MPI_COMM_SELF%MPI_VAL) END PROGRAM testmpi [docutils] WARNING: unknown directive or role name: f:type /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:480: ERROR: Unknown directive type "f:type". .. f:type:: lammps_style This derived type is there to provide a convenient interface for the style constants used with :f:func:`extract_compute`, :f:func:`extract_fix`, and :f:func:`extract_variable`. Assuming your LAMMPS instance is called ``lmp``, these constants will be ``lmp%style%global``, ``lmp%style%atom``, and ``lmp%style%local``. These values are identical to the values described in :cpp:enum:`_LMP_STYLE_CONST` for the C library interface. :f integer(c_int) global: used to request global data :f integer(c_int) atom: used to request per-atom data :f integer(c_int) local: used to request local data [docutils] WARNING: unknown directive or role name: f:type /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:493: ERROR: Unknown directive type "f:type". .. f:type:: lammps_type This derived type is there to provide a convenient interface for the type constants used with :f:func:`extract_compute`, :f:func:`extract_fix`, and :f:func:`extract_variable`. Assuming your LAMMPS instance is called ``lmp``, these constants will be ``lmp%type%scalar``, ``lmp%type%vector``, and ``lmp%type%array``. These values are identical to the values described in :cpp:enum:`_LMP_TYPE_CONST` for the C library interface. :f integer(c_int) scalar: used to request scalars :f integer(c_int) vector: used to request vectors :f integer(c_int) array: used to request arrays (matrices) [docutils] WARNING: unknown directive or role name: f:type /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:506: ERROR: Unknown interpreted text role "f:type". [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:509: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: close([finalize]) This method will close down the LAMMPS instance through calling :cpp:func:`lammps_close`. If the *finalize* argument is present and has a value of ``.TRUE.``, then this subroutine also calls :cpp:func:`lammps_kokkos_finalize` and :cpp:func:`lammps_mpi_finalize`. :o finalize: shut down the MPI environment of the LAMMPS library if ``.TRUE.``. :otype finalize: logical,optional :to: :cpp:func:`lammps_close` :to: :cpp:func:`lammps_mpi_finalize` :to: :cpp:func:`lammps_kokkos_finalize` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:526: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: error(error_type, error_text) This method is a wrapper around the :cpp:func:`lammps_error` function and will dispatch an error through the LAMMPS Error class. .. versionadded:: 3Nov2022 :p error_type: constant to select which Error class function to call :ptype error_type: integer(c_int) :p character(len=\*) error_text: error message :to: :cpp:func:`lammps_error` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:540: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: file(filename) This method will call :cpp:func:`lammps_file` to have LAMMPS read and process commands from a file. :p character(len=\*) filename: name of file with LAMMPS commands :to: :cpp:func:`lammps_file` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:550: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: command(cmd) This method will call :cpp:func:`lammps_command` to have LAMMPS execute a single command. :p character(len=\*) cmd: single LAMMPS command :to: :cpp:func:`lammps_command` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:560: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: commands_list(cmds) This method will call :cpp:func:`lammps_commands_list` to have LAMMPS execute a list of input lines. :p character(len=\*) cmd [dimension(:)]: list of LAMMPS input lines :to: :cpp:func:`lammps_commands_list` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:570: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: commands_string(str) This method will call :cpp:func:`lammps_commands_string` to have LAMMPS execute a block of commands from a string. :p character(len=\*) str: LAMMPS input in string :to: :cpp:func:`lammps_commands_string` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:580: ERROR: Unknown directive type "f:function". .. f:function:: get_natoms() This function will call :cpp:func:`lammps_get_natoms` and return the number of atoms in the system. :to: :cpp:func:`lammps_get_natoms` :r real(c_double) natoms: number of atoms .. note:: If you would prefer to get the number of atoms in its native format (i.e., as a 32- or 64-bit integer, depending on how LAMMPS was compiled), this can be extracted with :f:func:`extract_global`. [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:596: ERROR: Unknown directive type "f:function". .. f:function:: get_thermo(name) This function will call :cpp:func:`lammps_get_thermo` and return the value of the corresponding thermodynamic keyword. .. versionadded:: 3Nov2022 :p character(len=\*) name: string with the name of the thermo keyword :to: :cpp:func:`lammps_get_thermo` :r value [real(c_double)]: value of the requested thermo property or `0.0_c_double` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:609: ERROR: Unknown directive type "f:function". .. f:function:: last_thermo(what, index) This function will call :cpp:func:`lammps_last_thermo` and returns either a string or a pointer to a cached copy of LAMMPS last thermodynamic output, depending on the data requested through *what*. Note that *index* uses 1-based indexing to access thermo output columns. .. versionadded:: 15Jun2023 Note that this function actually does not return a value, but rather associates the pointer on the left side of the assignment to point to internal LAMMPS data (with the exception of string data, which are copied and returned as ordinary Fortran strings). Pointers must be of the correct data type to point to said data (typically ``INTEGER(c_int)``, ``INTEGER(c_int64_t)``, or ``REAL(c_double)``). The pointer being associated with LAMMPS data is type-checked at run-time via an overloaded assignment operator. The pointers returned by this function point to temporary, read-only data that may be overwritten at any time, so their target values need to be copied to local storage if they are supposed to persist. For example, .. code-block:: fortran PROGRAM thermo USE LIBLAMMPS USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_double, c_int64_t, c_int TYPE(lammps) :: lmp INTEGER(KIND=c_int64_t), POINTER :: ntimestep, bval REAL(KIND=c_double), POINTER :: dval INTEGER(KIND=c_int), POINTER :: nfield, typ, ival INTEGER(KIND=c_int) :: i CHARACTER(LEN=11) :: key lmp = lammps() CALL lmp%file('in.sysinit') ntimestep = lmp%last_thermo('step', 0) nfield = lmp%last_thermo('num', 0) PRINT*, 'Last thermo output on step: ', ntimestep, ' Number of fields: ', nfield DO i=1, nfield key = lmp%last_thermo('keyword',i) typ = lmp%last_thermo('type',i) IF (typ == lmp%dtype%i32) THEN ival = lmp%last_thermo('data',i) PRINT*, key, ':', ival ELSE IF (typ == lmp%dtype%i64) THEN bval = lmp%last_thermo('data',i) PRINT*, key, ':', bval ELSE IF (typ == lmp%dtype%r64) THEN dval = lmp%last_thermo('data',i) PRINT*, key, ':', dval END IF END DO CALL lmp%close(.TRUE.) END PROGRAM thermo would extract the last timestep where thermo output was done and the number of columns it printed. Then it loops over the columns to print out column header keywords and the corresponding data. .. note:: If :f:func:`last_thermo` returns a string, the string must have a length greater than or equal to the length of the string (not including the terminal ``NULL`` character) that LAMMPS returns. If the variable's length is too short, the string will be truncated. As usual in Fortran, strings are padded with spaces at the end. If you use an allocatable string, the string **must be allocated** prior to calling this function. :p character(len=\*) what: string with the name of the thermo keyword :p integer(c_int) index: 1-based column index :to: :cpp:func:`lammps_last_thermo` :r pointer [polymorphic]: pointer to LAMMPS data. The left-hand side of the assignment should be either a string (if expecting string data) or a C-compatible pointer (e.g., ``INTEGER(c_int), POINTER :: nlocal``) to the extracted property. .. warning:: Modifying the data in the location pointed to by the returned pointer may lead to inconsistent internal data and thus may cause failures, crashes, or bogus simulations. In general, it is much better to use a LAMMPS input command that sets or changes these parameters. Using an input command will take care of all side effects and necessary updates of settings derived from such settings. [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:699: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: extract_box([boxlo][, boxhi][, xy][, yz][, xz][, pflags][, boxflag]) This subroutine will call :cpp:func:`lammps_extract_box`. All parameters are optional, though obviously at least one should be present. The parameters *pflags* and *boxflag* are stored in LAMMPS as integers, but should be declared as ``LOGICAL`` variables when calling from Fortran. .. versionadded:: 3Nov2022 :o real(c_double) boxlo [dimension(3),optional]: vector in which to store lower-bounds of simulation box :o real(c_double) boxhi [dimension(3),optional]: vector in which to store upper-bounds of simulation box :o real(c_double) xy [optional]: variable in which to store *xy* tilt factor :o real(c_double) yz [optional]: variable in which to store *yz* tilt factor :o real(c_double) xz [optional]: variable in which to store *xz* tilt factor :o pflags: vector in which to store periodicity flags (``.TRUE.`` means periodic in that dimension) :otype pflags: logical,dimension(3),optional :o boxflag: variable in which to store boolean denoting whether the box will change during a simulation (``.TRUE.`` means box will change) :otype boxflag: logical,optional :to: :cpp:func:`lammps_extract_box` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:741: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: reset_box(boxlo, boxhi, xy, yz, xz) This subroutine will call :cpp:func:`lammps_reset_box`. All parameters are required. .. versionadded:: 3Nov2022 :p real(c_double) boxlo [dimension(3)]: vector of three doubles containing the lower box boundary :p real(c_double) boxhi [dimension(3)]: vector of three doubles containing the upper box boundary :p real(c_double) xy: *x--y* tilt factor :p real(c_double) yz: *y--z* tilt factor :p real(c_double) xz: *x--z* tilt factor :to: :cpp:func:`lammps_reset_box` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:759: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: memory_usage(meminfo) This subroutine will call :cpp:func:`lammps_memory_usage` and store the result in the three-element array *meminfo*. .. versionadded:: 3Nov2022 :p real(c_double) meminfo [dimension(3)]: vector of three doubles in which to store memory usage data :to: :cpp:func:`lammps_memory_usage` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:772: ERROR: Unknown directive type "f:function". .. f:function:: get_mpi_comm() This function returns a Fortran representation of the LAMMPS "world" communicator. .. versionadded:: 3Nov2022 :to: :cpp:func:`lammps_get_mpi_comm` :r comm: Fortran integer equivalent to the MPI communicator LAMMPS is using :rtype comm: integer .. note:: The C library interface currently returns type ``int`` instead of type ``MPI_Fint``, which is the C type corresponding to Fortran ``INTEGER`` types of the default kind. On most compilers, these are the same anyway, but this interface exchanges values this way to avoid warning messages. .. note:: The :f:mod:`MPI_F08` module, which defines Fortran 2008 bindings for MPI, is not directly supported by this function. However, you should be able to convert between the two using the `MPI_VAL` member of the communicator. For example, .. code-block:: fortran USE MPI_F08 USE LIBLAMMPS TYPE(lammps) :: lmp TYPE(MPI_Comm) :: comm ! ... [commands to set up LAMMPS/etc.] comm%MPI_VAL = lmp%get_mpi_comm() should assign an :f:mod:`MPI_F08` communicator properly. [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:812: ERROR: Unknown directive type "f:function". .. f:function:: extract_setting(keyword) Query LAMMPS about global settings. See the documentation for the :cpp:func:`lammps_extract_setting` function from the C library. .. versionadded:: 3Nov2022 :p character(len=\*) keyword: string containing the name of the thermo keyword :to: :cpp:func:`lammps_extract_setting` :r integer(c_int) setting: value of the queried setting or :math:`-1` if unknown [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:826: ERROR: Unknown directive type "f:function". .. f:function:: extract_global(name) This function calls :cpp:func:`lammps_extract_global` and returns either a string or a pointer to internal global LAMMPS data, depending on the data requested through *name*. .. versionadded:: 3Nov2022 Note that this function actually does not return a value, but rather associates the pointer on the left side of the assignment to point to internal LAMMPS data (with the exception of string data, which are copied and returned as ordinary Fortran strings). Pointers must be of the correct data type to point to said data (typically ``INTEGER(c_int)``, ``INTEGER(c_int64_t)``, or ``REAL(c_double)``) and have compatible kind and rank. The pointer being associated with LAMMPS data is type-, kind-, and rank-checked at run-time via an overloaded assignment operator. The pointers returned by this function are generally persistent; therefore it is not necessary to call the function again unless a :doc:`clear` command has been issued, which wipes out and recreates the contents of the :cpp:class:`LAMMPS ` class. For example, .. code-block:: fortran PROGRAM demo USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int64_t, c_int, c_double USE LIBLAMMPS TYPE(lammps) :: lmp INTEGER(c_int), POINTER :: nlocal => NULL() INTEGER(c_int64_t), POINTER :: ntimestep => NULL() REAL(c_double), POINTER :: dt => NULL() CHARACTER(LEN=10) :: units lmp = lammps() ! other commands nlocal = lmp%extract_global('nlocal') ntimestep = lmp%extract_global('ntimestep') dt = lmp%extract_global('dt') units = lmp%extract_global('units') ! more commands lmp.close(.TRUE.) END PROGRAM demo would extract the number of atoms on this processor, the current time step, the size of the current time step, and the units being used into the variables *nlocal*, *ntimestep*, *dt*, and *units*, respectively. .. note:: If :f:func:`extract_global` returns a string, the string must have a length greater than or equal to the length of the string (not including the terminal ``NULL`` character) that LAMMPS returns. If the variable's length is too short, the string will be truncated. As usual in Fortran, strings are padded with spaces at the end. If you use an allocatable string, the string **must be allocated** prior to calling this function, but you can automatically reallocate it to the correct length after the function returns, viz., .. code-block :: fortran PROGRAM test USE LIBLAMMPS TYPE(lammps) :: lmp CHARACTER(LEN=:), ALLOCATABLE :: str lmp = lammps() CALL lmp%command('units metal') ALLOCATE(CHARACTER(LEN=80) :: str) str = lmp%extract_global('units') str = TRIM(str) ! re-allocates to length len_trim(str) here PRINT*, LEN(str), LEN_TRIM(str) END PROGRAM test will print the number 5 (the length of the word "metal") twice. :p character(len=\*) name: string with the name of the property to extract :to: :cpp:func:`lammps_extract_global` :r pointer [polymorphic]: pointer to LAMMPS data. The left-hand side of the assignment should be either a string (if expecting string data) or a C-compatible pointer (e.g., ``INTEGER(c_int), POINTER :: nlocal``) to the extracted property. If expecting vector data, the pointer should have dimension ":". .. warning:: Modifying the data in the location pointed to by the returned pointer may lead to inconsistent internal data and thus may cause failures, crashes, or bogus simulations. In general, it is much better to use a LAMMPS input command that sets or changes these parameters. Using an input command will take care of all side effects and necessary updates of settings derived from such settings. [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:921: ERROR: Unknown directive type "f:function". .. f:function:: extract_atom(name) This function calls :cpp:func:`lammps_extract_atom` and returns a pointer to LAMMPS data tied to the :cpp:class:`Atom` class, depending on the data requested through *name*. .. versionadded:: 3Nov2022 Note that this function actually does not return a pointer, but rather associates the pointer on the left side of the assignment to point to internal LAMMPS data. Pointers must be of the correct type, kind, and rank (e.g., ``INTEGER(c_int), DIMENSION(:)`` for "type", "mask", or "id"; ``INTEGER(c_int64_t), DIMENSION(:)`` for "id" if LAMMPS was compiled with the ``-DLAMMPS_BIGBIG`` flag; ``REAL(c_double), DIMENSION(:,:)`` for "x", "v", or "f"; and so forth). The pointer being associated with LAMMPS data is type-, kind-, and rank-checked at run-time. :p character(len=\*) name: string with the name of the property to extract :to: :cpp:func:`lammps_extract_atom` :r pointer: pointer to LAMMPS data. The left-hand side of the assignment should be a C-interoperable pointer of appropriate kind and rank (e.g., ``INTEGER(c_int), POINTER :: mask(:)``) to the extracted property. If expecting vector data, the pointer should have dimension ":"; if expecting matrix data, the pointer should have dimension ":,:". :rtype pointer: polymorphic .. warning:: Pointers returned by this function are generally not persistent, as per-atom data may be redistributed, reallocated, and reordered at every re-neighboring operation. It is advisable to re-bind pointers using :f:func:`extract_atom` between runs. .. admonition:: Array index order Two-dimensional arrays returned from :f:func:`extract_atom` will be **transposed** from equivalent arrays in C, and they will be indexed from 1 instead of 0. For example, in C, .. code-block:: c void *lmp; double **x; /* more code to setup, etc. */ x = lammps_extract_atom(lmp, "x"); printf("%f\n", x[5][1]); will print the *y*-coordinate of the sixth atom on this processor. Conversely, .. code-block:: fortran TYPE(lammps) :: lmp REAL(c_double), DIMENSION(:,:), POINTER :: x => NULL() ! more code to setup, etc. x = lmp%extract_atom("x") PRINT '(f0.6)', x(2,6) will print the *y*-coordinate of the sixth atom on this processor (note the transposition of the two indices). This is not a choice, but rather a consequence of the different conventions adopted by the Fortran and C standards decades ago: in C, the block of data .. parsed-literal:: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 interpreted as a :math:`4\times4` matrix would be .. math:: \begin{bmatrix} 1 & 2 & 3 & 4 \\ 5 & 6 & 7 & 8 \\ 9 & 10 & 11 & 12 \\ 13 & 14 & 15 & 16 \end{bmatrix}, that is, in row-major order. In Fortran, the same block of data is interpreted in column-major order, namely, .. math:: \begin{bmatrix} 1 & 5 & 9 & 13 \\ 2 & 6 & 10 & 14 \\ 3 & 7 & 11 & 15 \\ 4 & 8 & 12 & 16 \end{bmatrix}. This difference in interpretation of the same block of data by the two languages means, in effect, that matrices from C or C++ will be transposed when interpreted in Fortran. .. note:: If you would like the indices to start at 0 instead of 1 (which follows typical notation in C and C++, but not Fortran), you can create another pointer and associate it thus: .. code-block:: fortran REAL(c_double), DIMENSION(:,:), POINTER :: x, x0 x = lmp%extract_atom("x") x0(0:,0:) => x The above would cause the dimensions of *x* to be (1:3, 1:nmax) and those of *x0* to be (0:2, 0:nmax\ :math:`-`\ 1). [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1032: ERROR: Unknown directive type "f:function". .. f:function:: extract_compute(id, style, type) This function calls :cpp:func:`lammps_extract_compute` and returns a pointer to LAMMPS data tied to the :cpp:class:`Compute` class, specifically data provided by the compute identified by *id*. Computes may provide global, per-atom, or local data, and those data may be a scalar, a vector, or an array. Since computes may provide multiple kinds of data, the user is required to specify which set of data is to be returned through the *style* and *type* variables. .. versionadded:: 3Nov2022 Note that this function actually does not return a value, but rather associates the pointer on the left side of the assignment to point to internal LAMMPS data. Pointers must be of the correct data type to point to said data (i.e., ``REAL(c_double)``) and have compatible rank. The pointer being associated with LAMMPS data is type-, kind-, and rank-checked at run-time via an overloaded assignment operator. For example, .. code-block:: fortran TYPE(lammps) :: lmp REAL(c_double), DIMENSION(:), POINTER :: COM ! code to setup, create atoms, etc. CALL lmp%command('compute COM all com') COM = lmp%extract_compute('COM', lmp%style%global, lmp%style%type) will bind the variable *COM* to the center of mass of the atoms created in your simulation. The vector in this case has length 3; the length (or, in the case of array data, the number of rows and columns) is determined for you based on data from the :cpp:class:`Compute` class. .. admonition:: Array index order Two-dimensional arrays returned from :f:func:`extract_compute` will be **transposed** from equivalent arrays in C, and they will be indexed from 1 instead of 0. See the note at :f:func:`extract_atom` for further details. The following combinations are possible (assuming ``lmp`` is the name of your LAMMPS instance): .. list-table:: :header-rows: 1 :widths: auto * - Style - Type - Type to assign to - Returned data * - ``lmp%style%global`` - ``lmp%type%scalar`` - ``REAL(c_double), POINTER`` - Global scalar * - ``lmp%style%global`` - ``lmp%type%vector`` - ``REAL(c_double), DIMENSION(:), POINTER`` - Global vector * - ``lmp%style%global`` - ``lmp%type%array`` - ``REAL(c_double), DIMENSION(:,:), POINTER`` - Global array * - ``lmp%style%atom`` - ``lmp%type%vector`` - ``REAL(c_double), DIMENSION(:), POINTER`` - Per-atom vector * - ``lmp%style%atom`` - ``lmp%type%array`` - ``REAL(c_double), DIMENSION(:,:), POINTER`` - Per-atom array * - ``lmp%style%local`` - ``lmp%type%vector`` - ``REAL(c_double), DIMENSION(:), POINTER`` - Local vector * - ``lmp%style%local`` - ``lmp%type%array`` - ``REAL(c_double), DIMENSION(:,:), POINTER`` - Local array :p character(len=\*) id: compute ID from which to extract data :p integer(c_int) style: value indicating the style of data to extract (global, per-atom, or local) :p integer(c_int) type: value indicating the type of data to extract (scalar, vector, or array) :to: :cpp:func:`lammps_extract_compute` :r pointer: pointer to LAMMPS data. The left-hand side of the assignment should be a C-compatible pointer (e.g., ``REAL(c_double), POINTER :: x``) to the extracted property. If expecting vector data, the pointer should have dimension ":"; if expecting array (matrix) data, the pointer should have dimension ":,:". :rtype pointer: polymorphic .. note:: If the compute's data are not already computed for the current step, the compute will be invoked. LAMMPS cannot easily check at that time if it is valid to invoke a compute, so it may fail with an error. The caller has to check to avoid such an error. .. warning:: The pointers returned by this function are generally not persistent, since the computed data may be re-distributed, re-allocated, and re-ordered at every invocation. It is advisable to re-invoke this function before the data are accessed or make a copy if the data are to be used after other LAMMPS commands have been issued. Do **not** modify the data returned by this function. [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1144: ERROR: Unknown directive type "f:function". .. f:function:: extract_fix(id, style, type[, nrow][, ncol]) This function calls :cpp:func:`lammps_extract_fix` and returns a pointer to LAMMPS data tied to the :cpp:class:`Fix` class, specifically data provided by the fix identified by *id*. Fixes may provide global, per-atom, or local data, and those data may be a scalar, a vector, or an array. Since many fixes provide multiple kinds of data, the user is required to specify which set of data is to be returned through the *style* and *type* variables. .. versionadded:: 3Nov2022 Global data are calculated at the time they are requested and are only available element-by-element. As such, the user is expected to provide the *nrow* variable to specify which element of a global vector or the *nrow* and *ncol* variables to specify which element of a global array the user wishes LAMMPS to return. The *ncol* variable is optional for global scalar or vector data, and both *nrow* and *ncol* are optional when a global scalar is requested, as well as when per-atom or local data are requested. The following combinations are possible (assuming ``lmp`` is the name of your LAMMPS instance): .. list-table:: :header-rows: 1 :widths: auto * - Style - Type - nrow - ncol - Type to assign to - Returned data * - ``lmp%style%global`` - ``lmp%type%scalar`` - Ignored - Ignored - ``REAL(c_double)`` - Global scalar * - ``lmp%style%global`` - ``lmp%type%vector`` - Required - Ignored - ``REAL(c_double)`` - Element of global vector * - ``lmp%style%global`` - ``lmp%type%array`` - Required - Required - ``REAL(c_double)`` - Element of global array * - ``lmp%style%atom`` - ``lmp%type%scalar`` - - - - (not allowed) * - ``lmp%style%atom`` - ``lmp%type%vector`` - Ignored - Ignored - ``REAL(c_double), DIMENSION(:), POINTER`` - Per-atom vector * - ``lmp%style%atom`` - ``lmp%type%array`` - Ignored - Ignored - ``REAL(c_double), DIMENSION(:,:), POINTER`` - Per-atom array * - ``lmp%style%local`` - ``lmp%type%scalar`` - - - - (not allowed) * - ``lmp%style%local`` - ``lmp%type%vector`` - Ignored - Ignored - ``REAL(c_double), DIMENSION(:), POINTER`` - Per-atom vector * - ``lmp%style%local`` - ``lmp%type%array`` - Ignored - Ignored - ``REAL(c_double), DIMENSION(:,:), POINTER`` - Per-atom array In the case of global data, this function returns a value of type ``REAL(c_double)``. For per-atom or local data, this function does not return a value but instead associates the pointer on the left side of the assignment to point to internal LAMMPS data. Pointers must be of the correct type and kind to point to said data (i.e., ``REAL(c_double)``) and have compatible rank. The pointer being associated with LAMMPS data is type-, kind-, and rank-checked at run-time via an overloaded assignment operator. For example, .. code-block:: fortran TYPE(lammps) :: lmp REAL(c_double) :: dr, dx, dy, dz ! more code to set up, etc. lmp%command('fix george all recenter 2 2 2') ! more code dr = lmp%extract_fix("george", lmp%style%global, lmp%style%scalar) dx = lmp%extract_fix("george", lmp%style%global, lmp%style%vector, 1) dy = lmp%extract_fix("george", lmp%style%global, lmp%style%vector, 2) dz = lmp%extract_fix("george", lmp%style%global, lmp%style%vector, 3) will extract the global scalar calculated by :doc:`fix recenter ` into the variable *dr* and the three elements of the global vector calculated by fix recenter into the variables *dx*, *dy*, and *dz*, respectively. If asked for per-atom or local data, :f:func:`extract_compute` returns a pointer to actual LAMMPS data. The pointer so returned will have the appropriate size to match the internal data, and will be type/kind/rank-checked at the time of the assignment. For example, .. code-block:: fortran TYPE(lammps) :: lmp REAL(c_double), DIMENSION(:), POINTER :: r ! more code to set up, etc. lmp%command('fix state all store/state 0 x y z') ! more code r = lmp%extract_fix('state', lmp%style%atom, lmp%type%array) will bind the pointer *r* to internal LAMMPS data representing the per-atom array computed by :doc:`fix store/state ` when three inputs are specified. Similarly, .. code-block:: fortran TYPE(lammps) :: lmp REAL(c_double), DIMENSION(:), POINTER :: x ! more code to set up, etc. lmp%command('fix state all store/state 0 x') ! more code x = lmp%extract_fix('state', lmp%style%atom, lmp%type%vector) will associate the pointer *x* with internal LAMMPS data corresponding to the per-atom vector computed by :doc:`fix store/state ` when only one input is specified. Similar examples with ``lmp%style%atom`` replaced by ``lmp%style%local`` will extract local data from fixes that define local vectors and/or arrays. .. warning:: The pointers returned by this function for per-atom or local data are generally not persistent, since the computed data may be redistributed, reallocated, and reordered at every invocation of the fix. It is thus advisable to re-invoke this function before the data are accessed or to make a copy if the data are to be used after other LAMMPS commands have been issued. .. note:: LAMMPS cannot easily check if it is valid to access the data, so it may fail with an error. The caller has to avoid such an error. :p character(len=\*) id: string with the name of the fix from which to extract data :p integer(c_int) style: value indicating the style of data to extract (global, per-atom, or local) :p integer(c_int) type: value indicating the type of data to extract (scalar, vector, or array) :p integer(c_int) nrow: row index (used only for global vectors and arrays) :p integer(c_int) ncol: column index (only used for global arrays) :to: :cpp:func:`lammps_extract_fix` :r data: LAMMPS data (for global data) or a pointer to LAMMPS data (for per-atom or local data). The left-hand side of the assignment should be of type ``REAL(c_double)`` and have appropriate rank (i.e., ``DIMENSION(:)`` if expecting per-atom or local vector data and ``DIMENSION(:,:)`` if expecting per-atom or local array data). If expecting local or per-atom data, it should have the ``POINTER`` attribute, but if expecting global data, it should be an ordinary (non-``POINTER``) variable. :rtype data: polymorphic .. admonition:: Array index order Two-dimensional global, per-atom, or local array data from :f:func:`extract_fix` will be **transposed** from equivalent arrays in C (or in the ordinary LAMMPS interface accessed through thermodynamic output), and they will be indexed from 1, not 0. This is true even for global data, which are returned as scalars---this is done primarily so the interface is consistent, as there is no choice but to transpose the indices for per-atom or local array data. See the similar note under :f:func:`extract_atom` for further details. [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1337: ERROR: Unknown directive type "f:function". .. f:function:: extract_variable(name[,group]) This function calls :cpp:func:`lammps_extract_variable` and returns a scalar, vector, or string containing the value of the variable identified by *name*. When the variable is an *equal*-style variable (or one compatible with that style such as *internal*), the variable is evaluated and the corresponding value returned. When the variable is an *atom*-style variable, the variable is evaluated and a vector of values is returned. With all other variables, a string is returned. The *group* argument is only used for *atom* style variables and is ignored otherwise. If *group* is absent for *atom*-style variables, the group is assumed to be "all". .. versionadded:: 3Nov2022 This function returns the values of the variables, not pointers to them. Vectors pointing to *atom*-style variables should be of type ``REAL(c_double)``, be of rank 1 (i.e., ``DIMENSION(:)``), and have the ``ALLOCATABLE`` attribute. .. note:: Unlike the C library interface, the Fortran interface does not require you to deallocate memory when you are through; this is done for you, behind the scenes. For example, .. code-block:: fortran TYPE(lammps) :: lmp REAL(c_double) :: area ! more code to set up, etc. lmp%command('variable A equal lx*ly') ! more code area = lmp%extract_variable("A") will extract the *x*\ --*y* cross-sectional area of the simulation into the variable *area*. :p character(len=\*) name: variable name to evaluate :o character(len=\*) group [optional]: group for which to extract per-atom data (if absent, use "all") :to: :cpp:func:`lammps_extract_variable` :r data: scalar of type ``REAL(c_double)`` (for *equal*-style variables and others that are *equal*-compatible), vector of type ``REAL(c_double), DIMENSION(:), ALLOCATABLE`` for *atom*- or *vector*-style variables, or ``CHARACTER(LEN=*)`` for *string*-style and compatible variables. Strings whose length is too short to hold the result will be truncated. Allocatable strings must be allocated before this function is called; see note at :f:func:`extract_global` regarding allocatable strings. Allocatable arrays (for *atom*- and *vector*-style data) will be reallocated on assignment. :rtype data: polymorphic [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1401: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: set_variable(name, str) Set the value of a string-style variable. .. deprecated:: 7Feb2024 This function assigns a new value from the string *str* to the string-style variable *name*\ . If *name* does not exist or is not a string-style variable, an error is generated. .. warning:: This subroutine is deprecated and :f:subr:`set_string_variable` should be used instead. :p character(len=*) name: name of the variable :p character(len=*) str: new value to assign to the variable :to: :cpp:func:`lammps_set_variable` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1422: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: set_string_variable(name, str) Set the value of a string-style variable. .. versionadded:: 7Feb2024 This function assigns a new value from the string *str* to the string-style variable *name*\ . If *name* does not exist or is not a string-style variable, an error is generated. :p character(len=*) name: name of the variable :p character(len=*) str: new value to assign to the variable :to: :cpp:func:`lammps_set_string_variable` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1438: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: set_internal_variable(name, val) Set the value of a internal-style variable. .. versionadded:: 7Feb2024 This function assigns a new value from the floating-point number *val* to the internal-style variable *name*\ . If *name* does not exist or is not an internal-style variable, an error is generated. :p character(len=*) name: name of the variable :p read(c_double) val: new value to assign to the variable :to: :cpp:func:`lammps_set_internal_variable` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1454: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: gather_atoms(name, count, data) This function calls :cpp:func:`lammps_gather_atoms` to gather the named atom-based entity for all atoms on all processors and return it in the vector *data*. The vector *data* will be ordered by atom ID, which requires consecutive atom IDs (1 to *natoms*). .. versionadded:: 3Nov2022 If you need a similar array but have non-consecutive atom IDs, see :f:func:`gather_atoms_concat`; for a similar array but for a subset of atoms, see :f:func:`gather_atoms_subset`. The *data* array will be ordered in groups of *count* values, sorted by atom ID (e.g., if *name* is *x* and *count* = 3, then *data* = [*x*\ (1,1), *x*\ (2,1), *x*\ (3,1), *x*\ (1,2), *x*\ (2,2), *x*\ (3,2), *x*\ (1,3), :math:`\dots`]); *data* must be ``ALLOCATABLE`` and will be allocated to length (*count* :math:`\times` *natoms*), as queried by :f:func:`get_natoms`. This function is not compatible with ``-DLAMMPS_BIGBIG``. :p character(len=\*) name: desired quantity (e.g., *x* or *mask*) :p integer(c_int) count: number of per-atom values you expect per atom (e.g., 1 for *type*, *mask*, or *charge*; 3 for *x*, *v*, or *f*). Use *count* = 3 with *image* if you want a single image flag unpacked into *x*/*y*/*z* components. :p data: array into which to store the data. Array *must* have the ``ALLOCATABLE`` attribute and be of rank 1 (i.e., ``DIMENSION(:)``). If this array is already allocated, it will be reallocated to fit the length of the incoming data. It should have type ``INTEGER(c_int)`` if expecting integer data and ``REAL(c_double)`` if expecting floating-point data. :ptype data: polymorphic,dimension(:),allocatable :to: :cpp:func:`lammps_gather_atoms` .. note:: If you want data from this function to be accessible as a two-dimensional array, you can declare a rank-2 pointer and reassign it, like so: .. code-block:: fortran USE, INTRINSIC :: ISO_C_BINDING USE LIBLAMMPS TYPE(lammps) :: lmp REAL(c_double), DIMENSION(:), ALLOCATABLE, TARGET :: xdata REAL(c_double), DIMENSION(:,:), POINTER :: x ! other code to set up, etc. CALL lmp%gather_atoms('x',3,xdata) x(1:3,1:size(xdata)/3) => xdata You can then access the *y*\ -component of atom 3 with ``x(2,3)``. See the note about array index order at :f:func:`extract_atom`. [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1511: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: gather_atoms_concat(name, count, data) This function calls :cpp:func:`lammps_gather_atoms_concat` to gather the named atom-based entity for all atoms on all processors and return it in the vector *data*. .. versionadded:: 3Nov2022 The vector *data* will not be ordered by atom ID, and there is no restriction on the IDs being consecutive. If you need the IDs, you can do another :f:func:`gather_atoms_concat` with *name* set to ``id``. If you need a similar array but have consecutive atom IDs, see :f:func:`gather_atoms`; for a similar array but for a subset of atoms, see :f:func:`gather_atoms_subset`. This function is not compatible with ``-DLAMMPS_BIGBIG``. :p character(len=\*) name: desired quantity (e.g., *x* or *mask*) :p integer(c_int) count: number of per-atom values you expect per atom (e.g., 1 for *type*, *mask*, or *charge*; 3 for *x*, *v*, or *f*). Use *count* = 3 with *image* if you want a single image flag unpacked into *x*/*y*/*z* components. :p data: array into which to store the data. Array *must* have the ``ALLOCATABLE`` attribute and be of rank 1 (i.e., ``DIMENSION(:)``). If this array is already allocated, it will be reallocated to fit the length of the incoming data. It should have type ``INTEGER(c_int)`` if expecting integer data and ``REAL(c_double)`` if expecting floating-point data. :ptype data: polymorphic,dimension(:),allocatable :to: :cpp:func:`lammps_gather_atoms_concat` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1545: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: gather_atoms_subset(name, count, ids, data) This function calls :cpp:func:`lammps_gather_atoms_subset` to gather the named atom-based entity for the atoms in the array *ids* from all processors and return it in the vector *data*. .. versionadded:: 3Nov2022 This subroutine gathers data for the requested atom IDs and stores them in a one-dimensional allocatable array. The data will be ordered by atom ID, but there is no requirement that the IDs be consecutive. If you wish to return a similar array for *all* the atoms, use :f:func:`gather_atoms` or :f:func:`gather_atoms_concat`. The *data* array will be in groups of *count* values, sorted by atom ID in the same order as the array *ids* (e.g., if *name* is *x*, *count* = 3, and *ids* is [100, 57, 210], then *data* might look like [*x*\ (1,100), *x*\ (2,100), *x*\ (3,100), *x*\ (1,57), *x*\ (2,57), *x*\ (3,57), *x*\ (1,210), :math:`\dots`]; *ids* must be provided by the user, and *data* must be of rank 1 (i.e., ``DIMENSION(:)``) and have the ``ALLOCATABLE`` attribute. This function is not compatible with ``-DLAMMPS_BIGBIG``. :p character(len=\*) name: desired quantity (e.g., *x* or *mask*) :p integer(c_int) count: number of per-atom values you expect per atom (e.g., 1 for *type*, *mask*, or *charge*; 3 for *x*, *v*, or *f*). Use *count* = 3 with *image* if you want a single image flag unpacked into *x*/*y*/*z* components. :p integer(c_int) ids [dimension(:)]: atom IDs corresponding to the atoms to be gathered :p data: array into which to store the data. Array *must* have the ``ALLOCATABLE`` attribute and be of rank 1 (i.e., ``DIMENSION(:)``). If this array is already allocated, it will be reallocated to fit the length of the incoming data. It should have type ``INTEGER(c_int)`` if expecting integer data and ``REAL(c_double)`` if expecting floating-point data. :ptype data: polymorphic,dimension(:),allocatable :to: :cpp:func:`lammps_gather_atoms_subset` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1587: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: scatter_atoms(name, data) This function calls :cpp:func:`lammps_scatter_atoms` to scatter the named atom-based entities in *data* to all processors. .. versionadded:: 3Nov2022 This subroutine takes data stored in a one-dimensional array supplied by the user and scatters them to all atoms on all processors. The data must be ordered by atom ID, with the requirement that the IDs be consecutive. Use :f:func:`scatter_atoms_subset` to scatter data for some (or all) atoms, in any order. The *data* array needs to be ordered in groups of *count* values, sorted by atom ID (e.g., if *name* is *x* and *count* = 3, then *data* = [*x*\ (1,1), *x*\ (2,1), *x*\ (3,1), *x*\ (1,2), *x*\ (2,2), *x*\ (3,2), *x*\ (1,3), :math:`\dots`]); *data* must be of length *natoms* or 3\*\ *natoms*. :p character(len=\*) name: quantity to be scattered (e.g., *x* or *charge*) :p data: per-atom values packed in a one-dimensional array containing the data to be scattered. This array must have length *natoms* (e.g., for *type* or *charge*) or length *natoms*\ :math:`{}\times 3` (e.g., for *x* or *f*). The array *data* must be rank 1 (i.e., ``DIMENSION(:)``) and be of type ``INTEGER(c_int)`` (e.g., for *mask* or *type*) or of type ``REAL(c_double)`` (e.g., for *x* or *charge* or *f*). :ptype data: polymorphic,dimension(:) :to: :cpp:func:`lammps_scatter_atoms` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1618: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: scatter_atoms_subset(name, ids, data) This function calls :cpp:func:`lammps_scatter_atoms_subset` to scatter the named atom-based entities in *data* to all processors. .. versionadded:: 3Nov2022 This subroutine takes data stored in a one-dimensional array supplied by the user and scatters them to a subset of atoms on all processors. The array *data* contains data associated with atom IDs, but there is no requirement that the IDs be consecutive, as they are provided in a separate array, *ids*. Use :f:func:`scatter_atoms` to scatter data for all atoms, in order. The *data* array needs to be organized in groups of 1 or 3 values, depending on which quantity is being scattered, with the groups in the same order as the array *ids*. For example, if you want *data* to be the array [*x*\ (1,1), *x*\ (2,1), *x*\ (3,1), *x*\ (1,100), *x*\ (2,100), *x*\ (3,100), *x*\ (1,57), *x*\ (2,57), *x*\ (3,57)], then *ids* would be [1, 100, 57] and *name* would be *x*. :p character(len=\*) name: quantity to be scattered (e.g., *x* or *charge*) :p integer(c_int) ids [dimension(:)]: atom IDs corresponding to the atoms being scattered :p data: per-atom values packed into a one-dimensional array containing the data to be scattered. This array must have either the same length as *ids* (for *mask*, *type*, etc.) or three times its length (for *x*, *f*, etc.); the array must be rank 1 and be of type ``INTEGER(c_int)`` (e.g., for *mask* or *type*) or of type ``REAL(c_double)`` (e.g., for *charge*, *x*, or *f*). :ptype data: polymorphic,dimension(:) :to: :cpp:func:`lammps_scatter_atoms_subset` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1652: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: gather_bonds(data) Gather type and constituent atom information for all bonds. .. versionadded:: 3Nov2022 This function copies the list of all bonds into an allocatable array. The array will be filled with (bond type, bond atom 1, bond atom 2) for each bond. The array is allocated to the right length (i.e., three times the number of bonds). The array *data* must be of the same type as the LAMMPS ``tagint`` type, which is equivalent to either ``INTEGER(c_int)`` or ``INTEGER(c_int64_t)``, depending on whether ``-DLAMMPS_BIGBIG`` was used when LAMMPS was built. If the supplied array does not match, an error will result at run-time. An example of how to use this routine is below: .. code-block:: fortran PROGRAM bonds USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT USE LIBLAMMPS IMPLICIT NONE INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET :: bonds INTEGER(c_int), DIMENSION(:,:), POINTER :: bonds_array TYPE(lammps) :: lmp INTEGER :: i ! other commands to initialize LAMMPS, create bonds, etc. CALL lmp%gather_bonds(bonds) bonds_array(1:3, 1:SIZE(bonds)/3) => bonds DO i = 1, SIZE(bonds)/3 WRITE(OUTPUT_UNIT,'(A,1X,I4,A,I4,1X,I4)') 'bond', bonds_array(1,i), & '; type = ', bonds_array(2,i), bonds_array(3,i) END DO END PROGRAM bonds :p data: array into which to copy the result. \*The ``KIND`` parameter is either ``c_int`` or, if LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, kind ``c_int64_t``. :ptype data: integer(kind=\*),allocatable :to: :cpp:func:`lammps_gather_bonds` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1697: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: gather_angles(data) Gather type and constituent atom information for all angles. .. versionadded:: 8Feb2023 This function copies the list of all angles into an allocatable array. The array will be filled with (angle type, angle atom 1, angle atom 2, angle atom 3) for each angle. The array is allocated to the right length (i.e., four times the number of angles). The array *data* must be of the same type as the LAMMPS ``tagint`` type, which is equivalent to either ``INTEGER(c_int)`` or ``INTEGER(c_int64_t)``, depending on whether ``-DLAMMPS_BIGBIG`` was used when LAMMPS was built. If the supplied array does not match, an error will result at run-time. An example of how to use this routine is below: .. code-block:: fortran PROGRAM angles USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT USE LIBLAMMPS IMPLICIT NONE INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET :: angles INTEGER(c_int), DIMENSION(:,:), POINTER :: angles_array TYPE(lammps) :: lmp INTEGER :: i ! other commands to initialize LAMMPS, create angles, etc. CALL lmp%gather_angles(angles) angles_array(1:4, 1:SIZE(angles)/4) => angles DO i = 1, SIZE(angles)/4 WRITE(OUTPUT_UNIT,'(A,1X,I4,A,I4,1X,I4,1X,I4)') 'angle', angles_array(1,i), & '; type = ', angles_array(2,i), angles_array(3,i), angles_array(4,i) END DO END PROGRAM angles :p data: array into which to copy the result. \*The ``KIND`` parameter is either ``c_int`` or, if LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, kind ``c_int64_t``. :ptype data: integer(kind=\*),allocatable :to: :cpp:func:`lammps_gather_angles` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1742: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: gather(self, name, count, data) Gather the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entities from all processes, in order by atom ID. .. versionadded:: 22Dec2022 This subroutine gathers data from all processes and stores them in a one-dimensional allocatable array. The array *data* will be ordered by atom ID, which requires consecutive IDs (1 to *natoms*\ ). If you need a similar array but for non-consecutive atom IDs, see :cpp:func:`lammps_gather_concat`; for a similar array but for a subset of atoms, see :cpp:func:`lammps_gather_subset`. The *data* array will be ordered in groups of *count* values, sorted by atom ID (e.g., if *name* is *x*, then *data* is [x(1,1), x(2,1), x(3,1), x(1,2), x(2,2), x(3,2), x(1,3), :math:`\dots`]); *data* must be ``ALLOCATABLE`` and will be allocated to length (*count*\ :math:`{}\times{}`\ *natoms*), as queried by :f:func:`get_natoms`. This function will return an error if fix or compute data are requested and the fix or compute ID given does not have per-atom data. See the note about re-interpreting the vector as a matrix at :f:subr:`gather_atoms`. This function is not compatible with ``-DLAMMPS_BIGBIG``. :p character(len=\*) name: desired quantity (e.g., "x" or "mask" for atom properties, "f_id" for per-atom fix data, "c_id" for per-atom compute data, "d_name" or "i_name" for fix property/atom vectors with *count* = 1, "d2_name" or "i2_name" for fix property/atom vectors with *count*\ :math:`{}> 1`) :p integer(c_int) count: number of per-atom values (e.g., 1 for *type* or *charge*, 3 for *x* or *f*); use *count* = 3 with *image* if you want the image flags unpacked into (*x*,\ *y*,\ *z*) components. :p real(c_double) data [dimension(:),allocatable]: array into which to store the data. Array *must* have the ``ALLOCATABLE`` attribute and be of rank 1 (i.e., ``DIMENSION(:)``). If this array is already allocated, it will be reallocated to fit the length of the incoming data. :to: :cpp:func:`lammps_gather` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1784: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: gather_dihedrals(data) Gather type and constituent atom information for all dihedrals. .. versionadded:: 8Feb2023 This function copies the list of all dihedrals into an allocatable array. The array will be filled with (dihedral type, dihedral atom 1, dihedral atom 2, dihedral atom 3, dihedral atom 4) for each dihedral. The array is allocated to the right length (i.e., five times the number of dihedrals). The array *data* must be of the same type as the LAMMPS ``tagint`` type, which is equivalent to either ``INTEGER(c_int)`` or ``INTEGER(c_int64_t)``, depending on whether ``-DLAMMPS_BIGBIG`` was used when LAMMPS was built. If the supplied array does not match, an error will result at run-time. An example of how to use this routine is below: .. code-block:: fortran PROGRAM dihedrals USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT USE LIBLAMMPS IMPLICIT NONE INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET :: dihedrals INTEGER(c_int), DIMENSION(:,:), POINTER :: dihedrals_array TYPE(lammps) :: lmp INTEGER :: i ! other commands to initialize LAMMPS, create dihedrals, etc. CALL lmp%gather_dihedrals(dihedrals) dihedrals_array(1:5, 1:SIZE(dihedrals)/5) => dihedrals DO i = 1, SIZE(dihedrals)/5 WRITE(OUTPUT_UNIT,'(A,1X,I4,A,I4,1X,I4,1X,I4,1X,I4)') 'dihedral', dihedrals_array(1,i), & '; type = ', dihedrals_array(2,i), dihedrals_array(3,i), dihedrals_array(4,i), dihedrals_array(5,i) END DO END PROGRAM dihedrals :p data: array into which to copy the result. \*The ``KIND`` parameter is either ``c_int`` or, if LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, kind ``c_int64_t``. :ptype data: integer(kind=\*),allocatable :to: :cpp:func:`lammps_gather_dihedrals` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1830: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: gather_impropers(data) Gather type and constituent atom information for all impropers. .. versionadded:: 8Feb2023 This function copies the list of all impropers into an allocatable array. The array will be filled with (improper type, improper atom 1, improper atom 2, improper atom 3, improper atom 4) for each improper. The array is allocated to the right length (i.e., five times the number of impropers). The array *data* must be of the same type as the LAMMPS ``tagint`` type, which is equivalent to either ``INTEGER(c_int)`` or ``INTEGER(c_int64_t)``, depending on whether ``-DLAMMPS_BIGBIG`` was used when LAMMPS was built. If the supplied array does not match, an error will result at run-time. An example of how to use this routine is below: .. code-block:: fortran PROGRAM impropers USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : OUTPUT_UNIT USE LIBLAMMPS IMPLICIT NONE INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET :: impropers INTEGER(c_int), DIMENSION(:,:), POINTER :: impropers_array TYPE(lammps) :: lmp INTEGER :: i ! other commands to initialize LAMMPS, create impropers, etc. CALL lmp%gather_impropers(impropers) impropers_array(1:5, 1:SIZE(impropers)/5) => impropers DO i = 1, SIZE(impropers)/5 WRITE(OUTPUT_UNIT,'(A,1X,I4,A,I4,1X,I4,1X,I4,1X,I4)') 'improper', impropers_array(1,i), & '; type = ', impropers_array(2,i), impropers_array(3,i), impropers_array(4,i), impropers_array(5,i) END DO END PROGRAM impropers :p data: array into which to copy the result. \*The ``KIND`` parameter is either ``c_int`` or, if LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, kind ``c_int64_t``. :ptype data: integer(kind=\*),allocatable :to: :cpp:func:`lammps_gather_impropers` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1876: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: gather_concat(self, name, count, data) Gather the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entities from all processes, unordered. .. versionadded:: 22Dec2022 This subroutine gathers data for all atoms and stores them in a one-dimensional allocatable array. The data will be a concatenation of chunks from each processor's owned atoms, in whatever order the atoms are in on each processor. This process has no requirement that the atom IDs be consecutive. If you need the ID of each atom, you can do another call to either :f:subr:`gather_atoms_concat` or :f:subr:`gather_concat` with *name* set to ``id``. If you have consecutive IDs and want the data to be in order, use :f:subr:`gather`; for a similar array but for a subset of atoms, use :f:subr:`gather_subset`. The *data* array will be in groups of *count* values, with *natoms* groups total, but not in order by atom ID (e.g., if *name* is *x* and *count* is 3, then *data* might be something like [x(1,11), x(2,11), x(3,11), x(1,3), x(2,3), x(3,3), x(1,5), :math:`\dots`]); *data* must be ``ALLOCATABLE`` and will be allocated to length (*count* :math:`\times` *natoms*), as queried by :f:func:`get_natoms`. This function is not compatible with ``-DLAMMPS_BIGBIG``. :p character(len=\*) name: desired quantity (e.g., "x" or "mask" for atom properties, "f_id" for per-atom fix data, "c_id" for per-atom compute data, "d_name" or "i_name" for fix property/atom vectors with *count* = 1, "d2_name" or "i2_name" for fix property/atom vectors with *count*\ :math:`{}> 1`) :p integer(c_int) count: number of per-atom values you expect per atom (e.g., 1 for *type*, *mask*, or *charge*; 3 for *x*, *v*, or *f*). Use *count* = 3 with *image* if you want a single image flag unpacked into *x*/*y*/*z* components. :p data: array into which to store the data. Array *must* have the ``ALLOCATABLE`` attribute and be of rank 1 (i.e., ``DIMENSION(:)``). If this array is already allocated, it will be reallocated to fit the length of the incoming data. It should have type ``INTEGER(c_int)`` if expecting integer data and ``REAL(c_double)`` if expecting floating-point data. :ptype data: polymorphic,dimension(:),allocatable :to: :cpp:func:`lammps_gather_concat` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1922: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: gather_subset(name, count, ids, data) Gather the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entities from all processes for a subset of atoms. .. versionadded:: 22Dec2022 This subroutine gathers data for the requested atom IDs and stores them in a one-dimensional allocatable array. The data will be ordered by atom ID, but there is no requirement that the IDs be consecutive. If you wish to return a similar array for *all* the atoms, use :f:subr:`gather` or :f:subr:`gather_concat`. The *data* array will be in groups of *count* values, sorted by atom ID in the same order as the array *ids* (e.g., if *name* is *x*, *count* = 3, and *ids* is [100, 57, 210], then *data* might look like [*x*\ (1,100), *x*\ (2,100), *x*\ (3,100), *x*\ (1,57), *x*\ (2,57), *x*\ (3,57), *x*\ (1,210), :math:`\dots`]); *ids* must be provided by the user, and *data* must have the ``ALLOCATABLE`` attribute and be of rank 1 (i.e., ``DIMENSION(:)``). If *data* is already allocated, it will be reallocated to fit the length of the incoming data. This function is not compatible with ``-DLAMMPS_BIGBIG``. :p character(len=\*) name: quantity to be scattered :p integer(c_int) ids [dimension(:)]: atom IDs corresponding to the atoms being scattered (e.g., "x" or "f" for atom properties, "f_id" for per-atom fix data, "c_id" for per-atom compute data, "d_name" or "i_name" for fix property/atom vectors with *count* = 1, "d2_name" or "i2_name" for fix property/atom vectors with *count*\ :math:`{} > 1`) :p integer(c_int) count: number of per-atom values you expect per atom (e.g., 1 for *type*, *mask*, or *charge*; 3 for *x*, *v*, or *f*). Use *count* = 3 with *image* if you want a single image flag unpacked into *x*/*y*/*z* components. :p data: per-atom values packed into a one-dimensional array containing the data to be scattered. This array must have the ``ALLOCATABLE`` attribute and will be allocated either to the same length as *ids* (for *mask*, *type*, etc.) or to three times its length (for *x*, *f*, etc.); the array must be rank 1 and be of type ``INTEGER(c_int)`` (e.g., for *mask* or *type*) or of type ``REAL(c_double)`` (e.g., for *charge*, *x*, or *f*). :ptype data: polymorphic,dimension(:),allocatable :to: :cpp:func:`lammps_gather_subset` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:1969: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: scatter(name, data) This function calls :cpp:func:`lammps_scatter` to scatter the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entity in *data* to all processes. .. versionadded:: 22Dec2022 This subroutine takes data stored in a one-dimensional array supplied by the user and scatters them to all atoms on all processes. The data must be ordered by atom ID, with the requirement that the IDs be consecutive. Use :f:subr:`scatter_subset` to scatter data for some (or all) atoms, unordered. The *data* array needs to be ordered in groups of *count* values, sorted by atom ID (e.g., if *name* is *x* and *count* = 3, then *data* = [*x*\ (1,1), *x*\ (2,1), *x*\ (3,1), *x*\ (1,2), *x*\ (2,2), *x*\ (3,2), *x*\ (1,3), :math:`\dots`]); *data* must be of length (*count* :math:`\times` *natoms*). This function is not compatible with ``-DLAMMPS_BIGBIG``. :p character(len=*) name: desired quantity (e.g., "x" or "f" for atom properties, "f_id" for per-atom fix data, "c_id" for per-atom compute data, "d_name" or "i_name" for fix property/atom vectors with *count* = 1, "d2_name" or "i2_name" for fix property/atom vectors with *count*\ :math:`{} > 1`) :p data: per-atom values packed in a one-dimensional array; *data* should be of type ``INTEGER(c_int)`` or ``REAL(c_double)``, depending on the type of data being scattered, and be of rank 1 (i.e., ``DIMENSION(:)``). :ptype data: polymorphic,dimension(:) :to: :cpp:func:`lammps_scatter` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2002: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: scatter_subset(name, ids, data) This function calls :cpp:func:`lammps_scatter_subset` to scatter the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entities in *data* from a subset of atoms to all processes. .. versionadded:: 22Dec2022 This subroutine takes data stored in a one-dimensional array supplied by the user and scatters them to a subset of atoms on all processes. The array *data* contains data associated with atom IDs, but there is no requirement that the IDs be consecutive, as they are provided in a separate array. Use :f:subr:`scatter` to scatter data for all atoms, in order. The *data* array needs to be organized in groups of *count* values, with the groups in the same order as the array *ids*. For example, if you want *data* to be the array [x(1,1), x(2,1), x(3,1), x(1,100), x(2,100), x(3,100), x(1,57), x(2,57), x(3,57)], then *count* = 3 and *ids* = [1, 100, 57]. This function is not compatible with ``-DLAMMPS_BIGBIG``. :p character(len=\*) name: desired quantity (e.g., "x" or "mask" for atom properties, "f_id" for per-atom fix data, "c_id" for per-atom compute data, "d_name" or "i_name" for fix property/atom vectors with *count* = 1, "d2_name" or "i2_name" for fix property/atom vectors with *count*\ :math:`{}> 1`) :p integer(c_int) ids: list of atom IDs to scatter data for :p polymorphic data [dimension(:)]: per-atom values packed in a one-dimensional array of length *size(ids)* \* *count*. :to: :cpp:func:`lammps_scatter_subset` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2035: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: create_atoms([id,] type, x, [v,] [image,] [bexpand]) This method calls :cpp:func:`lammps_create_atoms` to create additional atoms from a given list of coordinates and a list of atom types. Additionally, the atom IDs, velocities, and image flags may be provided. .. versionadded:: 3Nov2022 :p integer(c_int) type [dimension(N)]: vector of :math:`N` atom types (required/see note below) :p real(c_double) x [dimension(3N)]: vector of :math:`3N\ x/y/z` positions of the new atoms, arranged as :math:`[x_1,y_1,z_1,x_2,y_2,\dotsc]` (required/see note below) :o integer(kind=\*) id [dimension(N),optional]: vector of :math:`N` atom IDs; if absent, LAMMPS will generate them for you. \*The ``KIND`` parameter should be ``c_int`` unless LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, in which case it should be ``c_int64_t``. :o real(c_double) v [dimension(3N),optional]: vector of :math:`3N` *x*\ /*y*\ /*z* velocities of the new atoms, arranged as :math:`[v_{1,x},v_{1,y},v_{1,z},v_{2,x}, \dotsc]`; if absent, they will be set to zero :o integer(kind=\*) image [dimension(N),optional]: vector of :math:`N` image flags; if absent, they are set to zero. \*The ``KIND`` parameter should be ``c_int`` unless LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, in which case it should be ``c_int64_t``. See note below. :o bexpand: if ``.TRUE.``, atoms outside of shrink-wrap boundaries will be created, not dropped, and the box dimensions will be extended. Default is ``.FALSE.`` :otype bexpand: logical,optional :to: :cpp:func:`lammps_create_atoms` .. note:: The *type* and *x* arguments are required, but they are declared ``OPTIONAL`` in the module because making them mandatory would require *id* to be present as well. To have LAMMPS generate the ids for you, use a call something like .. code-block:: fortran lmp%create_atoms(type=new_types, x=new_xs) .. note:: When LAMMPS has been compiled with ``-DLAMMPS_BIGBIG``, it is not possible to include the *image* parameter but omit the *id* parameter. Either *id* must be present, or both *id* and *image* must be absent. This is required because having all arguments be optional in both generic functions creates an ambiguous interface. This limitation does not exist if LAMMPS was not compiled with ``-DLAMMPS_BIGBIG``. [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2088: ERROR: Unknown directive type "f:function". .. f:function:: find_pair_neighlist(style[, exact][, nsub][, reqid]) Find index of a neighbor list requested by a pair style. .. versionadded:: 3Nov2022 This function determines which of the available neighbor lists for pair styles matches the given conditions. It first matches the style name. If *exact* is ``.TRUE.``, the name must match exactly; if ``.FALSE.``, a regular expression or sub-string match is done. If the pair style is *hybrid* or *hybrid/overlay*, the style is matched against the sub-styles instead. If the same pair style is used multiple times as a sub-style, the *nsub* argument must be :math:`> 0`; this argument represents the *n*\ th instance of the sub-style (same as for the :doc:`pair_coeff ` command, for example). In that case, *nsub*\ :math:`{} = 0` will not produce a match, and the function will return :math:`-1`. The final condition to be checked is the request ID (\ *reqid*\ ). This will usually be zero, but some pair styles request multiple neighbor lists and set the request ID to a value greater than zero. :p character(len=\*) style: String used to search for pair style instance. :o exact: Flag to control whether style should match exactly or only a regular expression/sub-string match is applied. Default: ``.TRUE.``. :otype exact: logical,optional :o integer(c_int) nsub [optional]: Match *nsub*\ th hybrid sub-style instance of the same style. Default: 0. :o integer(c_int) reqid [optional]: Request ID to identify the neighbor list in case there are multiple requests from the same pair style instance. Default: 0. :to: :cpp:func:`lammps_find_pair_neighlist` :r integer(c_int) index: Neighbor list index if found, otherwise :math:`-1`. [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2124: ERROR: Unknown directive type "f:function". .. f:function:: find_fix_neighlist(id[, reqid]) Find index of a neighbor list requested by a fix. .. versionadded:: 3Nov2022 The neighbor list request from a fix is identified by the fix ID and the request ID. The request ID is typically zero, but will be :math:`>0` for fixes with multiple neighbor list requests. :p character(len=\*) id: Identifier of fix instance :o integer(c_int) reqid [optional]: request ID to identify the neighbor list in cases in which there are multiple requests from the same fix. Default: 0. :to: :cpp:func:`lammps_find_fix_neighlist` :r index: neighbor list index if found, otherwise :math:`-1` :rtype index: integer(c_int) [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2144: ERROR: Unknown directive type "f:function". .. f:function:: find_compute_neighlist(id[, reqid]) Find index of a neighbor list requested by a compute. .. versionadded:: 3Nov2022 The neighbor list request from a compute is identified by the compute ID and the request ID. The request ID is typically zero, but will be :math:`> 0` in case a compute has multiple neighbor list requests. :p character(len=\*) id: Identifier of compute instance. :o integer(c_int) reqid [optional]: request ID to identify the neighbor list in cases in which there are multiple requests from the same compute. Default: 0. :to: :cpp:func:`lammps_find_compute_neighlist` :r index: neighbor list index if found, otherwise :math:`-1`. :rtype index: integer(c_int) [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2164: ERROR: Unknown directive type "f:function". .. f:function:: neighlist_num_elements(idx) Return the number of entries in the neighbor list with the given index. .. versionadded:: 3Nov2022 :p integer(c_int) idx: neighbor list index :to: :cpp:func:`lammps_neighlist_num_elements` :r inum: number of entries in neighbor list, or :math:`-1` if *idx* is not a valid index. :rtype inum: integer(c_int) :to: :cpp:func:`lammps_neighlist_num_elements` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2179: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: neighlist_element_neighbors(idx, element, iatom, neighbors) Return atom local index, number of neighbors, and array of neighbor local atom indices of a neighbor list entry. .. versionadded:: 3Nov2022 :p integer(c_int) idx: index of this neighbor list in the list of all neighbor lists :p integer(c_int) element: index of this neighbor list entry :p integer(c_int) iatom: local atom index (i.e., in the range [1,nlocal+nghost]; -1 if invalid or element value :p integer(c_int) neighbors [dimension(:),pointer]: pointer to an array of neighboring atom local indices :to: :cpp:func:`lammps_neighlist_element_neighbors` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2197: ERROR: Unknown directive type "f:function". .. f:function:: version() This method returns the numeric LAMMPS version like :cpp:func:`lammps_version` does. :to: :cpp:func:`lammps_version` :r version: LAMMPS version :rtype version: integer [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2208: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: get_os_info(buffer) This function can be used to retrieve detailed information about the hosting operating system and compiler/runtime environment. .. versionadded:: 3Nov2022 A suitable buffer has to be provided. The assembled text will be truncated so as not to overflow this buffer. The string is typically a few hundred bytes long. :p character(len=\*) buffer: string that will house the information. :to: :cpp:func:`lammps_get_os_info` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2225: ERROR: Unknown directive type "f:function". .. f:function:: config_has_mpi_support() This function is used to query whether LAMMPS was compiled with a real MPI library or in serial. .. versionadded:: 3Nov2022 :to: :cpp:func:`lammps_config_has_mpi_support` :r has_mpi: ``.FALSE.`` when compiled with STUBS, ``.TRUE.`` if complied with MPI. :rtype has_mpi: logical [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2239: ERROR: Unknown directive type "f:function". .. f:function:: config_has_gzip_support() Check if the LAMMPS library supports reading or writing compressed files via a pipe to gzip or similar compression programs. .. versionadded:: 3Nov2022 Several LAMMPS commands (e.g., :doc:`read_data`, :doc:`write_data`, :doc:`dump styles atom, custom, and xyz `) support reading and writing compressed files via creating a pipe to the ``gzip`` program. This function checks whether this feature was :ref:`enabled at compile time `. It does **not** check whether ``gzip`` or any other supported compression programs themselves are installed and usable. :to: :cpp:func:`lammps_config_has_gzip_support` :r has_gzip: :rtype has_gzip: logical [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2259: ERROR: Unknown directive type "f:function". .. f:function:: config_has_png_support() Check if the LAMMPS library supports writing PNG format images. .. versionadded:: 3Nov2022 The LAMMPS :doc:`dump style image ` supports writing multiple image file formats. Most of them, however, need support from an external library, and using that has to be :ref:`enabled at compile time `. This function checks whether support for the `PNG image file format `_ is available in the current LAMMPS library. :to: :cpp:func:`lammps_config_has_png_support` :r has_png: :rtype has_png: logical [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2278: ERROR: Unknown directive type "f:function". .. f:function:: config_has_jpeg_support() Check if the LAMMPS library supports writing JPEG format images. .. versionadded:: 3Nov2022 The LAMMPS :doc:`dump style image ` supports writing multiple image file formats. Most of them, however, need support from an external library, and using that has to be :ref:`enabled at compile time `. This function checks whether support for the `JPEG image file format `_ is available in the current LAMMPS library. :to: :cpp:func:`lammps_config_has_jpeg_support` :r has_jpeg: :rtype has_jpeg: logical [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2296: ERROR: Unknown directive type "f:function". .. f:function:: config_has_ffmpeg_support() Check if the LAMMPS library supports creating movie files via a pipe to ffmpeg. .. versionadded:: 3Nov2022 The LAMMPS :doc:`dump style movie ` supports generating movies from images on-the-fly via creating a pipe to the `ffmpeg `_ program. This function checks whether this feature was :ref:`enabled at compile time `. It does **not** check whether the ``ffmpeg`` itself is installed and usable. :to: :cpp:func:`lammps_config_has_ffmpeg_support` :r has_ffmpeg: :rtype has_ffmpeg: logical [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2316: ERROR: Unknown directive type "f:function". .. f:function:: config_has_exceptions() Check whether LAMMPS errors will throw C++ exceptions. .. versionadded:: 3Nov2022 When using the library interface, the library interface functions will "catch" exceptions, and then the error status can be checked by calling :f:func:`has_error`. The most recent error message can be retrieved via :f:func:`get_last_error_message`. This allows to restart a calculation or delete and recreate the LAMMPS instance when a C++ exception occurs. One application of using exceptions this way is the :ref:`lammps_shell`. :to: :cpp:func:`lammps_config_has_exceptions` :r has_exceptions: :rtype has_exceptions: logical [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2336: ERROR: Unknown directive type "f:function". .. f:function:: config_has_package(name) Check whether a specific package has been included in LAMMPS .. versionadded:: 3Nov2022 This function checks whether the LAMMPS library in use includes the specific :doc:`LAMMPS package ` provided as argument. :to: :cpp:func:`lammps_config_has_package` :r has_package: :rtype has_package: logical [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2351: ERROR: Unknown directive type "f:function". .. f:function:: config_package_count() Count the number of installed packages in the LAMMPS library. .. versionadded:: 3Nov2022 This function counts how many :doc:`LAMMPS packages ` are included in the LAMMPS library in use. It directly calls the C library function :cpp:func:`lammps_config_package_count`. :to: :cpp:func:`lammps_config_package_count` :r integer(c_int) npackages: number of packages installed [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2366: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: config_package_name(idx, buffer) Get the name of a package in the list of installed packages in the LAMMPS library. .. versionadded:: 3Nov2022 This subroutine copies the name of the package with the index *idx* into the provided string *buffer*. If the name of the package exceeds the length of the buffer, it will be truncated accordingly. If the index is out of range, *buffer* is set to an empty string. :p integer(c_int) idx: index of the package in the list of included packages :math:`(0 \le idx < \text{package count})` :p character(len=\*) buffer: string to hold the name of the package :to: :cpp:func:`lammps_config_package_name` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2385: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: installed_packages(package[, length]) Obtain a list of the names of enabled packages in the LAMMPS shared library and store it in *package*. .. versionadded:: 3Nov2022 This function is analogous to the :py:meth:`installed_packages ` function in the Python API. The optional argument *length* sets the length of each string in the vector *package* (default: 31). :p character(len=:) package [dimension(:),allocatable]: list of packages; *must* have the ``ALLOCATABLE`` attribute and be of rank 1 (i.e., ``DIMENSION(:)``) with allocatable length. :o length: length of each string in the list. Default: 31. :otype length: integer,optional :to: :cpp:func:`lammps_config_package_count` :to: :cpp:func:`lammps_config_package_name` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2407: ERROR: Unknown directive type "f:function". .. f:function:: config_accelerator(package, category, setting) This function calls :cpp:func:`lammps_config_accelerator` to check the availability of compile time settings of included :doc:`accelerator packages ` in LAMMPS. .. versionadded:: 3Nov2022 Supported packages names are "GPU", "KOKKOS", "INTEL", and "OPENMP". Supported categories are "api" with possible settings "cuda", "hip", "phi", "pthreads", "opencl", "openmp", and "serial"; and "precision" with possible settings "double", "mixed", and "single". :p character(len=\*) package: string with the name of the accelerator package :p character(len=\*) category: string with the name of the setting :p character(len=\*) setting: string with the name of the specific setting :to: :cpp:func:`lammps_config_accelerator` :r available: ``.TRUE.`` if the combination of package, category, and setting is available, otherwise ``.FALSE.``. :rtype available: logical [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2432: ERROR: Unknown directive type "f:function". .. f:function:: has_gpu_device() Checks for the presence of a viable GPU package device. .. versionadded:: 3Nov2022 This function calls :cpp:func:`lammps_has_gpu_device`, which checks at runtime whether an accelerator device is present that can be used with the :doc:`GPU package `. More detailed information about the available device or devices can be obtained by calling the :f:subr:`get_gpu_device_info` subroutine. :to: :cpp:func:`lammps_has_gpu_device` :r available: ``.TRUE.`` if a viable device is available, ``.FALSE.`` if not. :rtype available: logical [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2452: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: get_gpu_device_info(buffer) Get GPU package device information. .. versionadded:: 3Nov2022 Calls :cpp:func:`lammps_get_gpu_device_info` to retrieve detailed information about any accelerator devices that are viable for use with the :doc:`GPU package `. It will fill *buffer* with a string that is equivalent to the output of the ``nvc_get_device`` or ``ocl_get_device`` or ``hip_get_device`` tools that are compiled alongside LAMMPS if the GPU package is enabled. A suitable-length Fortran string has to be provided. The assembled text will be truncated so as not to overflow this buffer. This string can be several kilobytes long if multiple devices are present. :p character(len=\*) buffer: string into which to copy the information. :to: :cpp:func:`lammps_get_gpu_device_info` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2474: ERROR: Unknown directive type "f:function". .. f:function:: has_style(category, name) Check whether a specific style has been included in LAMMPS. .. versionadded:: 3Nov2022 This function calls :cpp:func:`lammps_has_style` to check whether the LAMMPS library in use includes the specific style *name* associated with a specific *category* provided as arguments. Please see :cpp:func:`lammps_has_style` for a list of valid categories. :p character(len=\*) category: category of the style :p character(len=\*) name: name of the style :to: :cpp:func:`lammps_has_style` :r has_style: ``.TRUE.`` if included, ``.FALSE.`` if not. :rtype has_style: logical [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2493: ERROR: Unknown directive type "f:function". .. f:function:: style_count(category) Count the number of styles of *category* in the LAMMPS library. .. versionadded:: 3Nov2022 This function counts how many styles in the provided *category* are included in the LAMMPS library currently in use. Please see :cpp:func:`lammps_has_style` for a list of valid categories. :p character(len=\*) category: category of styles to count :to: :cpp:func:`lammps_style_count` :r integer(c_int) count: number of styles in *category* [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2509: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: style_name(category, idx, buffer) Look up the name of a style by index in the list of styles of a given category in the LAMMPS library. .. versionadded:: 3Nov2022 This function calls :cpp:func:`lammps_style_name` and copies the name of the *category* style with index *idx* into the provided string *buffer*. The length of *buffer* must be long enough to contain the name of the style; if it is too short, the name will be truncated accordingly. If *idx* is out of range, *buffer* will be the empty string and a warning will be issued. :p character(len=\*) category: category of styles :p integer(c_int) idx: index of the style in the list of *category* styles :math:`(1 \leq idx \leq \text{style count})` :p character(len\*) buffer: string buffer to copy the name of the style into :to: :cpp:func:`lammps_style_name` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2532: ERROR: Unknown directive type "f:function". .. f:function:: has_id(category, name) This function checks if the current LAMMPS instance a *category* ID of the given *name* exists. Valid categories are: *compute*\ , *dump*\ , *fix*\ , *group*\ , *molecule*\ , *region*\ , and *variable*\ . .. versionadded:: 3Nov2022 :p character(len=\*) category: category of the ID :p character(len=\*) name: name of the ID :to: :cpp:func:`lammps_has_id` :r has_id: ``.TRUE.`` if *category* style *name* exists, ``.FALSE.`` if not. :rtype has_id: logical [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2548: ERROR: Unknown directive type "f:function". .. f:function:: id_count(category) This function counts how many IDs in the provided *category* are defined in the current LAMMPS instance. Please see :f:func:`has_id` for a list of valid categories. .. versionadded:: 3Nov2022 :p character(len=\*) category: category of the ID :to: :cpp:func:`lammps_id_count` :r count: number of IDs in *category* :rtype count: integer(c_int) [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2563: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: id_name(category, idx, buffer) Look up the name of an ID by index in the list of IDs of a given category. .. versionadded:: 3Nov2022 This function copies the name of the *category* ID with the index *idx* into the provided string *buffer*\ . The length of the buffer must be long enough to hold the string; if the name of the style exceeds the length of the buffer, it will be truncated accordingly. If *buffer* is ``ALLOCATABLE``, it must be allocated *before* the function is called. If *idx* is out of range, *buffer* is set to an empty string and a warning is issued. :p character(len=\*) category: category of IDs :p integer(c_int) idx: index of the ID in the list of *category* styles (:math:`0 \leq idx < count`) :p character(len=\*) buffer: string into which to copy the name of the style :to: :cpp:func:`lammps_id_name` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2586: ERROR: Unknown directive type "f:function". .. f:function:: plugin_count() This function counts the number of loaded plugins. .. versionadded:: 3Nov2022 :to: :cpp:func:`lammps_plugin_count` :r n: number of loaded plugins :rtype n: integer(c_int) [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2598: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: plugin_name(idx, stylebuf, namebuf) Look up the style and name of a plugin by its index in the list of plugins. .. versionadded:: 3Nov2022 This function copies the name of the *style* plugin with the index *idx* into the provided C-style string buffer. The length of the buffer must be provided as *buf_size* argument. If the name of the style exceeds the length of the buffer, it will be truncated accordingly. If the index is out of range, both strings are set to the empty string and a warning is printed. :p integer(c_int) idx: index of the plugin in the list all or *style* plugins :p character(len=\*) stylebuf: string into which to copy the style of the plugin :p character(len=\*) namebuf: string into which to copy the style of the plugin :to: :cpp:func:`lammps_plugin_name` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2621: ERROR: Unknown directive type "f:function". .. f:function:: encode_image_flags(ix, iy, iz) Encodes three integer image flags into a single imageint. .. versionadded:: 3Nov2022 This function performs the bit-shift, addition, and bit-wise OR operations necessary to combine the values of three integers representing the image flags in the :math:`x`-, :math:`y`-, and :math:`z`-directions. Unless LAMMPS is compiled with ``-DLAMMPS_BIGBIG``, those integers are limited to 10-bit signed integers :math:`[-512,512)`. If ``-DLAMMPS_BIGBIG`` was used when compiling, then the return value is of kind ``c_int64_t`` instead of kind ``c_int``, and the valid range for the individual image flags becomes :math:`[-1048576,1048575)` (i.e., the range of a 21-bit signed integer). There is no check on whether the arguments conform to these requirements; values out of range will simply be wrapped back into the interval. :p integer(c_int) ix: image flag in :math:`x`-direction :p integer(c_int) iy: image flag in :math:`y`-direction :p integer(c_int) iz: image flag in :math:`z`-direction :r integer(kind=\*) imageint: encoded image flag. \*The ``KIND`` parameter is ``c_int`` unless LAMMPS was built with ``-DLAMMPS_BIGBIG``, in which case it is ``c_int64_t``. .. note:: The fact that the programmer does not know the ``KIND`` parameter of the return value until compile time means that it is impossible to define an interface that works for both sizes of ``imageint``. One side effect of this is that you must assign the return value of this function to a variable; it cannot be used as the argument to another function or as part of an array constructor. For example, .. code-block:: fortran my_images = [lmp%encode_image_flags(0,0,0), lmp%encode_image_flags(1,0,0)] will *not* work; instead, do something like .. code-block:: fortran my_images(1) = lmp%encode_image_flags(0,0,0) my_images(2) = lmp%encode_image_flags(1,0,0) [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2667: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: decode_image_flags(image, flags) This function does the reverse operation of :f:func:`encode_image_flags`: it takes the image flag and performs the bit-shift and bit-masking operations to decode it and stores the resulting three integers into the array *flags*. .. versionadded:: 3Nov2022 :p integer(kind=\*) image: encoded image flag. \*The ``KIND`` parameter is either ``c_int`` or, if LAMMPS was compiled with ``-DLAMMPS_BIGBIG``, ``c_int64_t``. Kind compatibility is checked at run-time. :p integer(c_int) flags [dimension(3)]: three-element vector where the decoded image flags will be stored. [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2684: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: set_fix_external_callback(id, callback, caller) Set the callback function for a :doc:`fix external ` instance with the given ID. .. versionadded:: 22Dec2022 Fix :doc:`external ` allows programs that are running LAMMPS through its library interface to modify certain LAMMPS properties on specific time steps, similar to the way other fixes do. This subroutine sets the callback function for use with the "pf/callback" mode. The function should have Fortran language bindings with the following interface, which depends on how LAMMPS was compiled: .. code-block:: fortran ABSTRACT INTERFACE SUBROUTINE external_callback(caller, timestep, ids, x, fexternal) USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double, c_int64_t CLASS(*), INTENT(INOUT) :: caller INTEGER(c_bigint), INTENT(IN) :: timestep INTEGER(c_tagint), DIMENSION(:), INTENT(IN) :: ids REAL(c_double), DIMENSION(:,:), INTENT(IN) :: x REAL(c_double), DIMENSION(:,:), INTENT(OUT) :: fexternal END SUBROUTINE external_callback END INTERFACE where ``c_bigint`` is ``c_int`` if ``-DLAMMPS_SMALLSMALL`` was used and ``c_int64_t`` otherwise; and ``c_tagint`` is ``c_int64_t`` if ``-DLAMMPS_BIGBIG`` was used and ``c_int`` otherwise. The argument *caller* to :f:subr:`set_fix_external_callback` is unlimited polymorphic (i.e., it can be any Fortran object you want to pass to the calling function) and will be available as the first argument to the callback function. It can be your LAMMPS instance, which you might need if the callback function needs access to the library interface. The argument must be a scalar; to pass non-scalar data, wrap those data in a derived type and pass an instance of the derived type to *caller*. The array *ids* is an array of length *nlocal* (as accessed from the :cpp:class:`Atom` class or through :f:func:`extract_global`). The arrays *x* and *fexternal* are :math:`3 \times {}`\ *nlocal* arrays; these are transposed from what they would look like in C (see note about array index order at :f:func:`extract_atom`). The callback mechanism is one of two ways that forces can be applied to a simulation with the help of :doc:`fix external `. The alternative is *array* mode, where one calls :f:func:`fix_external_get_force`. Please see the documentation for :doc:`fix external ` for more information about how to use the fix and couple it with external programs. :p character(len=*) id: ID of :doc:`fix external ` instance :p callback: subroutine :doc:`fix external ` should call :ptype callback: external :p class(*) caller [optional]: object you wish to pass to the callback procedure (must be a scalar; see note) :to: :cpp:func:`lammps_set_fix_external_callback` .. note:: The interface for your callback function must match types precisely with the abstract interface block given above. **The compiler probably will not be able to check this for you.** In particular, the first argument ("caller") must be of type ``CLASS(*)`` or you will probably get a segmentation fault or at least a misinterpretation of whatever is in memory there. You can resolve the object using the ``SELECT TYPE`` construct. An example callback function (assuming LAMMPS was compiled with ``-DLAMMPS_SMALLBIG``) that applies something akin to Hooke's Law (with each atom having a different *k* value) is shown below. .. code-block:: fortran MODULE stuff USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int, c_double, c_int64_t USE, INTRINSIC :: ISO_FORTRAN_ENV, ONLY : error_unit IMPLICIT NONE TYPE shield REAL(c_double), DIMENSION(:,:), ALLOCATABLE :: k ! assume k gets allocated to dimension(3,nlocal) at some point ! and assigned values END TYPE shield SUBROUTINE my_callback(caller, timestep, ids, x, fexternal) CLASS(*), INTENT(INOUT) :: caller INTEGER(c_int), INTENT(IN) :: timestep INTEGER(c_int64_t), INTENT(IN) :: ids REAL(c_double), INTENT(IN) :: x(:,:) REAL(c_double), INTENT(OUT) :: fexternal(:,:) SELECT TYPE (caller) TYPE IS (shield) fexternal = - caller%k * x CLASS DEFAULT WRITE(error_unit,*) 'UH OH...' END SELECT END SUBROUTINE my_callback END MODULE stuff ! then, when assigning the callback function, do this: PROGRAM example USE LIBLAMMPS USE stuff TYPE(lammps) :: lmp TYPE(shield) :: my_shield lmp = lammps() CALL lmp%command('fix ext all external pf/callback 1 1') CALL lmp%set_fix_external_callback('ext', my_callback, my_shield) END PROGRAM example [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2800: ERROR: Unknown directive type "f:function". .. f:function:: fix_external_get_force(id) Get pointer to the force array storage in a fix external instance with the given ID. .. versionadded:: 22Dec2022 Fix :doc:`external ` allows programs that are running LAMMPS through its library interfaces to add or modify certain LAMMPS properties on specific time steps, similar to the way other fixes do. This function provides access to the per-atom force storage in a fix external instance with the given fix-ID to be added to the individual atoms when using the "pf/array" mode. The *fexternal* array can be accessed like other "native" per-atom arrays accessible via the :f:func:`extract_atom` function. Please note that the array stores the forces for *local* atoms for each MPI rank, in the order determined by the neighbor list build. Because the underlying data structures can change as well as the order of atom as they migrate between MPI processes because of the domain decomposition parallelization, this function should be always called immediately before the forces are going to be set to get an up-to-date pointer. You can use, for example, :f:func:`extract_setting` to obtain the number of local atoms `nlocal` and then assume the dimensions of the returned force array as ``REAL(c_double) :: force(3,nlocal)``. This function is an alternative to the callback mechanism in fix external set up by :f:subr:`set_fix_external_callback`. The main difference is that this mechanism can be used when forces are to be pre-computed and the control alternates between LAMMPS and the external driver, while the callback mechanism can call an external subroutine to compute the force when the fix is triggered and needs them. Please see the documentation for :doc:`fix external ` for more information about how to use the fix and how to couple it with an external program. :p character(len=*) id: ID of :doc:`fix external ` instance :to: :cpp:func:`lammps_fix_external_get_force` :r fexternal: pointer to the per-atom force array allocated by the fix :rtype fexternal: real(c_double),dimension(3,nlocal) [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2844: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: fix_external_set_energy_global(id, eng) Set the global energy contribution for a :doc:`fix external ` instance with the given ID. .. versionadded:: 22Dec2022 This is a companion function to :f:func:`set_fix_external_callback` and :f:func:`fix_external_get_force` that also sets the contribution to the global energy from the external program. The value of the *eng* argument will be stored in the fix and applied on the current and all following time steps until changed by another call to this function. The energy is in energy units as determined by the current :doc:`units ` settings and is the **total** energy of the contribution. Thus, when running in parallel, all MPI processes have to call this function with the **same** value, and this will be returned as a scalar property of the fix external instance when accessed in LAMMPS input commands or from variables. Please see the documentation for :doc:`fix external ` for more information about how to use the fix and how to couple it with an external program. :p character(len=*) id: fix ID of fix external instance :p real(c_double) eng: total energy to be added to the global energy :to: :cpp:func:`lammps_fix_external_set_energy_global` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2872: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: fix_external_set_virial_global(id, virial) Set the global virial contribution for a fix external instance with the given ID. .. versionadded:: 22Dec2022 This is a companion function to :f:subr:`set_fix_external_callback` and :f:func:`fix_external_get_force` to set the contribution to the global virial from an external program. The six values of the *virial* array will be stored in the fix and applied on the current and all following time steps until changed by another call to this function. The components of the virial need to be stored in the following order: *xx*, *yy*, *zz*, *xy*, *xz*, *yz*. In LAMMPS, the virial is stored internally as `stress*volume` in units of `pressure*volume` as determined by the current :doc:`units ` settings and is the **total** contribution. Thus, when running in parallel, all MPI processes have to call this function with the **same** value, and this will then be added by fix external. Please see the documentation for :doc:`fix external ` for more information about how to use the fix and how to couple it with an external code. :p character(len=*) id: fix ID of fix external instance :p real(c_double) virial [dimension(6)]: the six global stress tensor components to be added to the global virial :to: :cpp:func:`lammps_fix_external_set_virial_global` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2904: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: fix_external_set_energy_peratom(id, eng) Set the per-atom energy contribution for a fix external instance with the given ID. .. versionadded:: 22Dec2022 This is a companion function to :f:subr:`set_fix_external_callback` to set the per-atom energy contribution due to the fix from the external program as part of the callback function. For this to work, the LAMMPS object must be passed as part of the *caller* argument when registering the callback function, or the callback function must otherwise have access to the LAMMPS object, such as through a module-based pointer. .. note:: This function is fully independent from :f:subr:`fix_external_set_energy_global` and will **NOT** add any contributions to the global energy tally and will **NOT** check whether the sum of the contributions added here are consistent with the global added energy. Please see the documentation for :doc:`fix external ` for more information about how to use the fix and how to couple it with an external code. :p character(len=*) id: fix ID of the fix external instance :p real(c_double) eng [dimension(:)]: array of length *nlocal* containing the energy to add to the per-atom energy :to: :cpp:func:`lammps_fix_external_set_energy_peratom` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2937: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: set_fix_external_set_virial_peratom(id, virial) This is a companion function to :f:subr:`set_fix_external_callback` to set the per-atom virial contribution due to the fix from the external program as part of the callback function. For this to work, the LAMMPS object must be passed as the *caller* argument when registering the callback function. .. versionadded:: 22Dec2022 .. note:: This function is fully independent from :f:subr:`fix_external_set_virial_global` and will **NOT** add any contributions to the global virial tally and **NOT** check whether the sum of the contributions added here are consistent with the global added virial. The order and units of the per-atom stress tensor elements are the same as for the global virial. The type and dimensions of the per-atom virial array must be ``REAL(c_double), DIMENSION(6,nlocal)``. Please see the documentation for :doc:`fix external ` for more information about how to use the fix and how to couple it with an external program. :p character(len=*) id: fix ID of fix external instance :p real(c_double) virial [dimension(:,:)]: an array of :math:`6 \times{}`\ *nlocal* components to be added to the per-atom virial :to: :cpp:func:`lammps_set_virial_peratom` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2969: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: fix_external_set_vector_length(id, length) Set the vector length for a global vector stored with fix external for analysis. .. versionadded:: 22Dec2022 This is a companion function to :f:subr:`set_fix_external_callback` and :f:func:`fix_external_get_force` to set the length of a global vector of properties that will be stored with the fix via :f:subr:`fix_external_set_vector`. This function needs to be called **before** a call to :f:subr:`fix_external_set_vector` and **before** a run or minimize command. When running in parallel, it must be called from **all** MPI processes with the same length argument. Please see the documentation for :doc:`fix external ` for more information about how to use the fix and how to couple it with an external program. :p character(len=*) id: fix ID of fix external instance :p integer(c_int) length: length of the global vector to be stored with the fix :to: :cpp:func:`lammps_fix_external_set_vector_length` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:2997: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: fix_external_set_vector(id, idx, val) Store a global vector value for a fix external instance with the given ID. .. versionadded:: 22Dec2022 This is a companion function to :f:subr:`set_fix_external_callback` and :f:func:`fix_external_get_force` to set the values of a global vector of properties that will be stored with the fix and can be accessed from within LAMMPS input commands (e.g., fix ave/time or variables) when used in a vector context. This function needs to be called **after** a call to :f:subr:`fix_external_set_vector_length` and **before** a run or minimize command. When running in parallel, it must be called from **all** MPI processes with the **same** *idx* and *val* parameters. The variable *val* is assumed to be extensive. .. note:: The index in the *idx* parameter is 1-based (i.e., the first element is set with *idx*\ :math:`{} = 1`, and the last element of the vector with *idx*\ :math:`{} = N`, where :math:`N` is the value of the *length* parameter of the call to :f:subr:`fix_external_set_vector_length`). Please see the documentation for :doc:`fix external ` for more information about how to use the fix and how to couple it with an external code. :p character(len=*) id: ID of fix external instance :p integer(c_int) idx: 1-based index in global vector :p integer(c_int) val: value to be stored in global vector at index *idx* :to: :cpp:func:`lammps_fix_external_set_vector` [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:3033: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: flush_buffers() This function calls :cpp:func:`lammps_flush_buffers`, which flushes buffered output to be written to screen and logfile. This can simplify capturing output from LAMMPS library calls. .. versionadded:: 3Nov2022 :to: :cpp:func:`lammps_flush_buffers` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:3045: ERROR: Unknown directive type "f:function". .. f:function:: is_running() Check if LAMMPS is currently inside a run or minimization. .. versionadded:: 3Nov2022 This function can be used from signal handlers or multi-threaded applications to determine if the LAMMPS instance is currently active. :to: :cpp:func:`lammps_is_running` :r is_running: ``.FALSE.`` if idle or ``.TRUE.`` if active :rtype is_running: logical [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:3060: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: force_timeout() Force a timeout to stop an ongoing run cleanly. .. versionadded:: 3Nov2022 This function can be used from signal handlers or multi-threaded applications to terminate an ongoing run cleanly. :to: :cpp:func:`lammps_force_timeout` [docutils] WARNING: unknown directive or role name: f:function /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:3073: ERROR: Unknown directive type "f:function". .. f:function:: has_error() Check if there is a (new) error message available. .. versionadded:: 3Nov2022 This function can be used to query if an error inside of LAMMPS has thrown a :ref:`C++ exception `. :to: :cpp:func:`lammps_has_error` :r has_error: ``.TRUE.`` if there is an error. :rtype has_error: logical [docutils] WARNING: unknown directive or role name: f:subroutine /build/reproducible-path/lammps-20240207+dfsg/doc/src/Fortran.rst:3088: ERROR: Unknown directive type "f:subroutine". .. f:subroutine:: get_last_error_message(buffer[,status]) Copy the last error message into the provided buffer. .. versionadded:: 3Nov2022 This function can be used to retrieve the error message that was set in the event of an error inside of LAMMPS that resulted in a :ref:`C++ exception `. A suitable buffer for a string has to be provided. If the internally-stored error message is longer than the string, it will be truncated accordingly. The optional argument *status* indicates the kind of error: a "1" indicates an error that occurred on all MPI ranks and is often recoverable, while a "2" indicates an abort that would happen only in a single MPI rank and thus may not be recoverable, as other MPI ranks may be waiting on the failing MPI rank(s) to send messages. :p character(len=\*) buffer: string buffer to copy the error message into :o integer(c_int) status [optional]: 1 when all ranks had the error, 2 on a single-rank error. :to: :cpp:func:`lammps_get_last_error_message` [docutils] looking for now-outdated files... none found pickling environment... done checking consistency... /build/reproducible-path/lammps-20240207+dfsg/doc/src/angle_coeff.rst: document is referenced in multiple toctrees: ['angles', 'commands_list'], selecting: commands_list <- angle_coeff /build/reproducible-path/lammps-20240207+dfsg/doc/src/angle_style.rst: document is referenced in multiple toctrees: ['angles', 'commands_list'], selecting: commands_list <- angle_style /build/reproducible-path/lammps-20240207+dfsg/doc/src/angle_write.rst: document is referenced in multiple toctrees: ['angles', 'commands_list'], selecting: commands_list <- angle_write /build/reproducible-path/lammps-20240207+dfsg/doc/src/bond_coeff.rst: document is referenced in multiple toctrees: ['bonds', 'commands_list'], selecting: commands_list <- bond_coeff /build/reproducible-path/lammps-20240207+dfsg/doc/src/bond_style.rst: document is referenced in multiple toctrees: ['bonds', 'commands_list'], selecting: commands_list <- bond_style /build/reproducible-path/lammps-20240207+dfsg/doc/src/bond_write.rst: document is referenced in multiple toctrees: ['bonds', 'commands_list'], selecting: commands_list <- bond_write /build/reproducible-path/lammps-20240207+dfsg/doc/src/compute_modify.rst: document is referenced in multiple toctrees: ['computes', 'commands_list'], selecting: computes <- compute_modify /build/reproducible-path/lammps-20240207+dfsg/doc/src/dihedral_coeff.rst: document is referenced in multiple toctrees: ['dihedrals', 'commands_list'], selecting: dihedrals <- dihedral_coeff /build/reproducible-path/lammps-20240207+dfsg/doc/src/dihedral_style.rst: document is referenced in multiple toctrees: ['dihedrals', 'commands_list'], selecting: dihedrals <- dihedral_style /build/reproducible-path/lammps-20240207+dfsg/doc/src/dihedral_write.rst: document is referenced in multiple toctrees: ['dihedrals', 'commands_list'], selecting: dihedrals <- dihedral_write /build/reproducible-path/lammps-20240207+dfsg/doc/src/dump.rst: document is referenced in multiple toctrees: ['dumps', 'commands_list'], selecting: dumps <- dump /build/reproducible-path/lammps-20240207+dfsg/doc/src/dump_adios.rst: document is referenced in multiple toctrees: ['dumps', 'commands_list'], selecting: dumps <- dump_adios /build/reproducible-path/lammps-20240207+dfsg/doc/src/dump_cfg_uef.rst: document is referenced in multiple toctrees: ['dumps', 'commands_list'], selecting: dumps <- dump_cfg_uef /build/reproducible-path/lammps-20240207+dfsg/doc/src/dump_h5md.rst: document is referenced in multiple toctrees: ['dumps', 'commands_list'], selecting: dumps <- dump_h5md /build/reproducible-path/lammps-20240207+dfsg/doc/src/dump_image.rst: document is referenced in multiple toctrees: ['dumps', 'commands_list'], selecting: dumps <- dump_image /build/reproducible-path/lammps-20240207+dfsg/doc/src/dump_modify.rst: document is referenced in multiple toctrees: ['dumps', 'commands_list'], selecting: dumps <- dump_modify /build/reproducible-path/lammps-20240207+dfsg/doc/src/dump_molfile.rst: document is referenced in multiple toctrees: ['dumps', 'commands_list'], selecting: dumps <- dump_molfile /build/reproducible-path/lammps-20240207+dfsg/doc/src/dump_netcdf.rst: document is referenced in multiple toctrees: ['dumps', 'commands_list'], selecting: dumps <- dump_netcdf /build/reproducible-path/lammps-20240207+dfsg/doc/src/dump_vtk.rst: document is referenced in multiple toctrees: ['dumps', 'commands_list'], selecting: dumps <- dump_vtk /build/reproducible-path/lammps-20240207+dfsg/doc/src/fix_modify.rst: document is referenced in multiple toctrees: ['fixes', 'commands_list'], selecting: fixes <- fix_modify /build/reproducible-path/lammps-20240207+dfsg/doc/src/fix_modify_atc_commands.rst: document is referenced in multiple toctrees: ['fixes', 'Manual'], selecting: fixes <- fix_modify_atc_commands /build/reproducible-path/lammps-20240207+dfsg/doc/src/improper_coeff.rst: document is referenced in multiple toctrees: ['impropers', 'commands_list'], selecting: impropers <- improper_coeff /build/reproducible-path/lammps-20240207+dfsg/doc/src/improper_style.rst: document is referenced in multiple toctrees: ['impropers', 'commands_list'], selecting: impropers <- improper_style /build/reproducible-path/lammps-20240207+dfsg/doc/src/pair_coeff.rst: document is referenced in multiple toctrees: ['pairs', 'commands_list'], selecting: pairs <- pair_coeff /build/reproducible-path/lammps-20240207+dfsg/doc/src/pair_modify.rst: document is referenced in multiple toctrees: ['pairs', 'commands_list'], selecting: pairs <- pair_modify /build/reproducible-path/lammps-20240207+dfsg/doc/src/pair_style.rst: document is referenced in multiple toctrees: ['pairs', 'commands_list'], selecting: pairs <- pair_style /build/reproducible-path/lammps-20240207+dfsg/doc/src/pair_write.rst: document is referenced in multiple toctrees: ['pairs', 'commands_list'], selecting: pairs <- pair_write done preparing documents... done copying assets... copying static files... Writing evaluated template result to /build/reproducible-path/lammps-20240207+dfsg/doc/html/_static/documentation_options.js Writing evaluated template result to /build/reproducible-path/lammps-20240207+dfsg/doc/html/_static/language_data.js Writing evaluated template result to /build/reproducible-path/lammps-20240207+dfsg/doc/html/_static/basic.css copying static files: done copying extra files... copying extra files: done copying assets: done writing output... [ 50%] Library writing output... [100%] Manual generating indices... genindex py-modindex done writing additional pages... search done dumping search index in English (code: en)... done dumping object inventory... done build succeeded, 196 warnings. The HTML pages are in html. ############################################ env: 'rst_anchor_check': No such file or directory Found 89 packages Parsed style names w/o suffixes from C++ tree in ../src: Angle styles: 26 Atom styles: 28 Body styles: 3 Bond styles: 25 Command styles: 51 Compute styles: 169 Dihedral styles: 17 Dump styles: 34 Fix styles: 265 Improper styles: 14 Integrate styles: 4 Kspace styles: 21 Minimize styles: 9 Pair styles: 287 Reader styles: 4 Region styles: 9 ---------------------------------------------------- Total number of styles (including suffixes): 1784 Total number of style index entries: 1278 ############################################ Build finished. The HTML pages are in doc/html. make[2]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg/doc' make[1]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg' debian/rules override_dh_auto_test-arch make[1]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg' mkdir test; cp examples/crack/* test/ cd test; /build/reproducible-path/lammps-20240207+dfsg/debian/build/lmp < in.crack LAMMPS (7 Feb 2024 - Update 1) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 1.1142771 1.9299846 1.1142771 Created orthogonal box = (0 0 -0.27856928) to (111.42771 77.199383 0.27856928) 1 by 1 by 1 MPI processor grid Created 8141 atoms using lattice units in orthogonal box = (-0.011142771 -0.0077199383 -0.27856928) to (111.43885 77.207103 0.27856928) create_atoms CPU = 0.002 seconds 302 atoms in group lower 302 atoms in group upper 604 atoms in group boundary 7537 atoms in group mobile 841 atoms in group leftupper 841 atoms in group leftlower Setting atom values ... 841 settings made for type Setting atom values ... 841 settings made for type Setting atom values ... 302 settings made for type Setting atom values ... 302 settings made for type WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:529) Generated 0 of 10 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 5 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 binsize = 1.4, bins = 80 56 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/2d bin: standard Setting up Verlet run ... Unit style : lj Current step : 0 Time step : 0.003 Per MPI rank memory allocation (min/avg/max) = 3.112 | 3.112 | 3.112 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0.065651733 -3.2595015 0 -3.1987287 -0.036239172 8605.5917 200 0.060086376 -3.2531936 0 -3.1975725 -0.23125026 8638.8101 400 0.060533553 -3.2509973 0 -3.1949623 -0.4305406 8679.2464 600 0.06082965 -3.2466949 0 -3.1903858 -0.6028531 8716.7569 800 0.061677224 -3.2413215 0 -3.1842278 -0.7482749 8756.226 1000 0.062383731 -3.2349273 0 -3.1771796 -0.87425132 8793.1116 1200 0.063709246 -3.2276094 0 -3.1686347 -0.98020161 8828.8863 1400 0.065404552 -3.2196608 0 -3.1591168 -1.0695384 8866.4893 1600 0.067579602 -3.2110378 0 -3.1484804 -1.1456387 8900.6772 1800 0.069324241 -3.2018536 0 -3.1376812 -1.2020999 8933.017 2000 0.071014927 -3.1921108 0 -3.1263733 -1.2430105 8963.9853 2200 0.072992881 -3.1818701 0 -3.1143017 -1.2701297 9004.4136 2400 0.075000723 -3.1712313 0 -3.1018043 -1.2830866 9034.9991 2600 0.076843477 -3.1601004 0 -3.0889675 -1.27924 9072.1325 2800 0.078671706 -3.1487747 0 -3.0759495 -1.2659604 9103.9526 3000 0.080713586 -3.1373277 0 -3.0626123 -1.2440673 9134.552 3200 0.08309469 -3.1260242 0 -3.0491047 -1.214547 9169.0003 3400 0.085424766 -3.1146623 0 -3.0355859 -1.1839326 9206.909 3600 0.087396485 -3.1029493 0 -3.0220477 -1.143412 9233.783 3800 0.089007987 -3.090822 0 -3.0084286 -1.1000791 9259.0348 4000 0.089813071 -3.0794078 0 -2.9962692 -1.062847 9281.82 4200 0.08584753 -3.0668559 0 -2.9873882 -1.037972 9308.8113 4400 0.086197517 -3.0559678 0 -2.9761761 -1.028843 9328.9666 4600 0.086766447 -3.0437627 0 -2.9634443 -1.0208785 9361.9925 4800 0.088195149 -3.0328502 0 -2.9512093 -1.0272063 9395.6122 5000 0.089415266 -3.0228825 0 -2.9401122 -1.0215336 9436.1637 Loop time of 4.01376 on 1 procs for 5000 steps with 8141 atoms Performance: 322888.940 tau/day, 1245.714 timesteps/s, 10.141 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3392 | 3.3392 | 3.3392 | 0.0 | 83.19 Neigh | 0.19943 | 0.19943 | 0.19943 | 0.0 | 4.97 Comm | 0.0030613 | 0.0030613 | 0.0030613 | 0.0 | 0.08 Output | 0.0015154 | 0.0015154 | 0.0015154 | 0.0 | 0.04 Modify | 0.36762 | 0.36762 | 0.36762 | 0.0 | 9.16 Other | | 0.103 | | | 2.57 Nlocal: 8141 ave 8141 max 8141 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 71389 ave 71389 max 71389 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71389 Ave neighs/atom = 8.7690701 Neighbor list builds = 100 Dangerous builds = 0 Total wall time: 0:00:04 rm -rf test mkdir test; cp examples/crack/* test/ cd test; mpirun -np 2 --allow-run-as-root /build/reproducible-path/lammps-20240207+dfsg/debian/build/lmp < in.crack LAMMPS (7 Feb 2024 - Update 1) WARNING: Using I/O redirection is unreliable with parallel runs. Better to use the -in switch to read input files. (src/lammps.cpp:552) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 1.1142771 1.9299846 1.1142771 Created orthogonal box = (0 0 -0.27856928) to (111.42771 77.199383 0.27856928) 2 by 1 by 1 MPI processor grid Created 8141 atoms using lattice units in orthogonal box = (-0.011142771 -0.0077199383 -0.27856928) to (111.43885 77.207103 0.27856928) create_atoms CPU = 0.001 seconds 302 atoms in group lower 302 atoms in group upper 604 atoms in group boundary 7537 atoms in group mobile 841 atoms in group leftupper 841 atoms in group leftlower Setting atom values ... 841 settings made for type Setting atom values ... 841 settings made for type Setting atom values ... 302 settings made for type Setting atom values ... 302 settings made for type WARNING: Temperature for thermo pressure is not for group all (src/thermo.cpp:529) Generated 0 of 10 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 1 steps, delay = 5 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 binsize = 1.4, bins = 80 56 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/2d bin: standard Setting up Verlet run ... Unit style : lj Current step : 0 Time step : 0.003 Per MPI rank memory allocation (min/avg/max) = 3.097 | 3.097 | 3.097 Mbytes Step Temp E_pair E_mol TotEng Press Volume 0 0.065993465 -3.2595015 0 -3.1984123 -0.035939913 8605.5917 200 0.060035253 -3.2531886 0 -3.1976149 -0.22757684 8638.5331 400 0.06054278 -3.2510706 0 -3.1950271 -0.42811733 8677.8288 600 0.060576995 -3.246816 0 -3.1907408 -0.60017647 8717.6131 800 0.060802753 -3.2413477 0 -3.1850635 -0.74499308 8756.4512 1000 0.061812114 -3.2349942 0 -3.1777756 -0.87130079 8796.9575 1200 0.06317147 -3.2277552 0 -3.1692783 -0.98010628 8823.1488 1400 0.065125405 -3.2198031 0 -3.1595175 -1.0690179 8858.8358 1600 0.06725411 -3.2111272 0 -3.148871 -1.1440993 8892.6607 1800 0.069389572 -3.2019689 0 -3.137736 -1.199078 8933.7591 2000 0.071276448 -3.1921621 0 -3.1261826 -1.239553 8969.0463 2200 0.073243486 -3.1818809 0 -3.1140805 -1.264839 8997.6559 2400 0.075063494 -3.1711703 0 -3.1016851 -1.2772278 9038.4932 2600 0.076789207 -3.1600658 0 -3.0889832 -1.2754953 9073.4997 2800 0.07875979 -3.1487143 0 -3.0758075 -1.2637926 9106.2245 3000 0.080591853 -3.1372361 0 -3.0626334 -1.2388824 9142.7862 3200 0.08227693 -3.125423 0 -3.0492605 -1.2055283 9169.4322 3400 0.084289444 -3.1136554 0 -3.03563 -1.1672422 9204.8205 3600 0.086720297 -3.1021183 0 -3.0218427 -1.126381 9233.2656 3800 0.089264018 -3.0909262 0 -3.0082959 -1.0899774 9265.4143 4000 0.091377688 -3.0795096 0 -2.9949227 -1.0580229 9297.6799 4200 0.092665135 -3.0678736 0 -2.9820949 -1.0390124 9331.6135 4400 0.09055434 -3.0560482 0 -2.9722234 -1.0323741 9362.2075 4600 0.088763719 -3.0446018 0 -2.9624346 -1.027693 9391.6949 4800 0.089467982 -3.0337452 0 -2.950926 -1.0232092 9427.4155 5000 0.089910902 -3.0237571 0 -2.9405279 -1.0174796 9452.031 Loop time of 2.51163 on 2 procs for 5000 steps with 8141 atoms Performance: 515999.419 tau/day, 1990.738 timesteps/s, 16.207 Matom-step/s 98.7% CPU use with 2 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6134 | 1.7812 | 1.949 | 12.6 | 70.92 Neigh | 0.11017 | 0.11313 | 0.11608 | 0.9 | 4.50 Comm | 0.15976 | 0.33191 | 0.50405 | 29.9 | 13.21 Output | 0.0012394 | 0.0016296 | 0.0020199 | 1.0 | 0.06 Modify | 0.1771 | 0.19757 | 0.21803 | 4.6 | 7.87 Other | | 0.08619 | | | 3.43 Nlocal: 4070.5 ave 4085 max 4056 min Histogram: 1 0 0 0 0 0 0 0 0 1 Nghost: 207 ave 208 max 206 min Histogram: 1 0 0 0 0 0 0 0 0 1 Neighs: 35700 ave 35927 max 35473 min Histogram: 1 0 0 0 0 0 0 0 0 1 Total # of neighbors = 71400 Ave neighs/atom = 8.7704213 Neighbor list builds = 106 Dangerous builds = 0 Total wall time: 0:00:02 rm -rf test make[1]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg' dh_auto_test -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build -Nlammps -Nliblammps-dev -Nliblammps0t64 -Npython3-lammps create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3,sphinxdoc --sourcedirectory=cmake --builddirectory=/build/reproducible-path/lammps-20240207+dfsg/debian/build dh_testroot -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build dh_prep -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build dh_auto_install -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build -Nlammps-doc -Nlammps-data -Nlammps-examples cd debian/build && make -j12 install DESTDIR=/build/reproducible-path/lammps-20240207\+dfsg/debian/tmp AM_UPDATE_INFO_DIR=no "INSTALL=install --strip-program=true" make[1]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' /usr/bin/cmake -P /build/reproducible-path/lammps-20240207+dfsg/debian/build/CMakeFiles/VerifyGlobs.cmake /usr/bin/cmake -S/build/reproducible-path/lammps-20240207+dfsg/cmake -B/build/reproducible-path/lammps-20240207+dfsg/debian/build --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 preinstall make[2]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' make[2]: Nothing to be done for 'preinstall'. make[2]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' Install the project... /usr/bin/cmake -P cmake_install.cmake -- Install configuration: "None" -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/bin/lmp -- Set non-toolchain portion of runtime path of "/build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/bin/lmp" to "" -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/angle.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/atom.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/bond.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/citeme.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/comm.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/command.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/compute.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/dihedral.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/domain.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/error.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/exceptions.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/fix.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/force.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/group.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/improper.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/input.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/info.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/kspace.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/lammps.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/lattice.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/library.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/lmppython.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/lmptype.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/memory.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/modify.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/neighbor.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/neigh_list.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/output.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/pair.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/platform.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/pointers.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/region.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/timer.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/universe.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/update.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/utils.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/variable.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/fmt/core.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/include/lammps/fmt/format.h -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/liblammps.so.0 -- Set non-toolchain portion of runtime path of "/build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/liblammps.so.0" to "" -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/liblammps.so -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/pkgconfig/liblammps.pc -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/LAMMPS/LAMMPS_Targets.cmake -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/LAMMPS/LAMMPS_Targets-none.cmake -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/LAMMPS/LAMMPSConfig.cmake -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/cmake/LAMMPS/LAMMPSConfigVersion.cmake -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/share/man/man1/lmp.1 -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/etc/profile.d/lammps.sh -- Installing: /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/etc/profile.d/lammps.csh make[1]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg/debian/build' debian/rules execute_after_dh_auto_install-arch make[1]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg' LD_LIBRARY_PATH=/build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu \ CMAKE_PREFIX_PATH=/build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu/cmake \ pybuild --dir=/build/reproducible-path/lammps-20240207+dfsg/python --system=pyproject --name=lammps ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. I: pybuild plugin_pyproject:129: Building wheel for python3.13 with "build" module I: pybuild base:311: python3.13 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/lammps-20240207+dfsg/.pybuild/cpython3_3.13_lammps ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. * Building wheel... ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. running bdist_wheel running build running build_py creating build/lib/lammps copying lammps/data.py -> build/lib/lammps copying lammps/formats.py -> build/lib/lammps copying lammps/numpy_wrapper.py -> build/lib/lammps copying lammps/pylammps.py -> build/lib/lammps copying lammps/core.py -> build/lib/lammps copying lammps/constants.py -> build/lib/lammps copying lammps/__init__.py -> build/lib/lammps creating build/lib/lammps/mliap copying lammps/mliap/mliap_unified_lj.py -> build/lib/lammps/mliap copying lammps/mliap/__init__.py -> build/lib/lammps/mliap copying lammps/mliap/loader.py -> build/lib/lammps/mliap copying lammps/mliap/mliap_unified_abc.py -> build/lib/lammps/mliap copying lammps/mliap/pytorch.py -> build/lib/lammps/mliap installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/lammps copying build/lib/lammps/data.py -> build/bdist.linux-x86_64/wheel/./lammps copying build/lib/lammps/formats.py -> build/bdist.linux-x86_64/wheel/./lammps copying build/lib/lammps/numpy_wrapper.py -> build/bdist.linux-x86_64/wheel/./lammps copying build/lib/lammps/pylammps.py -> build/bdist.linux-x86_64/wheel/./lammps copying build/lib/lammps/core.py -> build/bdist.linux-x86_64/wheel/./lammps creating build/bdist.linux-x86_64/wheel/lammps/mliap copying build/lib/lammps/mliap/mliap_unified_lj.py -> build/bdist.linux-x86_64/wheel/./lammps/mliap copying build/lib/lammps/mliap/__init__.py -> build/bdist.linux-x86_64/wheel/./lammps/mliap copying build/lib/lammps/mliap/loader.py -> build/bdist.linux-x86_64/wheel/./lammps/mliap copying build/lib/lammps/mliap/mliap_unified_abc.py -> build/bdist.linux-x86_64/wheel/./lammps/mliap copying build/lib/lammps/mliap/pytorch.py -> build/bdist.linux-x86_64/wheel/./lammps/mliap copying build/lib/lammps/constants.py -> build/bdist.linux-x86_64/wheel/./lammps copying build/lib/lammps/__init__.py -> build/bdist.linux-x86_64/wheel/./lammps running install_egg_info running egg_info creating lammps.egg-info writing lammps.egg-info/PKG-INFO writing dependency_links to lammps.egg-info/dependency_links.txt writing top-level names to lammps.egg-info/top_level.txt writing manifest file 'lammps.egg-info/SOURCES.txt' reading manifest file 'lammps.egg-info/SOURCES.txt' writing manifest file 'lammps.egg-info/SOURCES.txt' Copying lammps.egg-info to build/bdist.linux-x86_64/wheel/./lammps-2024.2.7.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/lammps-2024.2.7.dist-info/WHEEL creating '/build/reproducible-path/lammps-20240207+dfsg/.pybuild/cpython3_3.13_lammps/.tmp-sty5pdcm/lammps-2024.2.7-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'lammps/__init__.py' adding 'lammps/constants.py' adding 'lammps/core.py' adding 'lammps/data.py' adding 'lammps/formats.py' adding 'lammps/numpy_wrapper.py' adding 'lammps/pylammps.py' adding 'lammps/mliap/__init__.py' adding 'lammps/mliap/loader.py' adding 'lammps/mliap/mliap_unified_abc.py' adding 'lammps/mliap/mliap_unified_lj.py' adding 'lammps/mliap/pytorch.py' adding 'lammps-2024.2.7.dist-info/METADATA' adding 'lammps-2024.2.7.dist-info/WHEEL' adding 'lammps-2024.2.7.dist-info/top_level.txt' adding 'lammps-2024.2.7.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Successfully built lammps-2024.2.7-py3-none-any.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.13 with "installer" module I: pybuild plugin_pyproject:178: Copying package built for python3.13 to destdir I: pybuild base:311: cd /build/reproducible-path/lammps-20240207+dfsg/.pybuild/cpython3_3.13_lammps/build; python3.13 -m unittest discover -v ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ---------------------------------------------------------------------- Ran 0 tests in 0.000s NO TESTS RAN I: pybuild plugin_pyproject:129: Building wheel for python3.12 with "build" module I: pybuild base:311: python3.12 -m build --skip-dependency-check --no-isolation --wheel --outdir /build/reproducible-path/lammps-20240207+dfsg/.pybuild/cpython3_3.12_lammps ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. * Building wheel... ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. running bdist_wheel running build running build_py creating build/lib/lammps copying lammps/data.py -> build/lib/lammps copying lammps/formats.py -> build/lib/lammps copying lammps/numpy_wrapper.py -> build/lib/lammps copying lammps/pylammps.py -> build/lib/lammps copying lammps/core.py -> build/lib/lammps copying lammps/constants.py -> build/lib/lammps copying lammps/__init__.py -> build/lib/lammps creating build/lib/lammps/mliap copying lammps/mliap/mliap_unified_lj.py -> build/lib/lammps/mliap copying lammps/mliap/__init__.py -> build/lib/lammps/mliap copying lammps/mliap/loader.py -> build/lib/lammps/mliap copying lammps/mliap/mliap_unified_abc.py -> build/lib/lammps/mliap copying lammps/mliap/pytorch.py -> build/lib/lammps/mliap installing to build/bdist.linux-x86_64/wheel running install running install_lib creating build/bdist.linux-x86_64/wheel creating build/bdist.linux-x86_64/wheel/lammps copying build/lib/lammps/data.py -> build/bdist.linux-x86_64/wheel/./lammps copying build/lib/lammps/formats.py -> build/bdist.linux-x86_64/wheel/./lammps copying build/lib/lammps/numpy_wrapper.py -> build/bdist.linux-x86_64/wheel/./lammps copying build/lib/lammps/pylammps.py -> build/bdist.linux-x86_64/wheel/./lammps copying build/lib/lammps/core.py -> build/bdist.linux-x86_64/wheel/./lammps creating build/bdist.linux-x86_64/wheel/lammps/mliap copying build/lib/lammps/mliap/mliap_unified_lj.py -> build/bdist.linux-x86_64/wheel/./lammps/mliap copying build/lib/lammps/mliap/__init__.py -> build/bdist.linux-x86_64/wheel/./lammps/mliap copying build/lib/lammps/mliap/loader.py -> build/bdist.linux-x86_64/wheel/./lammps/mliap copying build/lib/lammps/mliap/mliap_unified_abc.py -> build/bdist.linux-x86_64/wheel/./lammps/mliap copying build/lib/lammps/mliap/pytorch.py -> build/bdist.linux-x86_64/wheel/./lammps/mliap copying build/lib/lammps/constants.py -> build/bdist.linux-x86_64/wheel/./lammps copying build/lib/lammps/__init__.py -> build/bdist.linux-x86_64/wheel/./lammps running install_egg_info running egg_info creating lammps.egg-info writing lammps.egg-info/PKG-INFO writing dependency_links to lammps.egg-info/dependency_links.txt writing top-level names to lammps.egg-info/top_level.txt writing manifest file 'lammps.egg-info/SOURCES.txt' reading manifest file 'lammps.egg-info/SOURCES.txt' writing manifest file 'lammps.egg-info/SOURCES.txt' Copying lammps.egg-info to build/bdist.linux-x86_64/wheel/./lammps-2024.2.7.egg-info running install_scripts creating build/bdist.linux-x86_64/wheel/lammps-2024.2.7.dist-info/WHEEL creating '/build/reproducible-path/lammps-20240207+dfsg/.pybuild/cpython3_3.12_lammps/.tmp-spyf2rvf/lammps-2024.2.7-py3-none-any.whl' and adding 'build/bdist.linux-x86_64/wheel' to it adding 'lammps/__init__.py' adding 'lammps/constants.py' adding 'lammps/core.py' adding 'lammps/data.py' adding 'lammps/formats.py' adding 'lammps/numpy_wrapper.py' adding 'lammps/pylammps.py' adding 'lammps/mliap/__init__.py' adding 'lammps/mliap/loader.py' adding 'lammps/mliap/mliap_unified_abc.py' adding 'lammps/mliap/mliap_unified_lj.py' adding 'lammps/mliap/pytorch.py' adding 'lammps-2024.2.7.dist-info/METADATA' adding 'lammps-2024.2.7.dist-info/WHEEL' adding 'lammps-2024.2.7.dist-info/top_level.txt' adding 'lammps-2024.2.7.dist-info/RECORD' removing build/bdist.linux-x86_64/wheel Successfully built lammps-2024.2.7-py3-none-any.whl I: pybuild plugin_pyproject:144: Unpacking wheel built for python3.12 with "installer" module I: pybuild plugin_pyproject:178: Copying package built for python3.12 to destdir I: pybuild base:311: cd /build/reproducible-path/lammps-20240207+dfsg/.pybuild/cpython3_3.12_lammps/build; python3.12 -m unittest discover -v ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. ---------------------------------------------------------------------- Ran 0 tests in 0.000s NO TESTS RAN make[1]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg' dh_install -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build dh_installdocs -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build debian/rules override_dh_sphinxdoc make[1]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg' echo "sphinx and dh_sphinx are broken for lammps docs. See Bug#1059621" sphinx and dh_sphinx are broken for lammps docs. See Bug#1059621 make[1]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg' dh_installchangelogs -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build debian/rules override_dh_installexamples make[1]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg' dh_installexamples -X.gitignore make[1]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg' debian/rules override_dh_installman-arch make[1]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg' sed -i 's|TH LAMMPS|TH LAMMPS \"1\"|g' /build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/share/man/man1/lmp.1 dh_installman -a make[1]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg' dh_installman -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build -Nlammps -Nliblammps-dev -Nliblammps0t64 -Npython3-lammps debian/rules execute_before_dh_python3-arch make[1]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg' set -e; \ cd python/examples; \ LD_LIBRARY_PATH=/build/reproducible-path/lammps-20240207+dfsg/debian/tmp/usr/lib/x86_64-linux-gnu \ PYTHONPATH=/build/reproducible-path/lammps-20240207+dfsg/debian/python3-lammps/usr/lib/python3.12/dist-packages:${PYTHONPATH} \ python3 demo.py ERROR: ld.so: object 'libfakeroot-sysv.so' from LD_PRELOAD cannot be preloaded (cannot open shared object file): ignored. LAMMPS (7 Feb 2024 - Update 1) Python output: Natoms, mass, x[0][0] coord = 4000 1.0 16.767988851705528 Temperature from compute = 0.7571533403732014 Energy from equal-style variable = -5.758142569688168 Velocity component from atom-style variable = -1.0131655567386921 Volume from get_thermo = 4738.213693437576 Natoms from get_natoms = 4000 Global coords from gather_atoms = 16.767988851705528 16.621004261651628 0.14158807746974947 Changed x[0][0] via scatter_atoms = 17.767988851705528 OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962 Created orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962) 1 by 1 by 1 MPI processor grid Created 4000 atoms using lattice units in orthogonal box = (0 0 0) to (16.795962 16.795962 16.795962) create_atoms CPU = 0.001 seconds Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule Neighbor list info ... update: every = 20 steps, delay = 0 steps, check = no max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 2.8 ghost atom cutoff = 2.8 binsize = 1.4, bins = 12 12 12 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut, perpetual attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : lj Current step : 0 Time step : 0.005 Per MPI rank memory allocation (min/avg/max) = 3.763 | 3.763 | 3.763 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.44 -6.7733681 0 -4.6139081 -5.0199732 100 0.75715334 -5.7581426 0 -4.6226965 0.20850222 Loop time of 0.267945 on 1 procs for 100 steps with 4000 atoms Performance: 161226.981 tau/day, 373.211 timesteps/s, 1.493 Matom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22292 | 0.22292 | 0.22292 | 0.0 | 83.20 Neigh | 0.036041 | 0.036041 | 0.036041 | 0.0 | 13.45 Comm | 0.0044844 | 0.0044844 | 0.0044844 | 0.0 | 1.67 Output | 4.7018e-05 | 4.7018e-05 | 4.7018e-05 | 0.0 | 0.02 Modify | 0.0036496 | 0.0036496 | 0.0036496 | 0.0 | 1.36 Other | | 0.0008035 | | | 0.30 Nlocal: 4000 ave 4000 max 4000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5754 ave 5754 max 5754 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 150362 ave 150362 max 150362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 150362 Ave neighs/atom = 37.5905 Neighbor list builds = 5 Dangerous builds not checked Total wall time: 0:00:00 make[1]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg' dh_python3 -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build dh_installsystemduser -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build dh_lintian -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build dh_perl -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build dh_link -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build dh_strip_nondeterminism -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build debian/rules override_dh_compress make[1]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg' dh_compress -X.pdf make[1]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg' dh_fixperms -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build debian/rules execute_after_dh_fixperms-indep make[1]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg' find /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/ -type f -a -not -name *.sh -print -exec chmod 644 {} \; /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/qeq/data.CHO /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/qeq/log.30Nov23.reaxff.g++.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/qeq/ffield.reax.cho /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/qeq/log.20Apr21.qeq.buck.g++.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/qeq/param.qeq2 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/qeq/buck.inc /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/qeq/param.qeq.reax /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/qeq/in.qeq.buck /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/qeq/log.30Nov23.reaxff.g++.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/qeq/param.qeq1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/qeq/data.aC /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/qeq/in.qeq.reaxff /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/qeq/log.20Apr21.qeq.buck.g++.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/log.10Feb21.in.lammps.melt.clang.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/plugin/CMakeLists.txt /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/plugin/kimplugin.cpp /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/plugin/README.txt /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/in.kim-sm.melt /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/in.kim-pm-property /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/log.10Feb21.in.kim-pm-query.melt.clang.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/log.10Feb21.in.kim-pm.melt.clang.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/log.10Feb21.in.kim-pm.melt.clang.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/in.kim-pm.melt /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/log.10Feb21.in.kim-ex.melt.clang.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/log.10Feb21.in.kim-ex.melt.clang.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/in.kim-query /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/in.kim-ex.melt /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/log.10Feb21.in.kim-sm.melt.clang.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/in.lammps.melt /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/log.10Feb21.in.kim-pm-property.clang.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/log.10Feb21.in.kim-pm-query.melt.clang.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/log.10Feb21.in.kim-pm-property.clang.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/log.10Feb21.in.kim-query.clang.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/in.kim-pm-query.melt /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/log.10Feb21.in.kim-sm.melt.clang.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/kim/log.10Feb21.in.lammps.melt.clang.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/threebody/log.29Sep21.threebody.g++.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/threebody/log.29Sep21.threebody.g++.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/threebody/in.mos2.sw.mod /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/threebody/in.threebody /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/threebody/log.27Oct21.mos2_sw_mod.g++.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/threebody/single_layer_MoS2.data /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/rigid/log.27Nov18.rigid.atomvar.g++.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/rigid/in.rigid.poems5 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/rigid/connected-bodies.dat /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/rigid/molecule.data /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/rigid/log.27Nov18.rigid.nve.g++.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/rigid/log.20Mar22.rigid.rigid.molecule.g++.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/rigid/log.20Mar22.rigid.small.infile.g++.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/rigid/in.rigid.small.infile /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/rigid/log.27Nov18.rigid.atomfile.g++.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/rigid/log.27Nov18.rigid.nve.g++.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/rigid/log.27Nov18.rigid.early.g++.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/rigid/data.rigid-property /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/rigid/log.27Nov18.rigid.nve.early.g++.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/rigid/connected-bodies2.dat /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/rigid/in.rigid.small /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/rigid/in.rigid.poems3 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/rigid/log.20Mar22.rigid.molecule.g++.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/rigid/log.27Nov18.rigid.atomvar.g++.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/rigid/in.rigid.nve.early 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/build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/mdi/log.17Jun22.snapshot.engine.tcp.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/mdi/in.aimd.driver /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/mdi/log.17Jun22.aimdpy.mm.mpi.2 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/mdi/dump.17Jun22.snapshot.alone.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/mdi/log.17Jun22.series.driver.mpi.3 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/mdi/log.17Jun22.snapshot.engine.plugin.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/mdi/dump.17Jun22.series.driver.plugin.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/mdi/sequence_driver.py /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/mdi/log.17Jun22.sequence.engine.tcp.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/multi/log.30Nov20.granular.old.intel.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/multi/log.30Nov20.granular.intel.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/multi/in.granular /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/multi/log.30Nov20.granular.old.intel.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/multi/log.30Nov20.powerlaw.intel.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/multi/log.30Nov20.powerlaw.intel.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/multi/log.30Nov20.colloid.intel.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/multi/log.30Nov20.granular.intel.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/multi/data.powerlaw /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/multi/log.30Nov20.colloid.intel.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/multi/log.30Nov20.colloid.old.intel.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/multi/in.colloid /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/multi/in.powerlaw /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/multi/log.30Nov20.colloid.old.intel.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/coreshell/log.27Nov18.coreshell.g++.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/coreshell/in.coreshell.dsf /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/coreshell/log.27Nov18.coreshell.thermostats.g++.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/coreshell/log.27Nov18.coreshell.wolf.g++.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/coreshell/log.27Nov18.coreshell.wolf.g++.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/coreshell/log.27Nov18.coreshell.dsf.g++.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/coreshell/in.coreshell.wolf /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/coreshell/data.coreshell /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/coreshell/log.27Nov18.coreshell.g++.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/coreshell/in.coreshell.thermostats /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/coreshell/in.coreshell /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/coreshell/log.27Nov18.coreshell.dsf.g++.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/coreshell/log.27Nov18.coreshell.thermostats.g++.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/UNITS/in.ar.real /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/UNITS/in.ar.lj /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/UNITS/log.ar.real.8Oct19.g++.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/UNITS/README /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/UNITS/log.ar.lj.8Oct19.g++.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/UNITS/log.ar.metal.8Oct19.g++.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/UNITS/log.ar.metal.8Oct19.g++.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/UNITS/log.ar.real.8Oct19.g++.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/UNITS/log.ar.lj.8Oct19.g++.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/UNITS/in.ar.metal /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/nemd/log.27Nov18.nemd.g++.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/nemd/in.nemd /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/nemd/log.27Nov18.nemd.g++.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/voronoi/in.voronoi.data /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/voronoi/log.27Nov18.voronoi.data.g++.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/voronoi/log.27Nov18.voronoi.2d.g++.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/voronoi/log.27Nov18.voronoi.data.g++.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/voronoi/in.voronoi.2d /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/voronoi/README /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/voronoi/log.27Nov18.voronoi.2d.g++.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/voronoi/log.27Nov18.voronoi.g++.4 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/voronoi/log.27Nov18.voronoi.g++.1 /build/reproducible-path/lammps-20240207+dfsg/debian/lammps-examples/usr/share/lammps/examples/voronoi/in.voronoi make[1]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg' dh_missing -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build debian/rules override_dh_dwz make[1]: Entering directory '/build/reproducible-path/lammps-20240207+dfsg' dh_dwz -Xliblammps.so.0 make[1]: Leaving directory '/build/reproducible-path/lammps-20240207+dfsg' dh_strip -a -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build dh_makeshlibs -a -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build dh_shlibdeps -a -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build dh_installdeb -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build dh_gencontrol -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build dpkg-gencontrol: warning: Depends field of package liblammps-dev: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package lammps-doc: substitution variable ${sphinxdoc:Depends} used, but is not defined dpkg-gencontrol: warning: Depends field of package python3-lammps: substitution variable ${shlibs:Depends} used, but is not defined dpkg-gencontrol: warning: package lammps-examples: substitution variable ${perl:Depends} unused, but is defined dh_md5sums -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build dh_builddeb -O--sourcedirectory=cmake -O--builddirectory=/build/reproducible-path/lammps-20240207\+dfsg/debian/build dpkg-deb: building package 'lammps-dbgsym' in '../lammps-dbgsym_20240207+dfsg-2_amd64.deb'. dpkg-deb: building package 'lammps' in '../lammps_20240207+dfsg-2_amd64.deb'. dpkg-deb: building package 'liblammps0t64' in '../liblammps0t64_20240207+dfsg-2_amd64.deb'. dpkg-deb: building package 'liblammps-dev' in '../liblammps-dev_20240207+dfsg-2_amd64.deb'. dpkg-deb: building package 'liblammps0t64-dbgsym' in '../liblammps0t64-dbgsym_20240207+dfsg-2_amd64.deb'. dpkg-deb: building package 'lammps-data' in '../lammps-data_20240207+dfsg-2_all.deb'. dpkg-deb: building package 'python3-lammps' in '../python3-lammps_20240207+dfsg-2_amd64.deb'. dpkg-deb: building package 'lammps-doc' in '../lammps-doc_20240207+dfsg-2_all.deb'. dpkg-deb: building package 'lammps-examples' in '../lammps-examples_20240207+dfsg-2_all.deb'. dpkg-genbuildinfo --build=binary -O../lammps_20240207+dfsg-2_amd64.buildinfo dpkg-genchanges --build=binary -O../lammps_20240207+dfsg-2_amd64.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) dpkg-genchanges: info: not including original source code in upload I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1128056 and its subdirectories I: Current time: Thu Jan 15 10:57:50 -12 2026 I: pbuilder-time-stamp: 1768517870 Fri Dec 13 16:34:53 UTC 2024 I: 1st build successful. Starting 2nd build on remote node infom01-amd64.debian.net. Fri Dec 13 16:34:53 UTC 2024 I: Preparing to do remote build '2' on infom01-amd64.debian.net. Fri Dec 13 16:51:53 UTC 2024 I: Deleting $TMPDIR on infom01-amd64.debian.net. Fri Dec 13 16:51:54 UTC 2024 I: lammps_20240207+dfsg-2_amd64.changes: Format: 1.8 Date: Fri, 13 Dec 2024 07:13:14 +0100 Source: lammps Binary: lammps lammps-data lammps-dbgsym lammps-doc lammps-examples liblammps-dev liblammps0t64 liblammps0t64-dbgsym python3-lammps Architecture: all amd64 Version: 20240207+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Science Maintainers Changed-By: Anton Gladky Description: lammps - Molecular Dynamics Simulator lammps-data - Molecular Dynamics Simulator. Data (potentials) lammps-doc - Molecular Dynamics Simulator (documentation) lammps-examples - Molecular Dynamics Simulator (examples) liblammps-dev - Molecular Dynamics Simulator (dev files) liblammps0t64 - Molecular Dynamics Simulator (shared library) python3-lammps - Molecular Dynamics Simulator Changes: lammps (20240207+dfsg-2) unstable; urgency=medium . * [e5b45dd] Fix autopkgtests * [019570b] d/control: set Standards-Version to 4.7.0 Checksums-Sha1: 2ffc514d56428ecc6d1bc2d422041d154726df83 9538064 lammps-data_20240207+dfsg-2_all.deb 68152aed01446f70aa22862b6b9f8cf5e5806ae3 22656 lammps-dbgsym_20240207+dfsg-2_amd64.deb db7f866e3453d608a663924dd0d6f9e21d191d9a 54074804 lammps-doc_20240207+dfsg-2_all.deb 416e8f9b5df821a38d2db0e71c8ad27606964c22 45429640 lammps-examples_20240207+dfsg-2_all.deb 4b457cd30089404ec5d530a648e5423a0b2fc8d0 31995 lammps_20240207+dfsg-2_amd64.buildinfo f92482932deef7ddad50091d31ff0e0347b7533d 18448 lammps_20240207+dfsg-2_amd64.deb f273e790e4afbc6b2bccf6ac5718bb1ed3f07059 114204 liblammps-dev_20240207+dfsg-2_amd64.deb 67748e6909a475e8549699d4a3f1fec072f3c811 85445476 liblammps0t64-dbgsym_20240207+dfsg-2_amd64.deb 216e1f44b4b10a844a7bf478acecf2e698f30679 7206724 liblammps0t64_20240207+dfsg-2_amd64.deb 93054efd489a46823bbf9631a8d52f4494ac8a49 72464 python3-lammps_20240207+dfsg-2_amd64.deb Checksums-Sha256: 4b2ed159e08785d544c05e7bdd8dd19d664841a952c70c097c7574dc4900437f 9538064 lammps-data_20240207+dfsg-2_all.deb 5347fb55764698551eecff25ac9ac8be7b39dfc7bd2feb70dde7bcc811f01aa5 22656 lammps-dbgsym_20240207+dfsg-2_amd64.deb 139286b5dd95e27c90fee10ae91a374419999f740df52796101aea604ebb5216 54074804 lammps-doc_20240207+dfsg-2_all.deb afcd77a37797ac21fc56a2eb25b969fed034de2163c5f8ccbc433d5519757c42 45429640 lammps-examples_20240207+dfsg-2_all.deb 50ff80321057fce2581c517d2f7666a22636bdda992f45a8b1ae5952d3bed69c 31995 lammps_20240207+dfsg-2_amd64.buildinfo 998c4e436521e9de8a34b2dc0a70d564b2f948a05153de1820ff565d0ac14ead 18448 lammps_20240207+dfsg-2_amd64.deb e4dc39ac2bc66c3762db482fd623f3a32fdf1127faea7645753ecfc69c86b001 114204 liblammps-dev_20240207+dfsg-2_amd64.deb 189212f7d376ab885f8ed85c06edd1245ebb37e9e98e2bb94b6441f69d8ec57a 85445476 liblammps0t64-dbgsym_20240207+dfsg-2_amd64.deb dd64773e74a93d7ff8db36c79fd27dcd9b22f984ea93847a91a1ff588fb79521 7206724 liblammps0t64_20240207+dfsg-2_amd64.deb f3403f0998f5e21533acd5497a26596ae083a925fad75b413dc8e10a3e81858c 72464 python3-lammps_20240207+dfsg-2_amd64.deb Files: 5a320bbbdd5c1f86a1a03e4b72d5d857 9538064 doc optional lammps-data_20240207+dfsg-2_all.deb 818e47ce22b2d9d3c394d7de668dca5c 22656 debug optional lammps-dbgsym_20240207+dfsg-2_amd64.deb 4d33c421269317c6dcaf801316da2c2b 54074804 doc optional lammps-doc_20240207+dfsg-2_all.deb 9a7cc73e034c1776dc167f02a110e827 45429640 doc optional lammps-examples_20240207+dfsg-2_all.deb 157a91d5e3302880217367eac71adca5 31995 science optional lammps_20240207+dfsg-2_amd64.buildinfo 637be8fa1870e5d76e4fdc10d40c6620 18448 science optional lammps_20240207+dfsg-2_amd64.deb 8cb0da60642afdbc9a157ec448b37758 114204 science optional liblammps-dev_20240207+dfsg-2_amd64.deb 9816752f3f29accf3a4de400b909e663 85445476 debug optional liblammps0t64-dbgsym_20240207+dfsg-2_amd64.deb 9d20dac449702155cad43ca499d96489 7206724 science optional liblammps0t64_20240207+dfsg-2_amd64.deb 654192a95fdfbbf03735d7c4c9b1a8d3 72464 python optional python3-lammps_20240207+dfsg-2_amd64.deb Fri Dec 13 16:51:56 UTC 2024 I: diffoscope 284 will be used to compare the two builds: Running as unit: rb-diffoscope-amd64_36-40557.service # Profiling output for: /usr/bin/diffoscope --timeout 7200 --html /srv/reproducible-results/rbuild-debian/r-b-build.UZ1wfsBI/lammps_20240207+dfsg-2.diffoscope.html --text /srv/reproducible-results/rbuild-debian/r-b-build.UZ1wfsBI/lammps_20240207+dfsg-2.diffoscope.txt --json /srv/reproducible-results/rbuild-debian/r-b-build.UZ1wfsBI/lammps_20240207+dfsg-2.diffoscope.json --profile=- /srv/reproducible-results/rbuild-debian/r-b-build.UZ1wfsBI/b1/lammps_20240207+dfsg-2_amd64.changes /srv/reproducible-results/rbuild-debian/r-b-build.UZ1wfsBI/b2/lammps_20240207+dfsg-2_amd64.changes ## command (total time: 0.000s) 0.000s 1 call cmp (internal) ## has_same_content_as (total time: 0.000s) 0.000s 1 call abc.DotChangesFile ## main (total time: 2.061s) 2.061s 2 calls outputs 0.000s 1 call cleanup ## recognizes (total time: 1.725s) 1.725s 12 calls diffoscope.comparators.binary.FilesystemFile ## specialize (total time: 0.000s) 0.000s 1 call specialize Finished with result: success Main processes terminated with: code=exited/status=0 Service runtime: 2.371s CPU time consumed: 2.371s Fri Dec 13 16:51:59 UTC 2024 I: diffoscope 284 found no differences in the changes files, and a .buildinfo file also exists. Fri Dec 13 16:51:59 UTC 2024 I: lammps from unstable built successfully and reproducibly on amd64. Fri Dec 13 16:52:01 UTC 2024 I: Submitting .buildinfo files to external archives: Fri Dec 13 16:52:01 UTC 2024 I: Submitting 36K b1/lammps_20240207+dfsg-2_amd64.buildinfo.asc Fri Dec 13 16:52:02 UTC 2024 I: Submitting 36K b2/lammps_20240207+dfsg-2_amd64.buildinfo.asc Fri Dec 13 16:52:03 UTC 2024 I: Done submitting .buildinfo files to http://buildinfo.debian.net/api/submit. Fri Dec 13 16:52:03 UTC 2024 I: Done submitting .buildinfo files. Fri Dec 13 16:52:03 UTC 2024 I: Removing signed lammps_20240207+dfsg-2_amd64.buildinfo.asc files: removed './b1/lammps_20240207+dfsg-2_amd64.buildinfo.asc' removed './b2/lammps_20240207+dfsg-2_amd64.buildinfo.asc'