--- /srv/reproducible-results/rbuild-debian/r-b-build.buWochGY/b1/lammps_20240207+dfsg-2_i386.changes +++ /srv/reproducible-results/rbuild-debian/r-b-build.buWochGY/b2/lammps_20240207+dfsg-2_i386.changes ├── Files │ @@ -1,10 +1,10 @@ │ │ 5a320bbbdd5c1f86a1a03e4b72d5d857 9538064 doc optional lammps-data_20240207+dfsg-2_all.deb │ b6073cec78b751ac4d4c591becb4e2f5 22616 debug optional lammps-dbgsym_20240207+dfsg-2_i386.deb │ - 4d33c421269317c6dcaf801316da2c2b 54074804 doc optional lammps-doc_20240207+dfsg-2_all.deb │ + 1254214445b08362fcf4ac30c41911ab 54074692 doc optional lammps-doc_20240207+dfsg-2_all.deb │ 9a7cc73e034c1776dc167f02a110e827 45429640 doc optional lammps-examples_20240207+dfsg-2_all.deb │ e1d8bc7c12571c6b7ac949f7887b936b 18436 science optional lammps_20240207+dfsg-2_i386.deb │ 36562ae73fc8ba2eaad450cfe2839e09 114184 science optional liblammps-dev_20240207+dfsg-2_i386.deb │ 5c030b36dda1862fa7a3b1b2504c001a 82540752 debug optional liblammps0t64-dbgsym_20240207+dfsg-2_i386.deb │ d880f0d36d9519bdef217c4f9c059bb8 7232860 science optional liblammps0t64_20240207+dfsg-2_i386.deb │ f632c62db1e91c8ebdb11cf259e12f27 72464 python optional python3-lammps_20240207+dfsg-2_i386.deb ├── lammps-doc_20240207+dfsg-2_all.deb │ ├── file list │ │ @@ -1,3 +1,3 @@ │ │ -rw-r--r-- 0 0 0 4 2024-12-13 06:13:14.000000 debian-binary │ │ --rw-r--r-- 0 0 0 29508 2024-12-13 06:13:14.000000 control.tar.xz │ │ --rw-r--r-- 0 0 0 54045104 2024-12-13 06:13:14.000000 data.tar.xz │ │ +-rw-r--r-- 0 0 0 29468 2024-12-13 06:13:14.000000 control.tar.xz │ │ +-rw-r--r-- 0 0 0 54045032 2024-12-13 06:13:14.000000 data.tar.xz │ ├── control.tar.xz │ │ ├── control.tar │ │ │ ├── ./md5sums │ │ │ │ ├── ./md5sums │ │ │ │ │┄ Files differ │ ├── data.tar.xz │ │ ├── data.tar │ │ │ ├── file list │ │ │ │ @@ -79,15 +79,15 @@ │ │ │ │ -rw-r--r-- 0 root (0) root (0) 32441 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/Howto_chunk.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 52098 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/Howto_cmake.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 34065 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/Howto_coreshell.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 14736 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/Howto_couple.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 12087 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/Howto_diffusion.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 16216 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/Howto_dispersion.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 15306 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/Howto_drude.html │ │ │ │ --rw-r--r-- 0 root (0) root (0) 64996 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/Howto_drude2.html │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 64977 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/Howto_drude2.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 14355 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/Howto_elastic.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 34846 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/Howto_github.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 14923 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/Howto_granular.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 16921 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/Howto_grid.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 15615 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/Howto_kappa.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 55118 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/Howto_lammps_gui.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 13303 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/Howto_library.html │ │ │ │ @@ -914,15 +914,15 @@ │ │ │ │ -rw-r--r-- 0 root (0) root (0) 44332 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/fix_store_force.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 48653 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/fix_store_state.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 52282 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/fix_temp_berendsen.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 54000 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/fix_temp_csvr.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 52614 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/fix_temp_rescale.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 44884 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/fix_temp_rescale_eff.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 49910 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/fix_tfmc.html │ │ │ │ --rw-r--r-- 0 root (0) root (0) 64696 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/fix_tgnh_drude.html │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 64713 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/fix_tgnh_drude.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 51467 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/fix_thermal_conductivity.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 50519 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/fix_ti_spring.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 47298 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/fix_tmd.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 66606 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/fix_ttm.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 45217 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/fix_tune_kspace.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 52738 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/fix_vector.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 51615 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/fix_viscosity.html │ │ │ │ @@ -984,15 +984,15 @@ │ │ │ │ -rw-r--r-- 0 root (0) root (0) 57802 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/molecule.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 52492 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/neb.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 47767 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/neb_spin.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 42869 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/neigh_modify.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 33157 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/neighbor.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 27929 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/newton.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 35406 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/next.html │ │ │ │ --rw-r--r-- 0 root (0) root (0) 44423 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/objects.inv │ │ │ │ +-rw-r--r-- 0 root (0) root (0) 44419 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/objects.inv │ │ │ │ -rw-r--r-- 0 root (0) root (0) 73336 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/package.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 61284 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/pair_adp.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 56190 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/pair_agni.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 67277 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/pair_aip_water_2dm.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 66576 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/pair_airebo.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 65617 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/pair_amoeba.html │ │ │ │ -rw-r--r-- 0 root (0) root (0) 63676 2024-12-13 06:13:14.000000 ./usr/share/doc/lammps/html/pair_atm.html │ │ │ ├── ./usr/share/doc/lammps/html/Howto_drude2.html │ │ │ │ @@ -471,15 +471,15 @@ │ │ │ │ fix NPT ATOMS npt temp 300. 300. 100 iso 1. 1. 500 │ │ │ │ fix_modify NPT temp TATOMS press thermo_press │ │ │ │ fix NVT DRUDES nvt temp 1. 1. 20 │ │ │ │ fix INVERSE all drude/transform/inverse │ │ │ │ │ │ │ │ │ │ │ │
Another option for thermalizing the Drude model is to use the │ │ │ │ -temperature-grouped Nose-Hoover (TGNH) thermostat proposed by (Son). │ │ │ │ +temperature-grouped Nose-Hoover (TGNH) thermostat proposed by (Son). │ │ │ │ This is implemented as fix tgnvt/drude and fix tgnpt/drude. │ │ │ │ It separates the kinetic energy into three contributions: │ │ │ │ the molecular center of mass (COM) motion, the motion of atoms or atom-Drude pairs relative to molecular COMs, │ │ │ │ and the relative motion of atom-Drude pairs. │ │ │ │ An independent Nose-Hoover chain is applied to each type of motion. │ │ │ │ When TGNH is used, the temperatures of molecular, atomic and Drude motion can be printed out with thermo_style command command.
│ │ │ │NVT simulation with TGNH thermostat
│ │ │ ├── ./usr/share/doc/lammps/html/fix_tgnh_drude.html │ │ │ │ @@ -441,15 +441,15 @@ │ │ │ │ │ │ │ │Example input scripts available: examples/PACKAGES/drude
│ │ │ │ │ │ │ │These commands are variants of the Nose-Hoover fix styles fix nvt and fix npt for thermalized Drude polarizable │ │ │ │ models. They apply temperature-grouped Nose-Hoover thermostat (TGNH) │ │ │ │ -proposed by (Son). When there are fast vibrational │ │ │ │ +proposed by (Son). When there are fast vibrational │ │ │ │ modes with frequencies close to Drude oscillators (e.g. double bonds or │ │ │ │ out-of-plane torsions), this thermostat can provide better kinetic │ │ │ │ energy equipartitioning.
│ │ │ │The difference between TGNH and the original Nose-Hoover thermostat is that,
│ │ │ │ TGNH separates the kinetic energy of the group into three contributions:
│ │ │ │ molecular center of mass (COM) motion,
│ │ │ │ motion of COM of atom-Drude pairs or non-polarizable atoms relative to molecular COM,
│ │ │ ├── ./usr/share/doc/lammps/html/objects.inv
│ │ │ │ ├── Sphinx inventory
│ │ │ │ │ @@ -1,12 +1,13 @@
│ │ │ │ │ # Sphinx inventory version 2
│ │ │ │ │ # Project: LAMMPS
│ │ │ │ │ # Version: 7 Feb 2024
│ │ │ │ │ # The remainder of this file is compressed using zlib.
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