| Offset 1, 11 lines modified | Offset 1, 11 lines modified | ||
| 1 | · | 1 | ·50164bf640ed8f67f30ac975730245e3·20582036·science·optional·gromacs-data_2020.6-2_all.deb |
| 2 | ·1962e74b4ffe4ed5b2a4540043bd0ab1·821244·debug·optional·gromacs-dbgsym_2020.6-2_amd64.deb | 2 | ·1962e74b4ffe4ed5b2a4540043bd0ab1·821244·debug·optional·gromacs-dbgsym_2020.6-2_amd64.deb |
| 3 | ·c89e38b6950ccadd5950da44347a4e95·85051644·debug·optional·gromacs-mpich-dbgsym_2020.6-2_amd64.deb | 3 | ·c89e38b6950ccadd5950da44347a4e95·85051644·debug·optional·gromacs-mpich-dbgsym_2020.6-2_amd64.deb |
| 4 | ·c10276216fd8d5c211ff981ea90314bd·6863660·science·optional·gromacs-mpich_2020.6-2_amd64.deb | 4 | ·c10276216fd8d5c211ff981ea90314bd·6863660·science·optional·gromacs-mpich_2020.6-2_amd64.deb |
| 5 | ·45e24b56e214da9decae4ce992b99a61·85056096·debug·optional·gromacs-openmpi-dbgsym_2020.6-2_amd64.deb | 5 | ·45e24b56e214da9decae4ce992b99a61·85056096·debug·optional·gromacs-openmpi-dbgsym_2020.6-2_amd64.deb |
| 6 | ·69a3120096c8b4e8f8a75f8c3b807c5d·6868232·science·optional·gromacs-openmpi_2020.6-2_amd64.deb | 6 | ·69a3120096c8b4e8f8a75f8c3b807c5d·6868232·science·optional·gromacs-openmpi_2020.6-2_amd64.deb |
| 7 | ·8496a4d5dec5e62b2d623337032b1837·137236·science·optional·gromacs_2020.6-2_amd64.deb | 7 | ·8496a4d5dec5e62b2d623337032b1837·137236·science·optional·gromacs_2020.6-2_amd64.deb |
| 8 | ·d | 8 | ·ad6076d479a24414b446089d0e7c5784·187296·libdevel·optional·libgromacs-dev_2020.6-2_amd64.deb |
| 9 | ·44d7388f5311fde7d077081582da588b·121103916·debug·optional·libgromacs5-dbgsym_2020.6-2_amd64.deb | 9 | ·44d7388f5311fde7d077081582da588b·121103916·debug·optional·libgromacs5-dbgsym_2020.6-2_amd64.deb |
| 10 | ·63983253290e5ee0f17bcfd917f6ba5f·11495956·libs·optional·libgromacs5_2020.6-2_amd64.deb | 10 | ·63983253290e5ee0f17bcfd917f6ba5f·11495956·libs·optional·libgromacs5_2020.6-2_amd64.deb |
| Offset 1, 3 lines modified | Offset 1, 3 lines modified | ||
| 1 | -rw-r--r--···0········0········0········4·2021-03-29·04:45:03.000000·debian-binary | 1 | -rw-r--r--···0········0········0········4·2021-03-29·04:45:03.000000·debian-binary |
| 2 | -rw-r--r--···0········0········0···3501 | 2 | -rw-r--r--···0········0········0···350124·2021-03-29·04:45:03.000000·control.tar.xz |
| 3 | -rw-r--r--···0········0········0·20231 | 3 | -rw-r--r--···0········0········0·20231720·2021-03-29·04:45:03.000000·data.tar.xz |
| Offset 63, 75 lines modified | Offset 63, 75 lines modified | ||
| 63 | </div><!--·top·--> | 63 | </div><!--·top·--> |
| 64 | <div·class="PageDoc"><div·class="header"> | 64 | <div·class="PageDoc"><div·class="header"> |
| 65 | ··<div·class="headertitle"> | 65 | ··<div·class="headertitle"> |
| 66 | <div·class="title">Todo·List·</div>··</div> | 66 | <div·class="title">Todo·List·</div>··</div> |
| 67 | </div><!--header--> | 67 | </div><!--header--> |
| 68 | <div·class="contents"> | 68 | <div·class="contents"> |
| 69 | <div·class="textblock"><dl·class="reflist"> | 69 | <div·class="textblock"><dl·class="reflist"> |
| 70 | <dt>Member·<a·class="el"·href="domdec__network_8h.xhtml#aa19abb9a9b9ce1ed0de5d259452f9e2c">ddSendrecv</a>··(const·gmx_domdec_t·*dd,·int·ddDimensionIndex,·int·direction,·T·*sendBuffer,·int·numElementsToSend,·T·*receiveBuffer,·int·numElementsToReceive)</dt> | ||
| 71 | <dd><a·class="anchor"·id="_todo000023"></a>This·function·template·is·deprecated,·new·calls·should·be·made·to·the·version·taking·ArrayRef·parameters·and·this·function·template·removed·when·unused.··</dd> | ||
| 72 | <dt>Member·<a·class="el"·href="state_8h.xhtml#aa4de64296c013fbd01f41b25c64a774c">df_history_t</a>··</dt> | ||
| 73 | <dd><a·class="anchor"·id="_todo000097"></a>Split·out·into·microstate·and·observables·history.··</dd> | ||
| 74 | <dt>Member·<a·class="el"·href="dir__separator_8h.xhtml#a0920890c442b665b0c6609fa796e9047">DIR_SEPARATOR</a>··</dt> | ||
| 75 | <dd><a·class="anchor"·id="_todo000160"></a>Get·rid·of·this·(Redmine·#950).·It·is·not·necessary·for·constructing·paths·on·the·systems·that·it·currently·supports,·and·is·not·reliable·in·parsing·input·paths·either,·since·Windows·needs·to·accept·both·instead·of·only·DIR_SEPARATOR.·At·the·very·least,·we·should·refactor·the·clients·of·this·header·so·that·they·operate·upon·path·objects·rather·than·raw·path·strings.··</dd> | ||
| 76 | <dt>Member·<a·class="el"·href="expfit_8h.xhtml#a560ea7d97277b9e0576776ec695fb9b3">fit_acf</a>··(int·ncorr,·int·fitfn,·const·gmx_output_env_t·*oenv,·gmx_bool·bVerbose,·real·tbeginfit,·real·tendfit,·real·dt,·real·c1[],·real·*fit)</dt> | ||
| 77 | <dd><a·class="anchor"·id="_todo000020"></a>check·parameters··</dd> | ||
| 70 | <dt>Member·<a·class="el"·href="classAtomProperties.xhtml#a076037cf4e1ac19d1dbab8bd405895e1">AtomProperties::atomNumberFromElement</a>··(const·char·*element)</dt> | 78 | <dt>Member·<a·class="el"·href="classAtomProperties.xhtml#a076037cf4e1ac19d1dbab8bd405895e1">AtomProperties::atomNumberFromElement</a>··(const·char·*element)</dt> |
| 71 | <dd><a·class="anchor"·id="_todo000151"></a>This·should·be·made·const·once·the·lazy·implementation·is·done·properly·for·the·class.··</dd> | 79 | <dd><a·class="anchor"·id="_todo000151"></a>This·should·be·made·const·once·the·lazy·implementation·is·done·properly·for·the·class.··</dd> |
| 72 | <dt>Member·<a·class="el"·href="classAtomProperties.xhtml#aa128b4b7662a21b904b8642eead5bfdd">AtomProperties::elementFromAtomNumber</a>··(int·atomNumber)</dt> | 80 | <dt>Member·<a·class="el"·href="classAtomProperties.xhtml#aa128b4b7662a21b904b8642eead5bfdd">AtomProperties::elementFromAtomNumber</a>··(int·atomNumber)</dt> |
| 73 | <dd><a·class="anchor"·id="_todo000150"></a>This·should·be·made·const·once·the·lazy·implementation·is·done·properly·for·the·class.··</dd> | 81 | <dd><a·class="anchor"·id="_todo000150"></a>This·should·be·made·const·once·the·lazy·implementation·is·done·properly·for·the·class.··</dd> |
| 74 | <dt>Class·<a·class="el"·href="structBondedInteractionList.xhtml">BondedInteractionList</a>··</dt> | 82 | <dt>Class·<a·class="el"·href="structBondedInteractionList.xhtml">BondedInteractionList</a>··</dt> |
| 75 | <dd><a·class="anchor"·id="_todo000040"></a>This·should·be·merged·with·<a·class="el"·href="structBondedInteraction.xhtml"·title="Information·about·single·bonded·interaction.">BondedInteraction</a>.··</dd> | 83 | <dd><a·class="anchor"·id="_todo000040"></a>This·should·be·merged·with·<a·class="el"·href="structBondedInteraction.xhtml"·title="Information·about·single·bonded·interaction.">BondedInteraction</a>.··</dd> |
| 76 | <dt>Member·<a·class="el"·href="gpu__utils_8h.xhtml#a7211e54946ef7b5f5ac17a321fc03b9b">buildSupportsNonbondedOnGpu</a>··(std::string·*error)</dt> | 84 | <dt>Member·<a·class="el"·href="gpu__utils_8h.xhtml#a7211e54946ef7b5f5ac17a321fc03b9b">buildSupportsNonbondedOnGpu</a>··(std::string·*error)</dt> |
| 77 | <dd><a·class="anchor"·id="_todo000049"></a>Move·this·to·NB·module·once·it·exists.··</dd> | 85 | <dd><a·class="anchor"·id="_todo000049"></a>Move·this·to·NB·module·once·it·exists.··</dd> |
| 78 | <dt>Member·<a·class="el"·href="hackblock_8h.xhtml#aebf7055bd2787b678b68cd10b985e280">clearModificationBlock</a>··(<a·class="el"·href="structMoleculePatchDatabase.xhtml"·title="A·set·of·modifications·to·apply·to·atoms.">MoleculePatchDatabase</a>·*globalPatches)</dt> | 86 | <dt>Member·<a·class="el"·href="hackblock_8h.xhtml#aebf7055bd2787b678b68cd10b985e280">clearModificationBlock</a>··(<a·class="el"·href="structMoleculePatchDatabase.xhtml"·title="A·set·of·modifications·to·apply·to·atoms.">MoleculePatchDatabase</a>·*globalPatches)</dt> |
| 79 | <dd><a·class="anchor"·id="_todo000041"></a>Remove·once·constructor/destructor·takes·care·of·all·of·this.··</dd> | 87 | <dd><a·class="anchor"·id="_todo000041"></a>Remove·once·constructor/destructor·takes·care·of·all·of·this.··</dd> |
| 80 | <dt>Member·<a·class="el"·href="hackblock_8h.xhtml#aecbab27ca8905331266d9ea02f925137">copyPreprocessResidues</a>··(const·<a·class="el"·href="structPreprocessResidue.xhtml"·title="Information·about·preprocessing·residues.">PreprocessResidue</a>·&s,·<a·class="el"·href="structPreprocessResidue.xhtml"·title="Information·about·preprocessing·residues.">PreprocessResidue</a>·*d,·t_symtab·*symtab)</dt> | 88 | <dt>Member·<a·class="el"·href="hackblock_8h.xhtml#aecbab27ca8905331266d9ea02f925137">copyPreprocessResidues</a>··(const·<a·class="el"·href="structPreprocessResidue.xhtml"·title="Information·about·preprocessing·residues.">PreprocessResidue</a>·&s,·<a·class="el"·href="structPreprocessResidue.xhtml"·title="Information·about·preprocessing·residues.">PreprocessResidue</a>·*d,·t_symtab·*symtab)</dt> |
| 81 | <dd><a·class="anchor"·id="_todo000042"></a>Remove·once·copy·can·be·done·directly.··</dd> | 89 | <dd><a·class="anchor"·id="_todo000042"></a>Remove·once·copy·can·be·done·directly.··</dd> |
| 82 | <dt>Member·<a·class="el"·href="domdec__network_8h.xhtml#aa19abb9a9b9ce1ed0de5d259452f9e2c">ddSendrecv</a>··(const·gmx_domdec_t·*dd,·int·ddDimensionIndex,·int·direction,·T·*sendBuffer,·int·numElementsToSend,·T·*receiveBuffer,·int·numElementsToReceive)</dt> | ||
| 83 | <dd><a·class="anchor"·id="_todo000023"></a>This·function·template·is·deprecated,·new·calls·should·be·made·to·the·version·taking·ArrayRef·parameters·and·this·function·template·removed·when·unused.··</dd> | ||
| 84 | <dt>Member·<a·class="el"·href="state_8h.xhtml#aa4de64296c013fbd01f41b25c64a774c">df_history_t</a>··</dt> | ||
| 85 | <dd><a·class="anchor"·id="_todo000097"></a>Split·out·into·microstate·and·observables·history.··</dd> | ||
| 86 | <dt>Member·<a·class="el"·href="dir__separator_8h.xhtml#a0920890c442b665b0c6609fa796e9047">DIR_SEPARATOR</a>··</dt> | ||
| 87 | <dd><a·class="anchor"·id="_todo000160"></a>Get·rid·of·this·(Redmine·#950).·It·is·not·necessary·for·constructing·paths·on·the·systems·that·it·currently·supports,·and·is·not·reliable·in·parsing·input·paths·either,·since·Windows·needs·to·accept·both·instead·of·only·DIR_SEPARATOR.·At·the·very·least,·we·should·refactor·the·clients·of·this·header·so·that·they·operate·upon·path·objects·rather·than·raw·path·strings.··</dd> | ||
| 88 | <dt>File·<a·class="el"·href="domdec__network_8h.xhtml">domdec_network.h</a>··</dt> | 90 | <dt>File·<a·class="el"·href="domdec__network_8h.xhtml">domdec_network.h</a>··</dt> |
| 89 | <dd><a·class="anchor"·id="_todo000022"></a>Wrap·the·raw·dd_bcast·in·md.cpp·into·a·higher-level·function·in·the·domdec·module,·then·this·file·can·be·module-internal.·</dd> | 91 | <dd><a·class="anchor"·id="_todo000022"></a>Wrap·the·raw·dd_bcast·in·md.cpp·into·a·higher-level·function·in·the·domdec·module,·then·this·file·can·be·module-internal.·</dd> |
| 90 | <dt>Member·<a·class="el"·href="expfit_8h.xhtml#a560ea7d97277b9e0576776ec695fb9b3">fit_acf</a>··(int·ncorr,·int·fitfn,·const·gmx_output_env_t·*oenv,·gmx_bool·bVerbose,·real·tbeginfit,·real·tendfit,·real·dt,·real·c1[],·real·*fit)</dt> | ||
| 91 | <dd><a·class="anchor"·id="_todo000020"></a>check·parameters··</dd> | ||
| 92 | <dt>Class·<a·class="el"·href="classgmx_1_1AbstractAnalysisArrayData.xhtml">gmx::AbstractAnalysisArrayData</a>··</dt> | 92 | <dt>Class·<a·class="el"·href="classgmx_1_1AbstractAnalysisArrayData.xhtml">gmx::AbstractAnalysisArrayData</a>··</dt> |
| 93 | <dd><a·class="anchor"·id="_todo000006"></a>·Add·support·for·multiple·data·sets.·</dd> | 93 | <dd><a·class="anchor"·id="_todo000006"></a>·Add·support·for·multiple·data·sets.·</dd> |
| 94 | <dt>Class·<a·class="el"·href="classgmx_1_1AbstractAnalysisData.xhtml">gmx::AbstractAnalysisData</a>··</dt> | 94 | <dt>Class·<a·class="el"·href="classgmx_1_1AbstractAnalysisData.xhtml">gmx::AbstractAnalysisData</a>··</dt> |
| 95 | <dd><a·class="anchor"·id="_todo000001"></a>·Improve·the·exception-handling·semantics.·In·most·cases,·it·doesn't·make·much·sense·to·continue·data·processing·after·one·module·fails,·but·having·the·alternative·would·not·hurt.·</dd> | 95 | <dd><a·class="anchor"·id="_todo000001"></a>·Improve·the·exception-handling·semantics.·In·most·cases,·it·doesn't·make·much·sense·to·continue·data·processing·after·one·module·fails,·but·having·the·alternative·would·not·hurt.·</dd> |
| 96 | <dt>Member·<a·class="el"·href="classgmx_1_1AbstractAnalysisData.xhtml#a90b99e3f700dbb8992a2d65a6b2a6de5">gmx::AbstractAnalysisData::addColumnModule</a>··(int·col,·int·span,·const·AnalysisDataModulePointer·&module)</dt> | 96 | <dt>Member·<a·class="el"·href="classgmx_1_1AbstractAnalysisData.xhtml#a90b99e3f700dbb8992a2d65a6b2a6de5">gmx::AbstractAnalysisData::addColumnModule</a>··(int·col,·int·span,·const·AnalysisDataModulePointer·&module)</dt> |
| 97 | <dd><p·class="startdd"><a·class="anchor"·id="_todo000003"></a>·Generalize·this·method·to·multiple·data·sets·(e.g.,·for·adding·modules·that·only·process·a·single·data·set).</p> | ||
| 98 | <p·class=" | 97 | <dd><p·class="startdd"><a·class="anchor"·id="_todo000002"></a>·This·method·doesn't·currently·work·in·all·cases·with·multipoint·data·or·with·multiple·data·sets.·In·particular,·if·the·added·module·requests·storage·and·uses·<a·class="el"·href="classgmx_1_1Abst[·...·truncated·by·diffoscope;·len:·157,·SHA:·43f69d8556c4caeed9663327eb34ac870552f520cc17b03ba4fc40e32b345929·...·]</p> |
| 98 | <p·class="enddd"><a·class="anchor"·id="_todo000003"></a>·Generalize·this·method·to·multiple·data·sets·(e.g.,·for·adding·modules·that·only·process·a·single·data·set).·</p> | ||
| 99 | </dd> | 99 | </dd> |
| 100 | <dt>Member·<a·class="el"·href="classgmx_1_1AbstractAnalysisData.xhtml#ae095550bd347b42db3c49e064bc44228">gmx::AbstractAnalysisData::applyModule</a>··(<a·class="el"·href="classgmx_1_1IAnalysisDataModule.xhtml"·title="Interface·for·a·module·that·gets·notified·whenever·data·is·added.">IAnalysisDataModule</a>·*module)</dt> | 100 | <dt>Member·<a·class="el"·href="classgmx_1_1AbstractAnalysisData.xhtml#ae095550bd347b42db3c49e064bc44228">gmx::AbstractAnalysisData::applyModule</a>··(<a·class="el"·href="classgmx_1_1IAnalysisDataModule.xhtml"·title="Interface·for·a·module·that·gets·notified·whenever·data·is·added.">IAnalysisDataModule</a>·*module)</dt> |
| 101 | <dd><a·class="anchor"·id="_todo000004"></a>·Currently,·this·method·may·not·work·correctly·if·<code>module</code>·requests·storage·(<a·class="el"·href="classgmx_1_1AbstractAnalysisData.xhtml#aa359ad884aa596dee5fd9e306ce8ea3f"·title="Adds·a·module·to·process·the·data.">addModule()</a>·has·the·same·problem·if·called·after·data·is·started).··</dd> | 101 | <dd><a·class="anchor"·id="_todo000004"></a>·Currently,·this·method·may·not·work·correctly·if·<code>module</code>·requests·storage·(<a·class="el"·href="classgmx_1_1AbstractAnalysisData.xhtml#aa359ad884aa596dee5fd9e306ce8ea3f"·title="Adds·a·module·to·process·the·data.">addModule()</a>·has·the·same·problem·if·called·after·data·is·started).··</dd> |
| 102 | <dt>Member·<a·class="el"·href="classgmx_1_1AbstractOptionStorage.xhtml#a9aa8495e558f50edd35b80754a508052">gmx::AbstractOptionStorage::processSet</a>··()=0</dt> | 102 | <dt>Member·<a·class="el"·href="classgmx_1_1AbstractOptionStorage.xhtml#a9aa8495e558f50edd35b80754a508052">gmx::AbstractOptionStorage::processSet</a>··()=0</dt> |
| 103 | <dd><a·class="anchor"·id="_todo000126"></a>·Improve·the·call·semantics.·</dd> | 103 | <dd><a·class="anchor"·id="_todo000126"></a>·Improve·the·call·semantics.·</dd> |
| 104 | <dt>Class·<a·class="el"·href="classgmx_1_1AnalysisData.xhtml">gmx::AnalysisData</a>··</dt> | 104 | <dt>Class·<a·class="el"·href="classgmx_1_1AnalysisData.xhtml">gmx::AnalysisData</a>··</dt> |
| 105 | <dd><a·class="anchor"·id="_todo000005"></a>·Parallel·implementation·is·not·complete.·</dd> | 105 | <dd><a·class="anchor"·id="_todo000005"></a>·Parallel·implementation·is·not·complete.·</dd> |
| 106 | <dt>Member·<a·class="el"·href="classgmx_1_1AnalysisDataPlotSettings.xhtml#a9431fa761d762a585a5c36c9595ad697">gmx::AnalysisDataPlotSettings::plotFormat</a>··()·const</dt> | 106 | <dt>Member·<a·class="el"·href="classgmx_1_1AnalysisDataPlotSettings.xhtml#a9431fa761d762a585a5c36c9595ad697">gmx::AnalysisDataPlotSettings::plotFormat</a>··()·const</dt> |
| 107 | <dd><a·class="anchor"·id="_todo000010"></a>Use·a·proper·enum.··</dd> | 107 | <dd><a·class="anchor"·id="_todo000010"></a>Use·a·proper·enum.··</dd> |
| 108 | <dt>Class·<a·class="el"·href="classgmx_1_1AnalysisDataStorage.xhtml">gmx::AnalysisDataStorage</a>··</dt> | 108 | <dt>Class·<a·class="el"·href="classgmx_1_1AnalysisDataStorage.xhtml">gmx::AnalysisDataStorage</a>··</dt> |
| 109 | <dd><a·class="anchor"·id="_todo000009"></a>·Proper·multi-threaded·implementation.·</dd> | 109 | <dd><a·class="anchor"·id="_todo000009"></a>·Proper·multi-threaded·implementation.·</dd> |
| 110 | <dt>Class·<a·class="el"·href="classgmx_1_1AnalysisNeighborhood.xhtml">gmx::AnalysisNeighborhood</a>··</dt> | 110 | <dt>Class·<a·class="el"·href="classgmx_1_1AnalysisNeighborhood.xhtml">gmx::AnalysisNeighborhood</a>··</dt> |
| 111 | <dd><a·class="anchor"·id="_todo000137"></a>·Generalize·the·exclusion·machinery·to·make·it·easier·to·use·for·other·cases·than·atom-atom·exclusions·from·the·topology.·</dd> | 111 | <dd><a·class="anchor"·id="_todo000137"></a>·Generalize·the·exclusion·machinery·to·make·it·easier·to·use·for·other·cases·than·atom-atom·exclusions·from·the·topology.·</dd> |
| 112 | <dt>Class·<a·class="el"·href="classgmx_1_1AnalysisNeighborhoodSearch.xhtml">gmx::AnalysisNeighborhoodSearch</a>··</dt> | 112 | <dt>Class·<a·class="el"·href="classgmx_1_1AnalysisNeighborhoodSearch.xhtml">gmx::AnalysisNeighborhoodSearch</a>··</dt> |
| 113 | <dd><p·class="startdd"><a·class="anchor"·id="_todo000139"></a>·Consider·removing·<a·class="el"·href="classgmx_1_1AnalysisNeighborhoodSearch.xhtml#a94cca278a9cee6a8ce84254bbecb9b90"·title="Calculates·the·minimum·distance·from·the·reference·points.">minimumDistance()</a>,·as·<a·class="el"·href="classgmx_1_1AnalysisNeighborhoodSearch.xhtml#a90f03798a665eb91af207b01331f7424"·title="Finds·the·closest·reference·point.">nearestPoint()</a>·already·returns·the·distance.</p> | ||
| 113 | < | 114 | <p·class="enddd"><a·class="anchor"·id="_todo000138"></a>·Make·it·such·that·<a·class="el"·href="classgmx_1_1AnalysisNeighborhoodSearch.xhtml#a5e749843e759e164b790eee1d8004489"·title="Clears·this·search.">reset()</a>·is·not·necessary·to·call·in·code·that·repe[·...·truncated·by·diffoscope;·len:·270,·SHA:·f1de101ce77d7ab23ce3e8317a6e3c51848c9152c19c8b369e000f1acf0560ee·...·]</p> |
| 114 | <p·class="enddd"><a·class="anchor"·id="_todo000139"></a>·Consider·removing·<a·class="el"·href="classgmx_1_1AnalysisNeighborhoodSearch.xhtml#a94cca278a9cee6a8ce84254bbecb9b90"·title="Calculates·the·minimum·distance·from·the·reference·points.">minimumDistance()</a>,·as·<a·class="el"·href="classgmx_1_1AnalysisNeighborhoodSearch.xhtml#a90f03798a665eb91af207b01331f7424"·title="Finds·the·closest·reference·point.">nearestPoint()</a>·already·returns·the·distance.·</p> | ||
| 115 | </dd> | 115 | </dd> |
| 116 | <dt>Class·<a·class="el"·href="classgmx_1_1ArrayRef.xhtml">gmx::ArrayRef<·T·></a>··</dt> | 116 | <dt>Class·<a·class="el"·href="classgmx_1_1ArrayRef.xhtml">gmx::ArrayRef<·T·></a>··</dt> |
| 117 | <dd><a·class="anchor"·id="_todo000157"></a>·This·class·is·not·complete.·There·are·likely·also·methods·missing·(not·required·for·current·usage).·</dd> | 117 | <dd><a·class="anchor"·id="_todo000157"></a>·This·class·is·not·complete.·There·are·likely·also·methods·missing·(not·required·for·current·usage).·</dd> |
| 118 | <dt>Class·<a·class="el"·href="classgmx_1_1Awh.xhtml">gmx::Awh</a>··</dt> | 118 | <dt>Class·<a·class="el"·href="classgmx_1_1Awh.xhtml">gmx::Awh</a>··</dt> |
| 119 | <dd><a·class="anchor"·id="_todo000012"></a><a·class="el"·href="classgmx_1_1Update.xhtml"·title="Contains·data·for·update·phase.">Update</a>·parameter·reading·and·checkpointing,·when·general·C++·framework·is·ready.··</dd> | 119 | <dd><a·class="anchor"·id="_todo000012"></a><a·class="el"·href="classgmx_1_1Update.xhtml"·title="Contains·data·for·update·phase.">Update</a>·parameter·reading·and·checkpointing,·when·general·C++·framework·is·ready.··</dd> |
| 120 | <dt>Member·<a·class="el"·href="namespacegmx.xhtml#ad95d30be525ee425b837e73681541507">gmx::BoxMatrix</a>··</dt> | 120 | <dt>Member·<a·class="el"·href="namespacegmx.xhtml#ad95d30be525ee425b837e73681541507">gmx::BoxMatrix</a>··</dt> |
| 121 | <dd><a·class="anchor"·id="_todo000152"></a>Implement·a·full·replacement·for·C-style·real[DIM][DIM]··</dd> | 121 | <dd><a·class="anchor"·id="_todo000152"></a>Implement·a·full·replacement·for·C-style·real[DIM][DIM]··</dd> |
| 122 | <dt>Member·<a·class="el"·href="classgmx_1_1CheckpointHandler.xhtml#a59e6140303fe71dc0f4ada1375b13153">gmx::CheckpointHandler::decideIfCheckpointingThisStep</a>··(bool·bNS,·bool·bFirstStep,·bool·bLastStep)</dt> | 122 | <dt>Member·<a·class="el"·href="classgmx_1_1CheckpointHandler.xhtml#a59e6140303fe71dc0f4ada1375b13153">gmx::CheckpointHandler::decideIfCheckpointingThisStep</a>··(bool·bNS,·bool·bFirstStep,·bool·bLastStep)</dt> |
| 123 | <dd><a·class="anchor"·id="_todo000066"></a>Change·these·bools·to·enums·to·make·calls·more·self-explanatory··</dd> | 123 | <dd><a·class="anchor"·id="_todo000066"></a>Change·these·bools·to·enums·to·make·calls·more·self-explanatory··</dd> |
| 124 | <dt>Class·<a·class="el"·href="classgmx_1_1CheckpointHelper.xhtml">gmx::CheckpointHelper</a>··</dt> | 124 | <dt>Class·<a·class="el"·href="classgmx_1_1CheckpointHelper.xhtml">gmx::CheckpointHelper</a>··</dt> |
| 125 | <dd><a·class="anchor"·id="_todo000112"></a>Develop·this·into·a·module·solely·providing·a·file·handler·to·modules·for·checkpoint·reading·and·writing.··</dd> | 125 | <dd><a·class="anchor"·id="_todo000112"></a>Develop·this·into·a·module·solely·providing·a·file·handler·to·modules·for·checkpoint·reading·and·writing.··</dd> |
| 126 | <dt>Member·<a·class="el"·href="namespacegmx.xhtml#a36a614356b557457126513747fbb559f">gmx::checkUserGpuIds</a>··(const·<a·class="el"·href="structgmx__gpu__info__t.xhtml"·title="Information·about·GPU·devices·on·this·physical·node.">gmx_gpu_info_t</a>·&gpu_info,·const·std::vector<·int·>·&compatibleGpus,·const·std::vector<·int·>·&gpuIds)</dt> | 126 | <dt>Member·<a·class="el"·href="namespacegmx.xhtml#a36a614356b557457126513747fbb559f">gmx::checkUserGpuIds</a>··(const·<a·class="el"·href="structgmx__gpu__info__t.xhtml"·title="Information·about·GPU·devices·on·this·physical·node.">gmx_gpu_info_t</a>·&gpu_info,·const·std::vector<·int·>·&compatibleGpus,·const·std::vector<·int·>·&gpuIds)</dt> |
| 127 | <dd><a·class="anchor"·id="_todo000149"></a>Note·that·the·selected·GPUs·can·be·different·on·each·rank,·and·the·IDs·of·compatible·GPUs·can·be·different·on·each·node,·so·this·routine·ought·to·do·communication·to·determine·whether·all·ranks·are·able·to·proceed.·Currently·this·relies·on·the·MPI·runtime·to·kill·the·other·processes·because·GROMACS·lacks·the·appropriate·infrastructure·to·do·a·good·job·of·coordinating·error·messages·and·behaviour·across·MPMD·ranks·and·multiple·simulations.·</dd> | 127 | <dd><a·class="anchor"·id="_todo000149"></a>Note·that·the·selected·GPUs·can·be·different·on·each·rank,·and·the·IDs·of·compatible·GPUs·can·be·different·on·each·node,·so·this·routine·ought·to·do·communication·to·determine·whether·all·ranks·are·able·to·proceed.·Currently·this·relies·on·the·MPI·runtime·to·kill·the·other·processes·because·GROMACS·lacks·the·appropriate·infrastructure·to·do·a·good·job·of·coordinating·error·messages·and·behaviour·across·MPMD·ranks·and·multiple·simulations.·</dd> |
| 128 | <dt>Class·<a·class="el"·href="classgmx_1_1ClfftInitializer.xhtml">gmx::ClfftInitializer</a>··</dt> | 128 | <dt>Class·<a·class="el"·href="classgmx_1_1ClfftInitializer.xhtml">gmx::ClfftInitializer</a>··</dt> |
| 129 | <dd><p·class="startdd"><a·class="anchor"·id="_todo000046"></a>Consider·making·a·composite·object·that·also·handles·on-demand·compilation,·managing·lifetime·of·PME·FFT·kernel·programs·to·avoid·exhausting·resources·and/or·recompiling·kernels·previously·used.·See·Redmine·#2535.</p> | ||
| 130 | <p·class=" | 129 | <dd><p·class="startdd"><a·class="anchor"·id="_todo000047"></a>Consider·implementing·an·appropriate·flavor·of·the·nifty·counter·idiom·so·that·both·static·initialization·and·deinitialization·can·work·in·a·fast,·leak-free,·and·thread-safe·way·without·imposing·[·...·truncated·by·diffoscope;·len:·51,·SHA:·fde9322f99e9e274bb05c85c125e3a5d787120b47bb311e56147b52d9c1d9603·...·]·</p> |
| 130 | <p·class="enddd"><a·class="anchor"·id="_todo000046"></a>Consider·making·a·composite·object·that·also·handles·on-demand·compilation,·managing·lifetime·of·PME·FFT·kernel·programs·to·avoid·exhausting·resources·and/or·recompiling·kernels·previously·used.·See·Redmine·#2535.·</p> | ||
| 131 | </dd> | 131 | </dd> |
| 132 | <dt>Class·<a·class="el"·href="classgmx_1_1compat_1_1not__null.xhtml">gmx::compat::not_null<·T·></a>··</dt> | 132 | <dt>Class·<a·class="el"·href="classgmx_1_1compat_1_1not__null.xhtml">gmx::compat::not_null<·T·></a>··</dt> |
| 133 | <dd><a·class="anchor"·id="_todo000015"></a>Eliminate·this·when·we·require·a·version·of·C++·that·supports·std::not_null.··</dd> | 133 | <dd><a·class="anchor"·id="_todo000015"></a>Eliminate·this·when·we·require·a·version·of·C++·that·supports·std::not_null.··</dd> |
| 134 | <dt>Member·<a·class="el"·href="classgmx_1_1Constraints.xhtml#a123bdbf22e047437544d48619ffa64c9">gmx::Constraints::setConstraints</a>··(const·<a·class="el"·href="structgmx__localtop__t.xhtml"·title="The·fully·written·out·topology·for·a·domain·over·its·lifetime.">gmx_localtop_t</a>·&top,·const·<a·class="el"·href="structt__mdatoms.xhtml"·title="Declares·mdatom·data·structure.">t_mdatoms</a>·&md)</dt> | 134 | <dt>Member·<a·class="el"·href="classgmx_1_1Constraints.xhtml#a123bdbf22e047437544d48619ffa64c9">gmx::Constraints::setConstraints</a>··(const·<a·class="el"·href="structgmx__localtop__t.xhtml"·title="The·fully·written·out·topology·for·a·domain·over·its·lifetime.">gmx_localtop_t</a>·&top,·const·<a·class="el"·href="structt__mdatoms.xhtml"·title="Declares·mdatom·data·structure.">t_mdatoms</a>·&md)</dt> |
| 135 | <dd><a·class="anchor"·id="_todo000068"></a>Make·this·a·callback·that·is·called·automatically·once·a·new·domain·has·been·made.··</dd> | 135 | <dd><a·class="anchor"·id="_todo000068"></a>Make·this·a·callback·that·is·called·automatically·once·a·new·domain·has·been·made.··</dd> |
| 136 | <dt>Member·<a·class="el"·href="classgmx_1_1ConstraintsElement.xhtml#a49afd5b53ba3b039418a0ea819f716b2">gmx::ConstraintsElement<·variable·>::elementSetup</a>··()·override</dt> | 136 | <dt>Member·<a·class="el"·href="classgmx_1_1ConstraintsElement.xhtml#a49afd5b53ba3b039418a0ea819f716b2">gmx::ConstraintsElement<·variable·>::elementSetup</a>··()·override</dt> |
| 137 | <dd><a·class="anchor"·id="_todo000113"></a>Should·this·rather·happen·at·grompp·time?·Right·position·of·this·operation·is·currently·depending·on·the·integrator·algorithm·(after·domdec,·before·compute·globals...),·so·doing·this·earlier·would·be·much·more·stable!··</dd> | 137 | <dd><a·class="anchor"·id="_todo000113"></a>Should·this·rather·happen·at·grompp·time?·Right·position·of·this·operation·is·currently·depending·on·the·integrator·algorithm·(after·domdec,·before·compute·globals...),·so·doing·this·earlier·would·be·much·more·stable!··</dd> |
| Offset 154, 16 lines modified | Offset 154, 16 lines modified | ||
| 154 | <dt>Member·<a·class="el"·href="namespacegmx.xhtml#a14ac652392d2a98ce5a3b3a3ca809206">gmx::getPageSize</a>··()</dt> | 154 | <dt>Member·<a·class="el"·href="namespacegmx.xhtml#a14ac652392d2a98ce5a3b3a3ca809206">gmx::getPageSize</a>··()</dt> |
| 155 | <dd><a·class="anchor"·id="_todo000156"></a>Move·this·function·into·sysinfo.cpp·where·other·OS-specific·code/includes·live··</dd> | 155 | <dd><a·class="anchor"·id="_todo000156"></a>Move·this·function·into·sysinfo.cpp·where·other·OS-specific·code/includes·live··</dd> |
| 156 | <dt>Member·<a·class="el"·href="classgmx_1_1GpuTaskAssignments.xhtml#a414447baa42eb2d6deabe6fe4bd64ff3">gmx::GpuTaskAssignments::initNonbondedDevice</a>··(const·t_commrec·*cr)·const</dt> | 156 | <dt>Member·<a·class="el"·href="classgmx_1_1GpuTaskAssignments.xhtml#a414447baa42eb2d6deabe6fe4bd64ff3">gmx::GpuTaskAssignments::initNonbondedDevice</a>··(const·t_commrec·*cr)·const</dt> |
| 157 | <dd><a·class="anchor"·id="_todo000148"></a>This·also·sets·up·DLB·for·device·sharing,·where·appropriate,·but·that·responsbility·should·move·elsewhere.··</dd> | 157 | <dd><a·class="anchor"·id="_todo000148"></a>This·also·sets·up·DLB·for·device·sharing,·where·appropriate,·but·that·responsbility·should·move·elsewhere.··</dd> |
| 158 | <dt>Member·<a·class="el"·href="classgmx_1_1GpuTaskAssignments.xhtml#a0949f5e2c2d5bc005db0c72a5857c85e">gmx::GpuTaskAssignments::reportGpuUsage</a>··(const·<a·class="el"·href="classgmx_1_1MDLogger.xhtml"·title="Declares·a·logging·interface.">MDLogger</a>·&mdlog,·bool·printHostName,·bool·useGpuForBonded,·PmeRunMode·pmeRunMode,·bool·useGpuForUpdate)</dt> | 158 | <dt>Member·<a·class="el"·href="classgmx_1_1GpuTaskAssignments.xhtml#a0949f5e2c2d5bc005db0c72a5857c85e">gmx::GpuTaskAssignments::reportGpuUsage</a>··(const·<a·class="el"·href="classgmx_1_1MDLogger.xhtml"·title="Declares·a·logging·interface.">MDLogger</a>·&mdlog,·bool·printHostName,·bool·useGpuForBonded,·PmeRunMode·pmeRunMode,·bool·useGpuForUpdate)</dt> |
| 159 | <dd><a·class="anchor"·id="_todo000147"></a>It·could·be·useful·to·report·also·whether·any·nodes·differed,·and·in·what·way.·</dd> | 159 | <dd><a·class="anchor"·id="_todo000147"></a>It·could·be·useful·to·report·also·whether·any·nodes·differed,·and·in·what·way.·</dd> |
| 160 | <dt>Class·<a·class="el"·href="classgmx_1_1GpuTaskAssignmentsBuilder.xhtml">gmx::GpuTaskAssignmentsBuilder</a>··</dt> | 160 | <dt>Class·<a·class="el"·href="classgmx_1_1GpuTaskAssignmentsBuilder.xhtml">gmx::GpuTaskAssignmentsBuilder</a>··</dt> |
| 161 | <dd><p·class="startdd"><a·class="anchor"·id="_todo000146"></a>Later·we·might·need·the·concept·of·computeTasksOnThisRank,·from·which·we·construct·gpuTasksOnThisRank.</p> | ||
| 162 | <p·class=" | 161 | <dd><p·class="startdd"><a·class="anchor"·id="_todo000145"></a>Later,·this·might·become·a·loop·over·all·registered·modules·relevant·to·the·mdp·inputs,·to·find·those·that·have·such·tasks.</p> |
| 162 | <p·class="enddd"><a·class="anchor"·id="_todo000146"></a>Later·we·might·need·the·concept·of·computeTasksOnThisRank,·from·which·we·construct·gpuTasksOnThisRank.·</p> | ||
| 163 | </dd> | 163 | </dd> |
| 164 | <dt>Member·<a·class="el"·href="classgmx_1_1GromacsException.xhtml#a1bd116912e67c096ae949ddae85afe06">gmx::GromacsException::prependContext</a>··(const·std::string·&context)</dt> | 164 | <dt>Member·<a·class="el"·href="classgmx_1_1GromacsException.xhtml#a1bd116912e67c096ae949ddae85afe06">gmx::GromacsException::prependContext</a>··(const·std::string·&context)</dt> |
| 165 | <dd><a·class="anchor"·id="_todo000162"></a>·The·added·information·is·currently·not·accessible·through·<a·class="el"·href="classgmx_1_1GromacsException.xhtml#a1c47abcf4fd5758615b74b11dcff50d5"·title="Returns·the·reason·string·for·the·exception.">what()</a>,·nor·through·any·other·means·except·for·calling·<a·class="el"·href="group__module__utility.xhtml#gac6287dc8a550a2d54429e44994e00e58"·title="Formats·a·standard·fatal·error·message·for·reporting·an·exception.">printFatalErrorMessage()</a>,·<a·class="el"·href="group__module__utility.xhtml#gac7703ad35b606758d2d12edc0a3d5217"·title="Formats·an·error·message·for·reporting·an·exception.">formatExceptionMessageToString()</a>·or·<a·class="el"·href="group__module__utility.xhtml#gac5e6f6ec944fb2484d6f273c9a0ff495"·title="Formats·an·error·message·for·reporting·an·exception.">formatExceptionMessageToFile()</a>.·See·<a·class="el"·href="classgmx_1_1ExceptionInitializer.xhtml"·title="Provides·information·for·Gromacs·exception·constructors.">ExceptionInitializer</a>·for·more·discussion.··</dd> | 165 | <dd><a·class="anchor"·id="_todo000162"></a>·The·added·information·is·currently·not·accessible·through·<a·class="el"·href="classgmx_1_1GromacsException.xhtml#a1c47abcf4fd5758615b74b11dcff50d5"·title="Returns·the·reason·string·for·the·exception.">what()</a>,·nor·through·any·other·means·except·for·calling·<a·class="el"·href="group__module__utility.xhtml#gac6287dc8a550a2d54429e44994e00e58"·title="Formats·a·standard·fatal·error·message·for·reporting·an·exception.">printFatalErrorMessage()</a>,·<a·class="el"·href="group__module__utility.xhtml#gac7703ad35b606758d2d12edc0a3d5217"·title="Formats·an·error·message·for·reporting·an·exception.">formatExceptionMessageToString()</a>·or·<a·class="el"·href="group__module__utility.xhtml#gac5e6f6ec944fb2484d6f273c9a0ff495"·title="Formats·an·error·message·for·reporting·an·exception.">formatExceptionMessageToFile()</a>.·See·<a·class="el"·href="classgmx_1_1ExceptionInitializer.xhtml"·title="Provides·information·for·Gromacs·exception·constructors.">ExceptionInitializer</a>·for·more·discussion.··</dd> |
| 166 | <dt>Member·<a·class="el"·href="classgmx_1_1HelpWriterContext.xhtml#a6bec872f46ecd34601df72141fca3739">gmx::HelpWriterContext::setReplacement</a>··(const·std::string·&search,·const·std::string·&replace)</dt> | 166 | <dt>Member·<a·class="el"·href="classgmx_1_1HelpWriterContext.xhtml#a6bec872f46ecd34601df72141fca3739">gmx::HelpWriterContext::setReplacement</a>··(const·std::string·&search,·const·std::string·&replace)</dt> |
| 167 | <dd><a·class="anchor"·id="_todo000125"></a>·Improve·semantics·if·the·same·<code>search</code>·item·is·set·multiple·times.··</dd> | 167 | <dd><a·class="anchor"·id="_todo000125"></a>·Improve·semantics·if·the·same·<code>search</code>·item·is·set·multiple·times.··</dd> |
| 168 | <dt>Class·<a·class="el"·href="classgmx_1_1HostAllocationPolicy.xhtml">gmx::HostAllocationPolicy</a>··</dt> | 168 | <dt>Class·<a·class="el"·href="classgmx_1_1HostAllocationPolicy.xhtml">gmx::HostAllocationPolicy</a>··</dt> |
| 169 | <dd><a·class="anchor"·id="_todo000051"></a>As·a·minor·optimization,·consider·also·having·a·stateless·version·of·this·policy,·which·might·be·slightly·faster·or·more·convenient·to·use·in·the·cases·where·it·is·known·at·compile·time·that·the·allocation·will·be·used·to·transfer·to·a·GPU.··</dd> | 169 | <dd><a·class="anchor"·id="_todo000051"></a>As·a·minor·optimization,·consider·also·having·a·stateless·version·of·this·policy,·which·might·be·slightly·faster·or·more·convenient·to·use·in·the·cases·where·it·is·known·at·compile·time·that·the·allocation·will·be·used·to·transfer·to·a·GPU.··</dd> |
| Offset 180, 16 lines modified | Offset 180, 16 lines modified | ||
| 180 | <p·class="enddd"><a·class="anchor"·id="_todo000081"></a>Modules·in·mdrun·should·acquire·proper·option·handling·so·that·all·of·these·declarations·and·defaults·are·local·to·the·modules.·</p> | 180 | <p·class="enddd"><a·class="anchor"·id="_todo000081"></a>Modules·in·mdrun·should·acquire·proper·option·handling·so·that·all·of·these·declarations·and·defaults·are·local·to·the·modules.·</p> |
| 181 | </dd> | 181 | </dd> |
| 182 | <dt>Member·<a·class="el"·href="classgmx_1_1LegacyMdrunOptions.xhtml#a38d4a34d2ac01acfe853e84393cf1fc6">gmx::LegacyMdrunOptions::oenv</a>··</dt> | 182 | <dt>Member·<a·class="el"·href="classgmx_1_1LegacyMdrunOptions.xhtml#a38d4a34d2ac01acfe853e84393cf1fc6">gmx::LegacyMdrunOptions::oenv</a>··</dt> |
| 183 | <dd><a·class="anchor"·id="_todo000083"></a>Clarify·initialization,·ownership,·and·lifetime.··</dd> | 183 | <dd><a·class="anchor"·id="_todo000083"></a>Clarify·initialization,·ownership,·and·lifetime.··</dd> |
| 184 | <dt>Class·<a·class="el"·href="classgmx_1_1MDAtoms.xhtml">gmx::MDAtoms</a>··</dt> | 184 | <dt>Class·<a·class="el"·href="classgmx_1_1MDAtoms.xhtml">gmx::MDAtoms</a>··</dt> |
| 185 | <dd><a·class="anchor"·id="_todo000075"></a>The·group-scheme·kernels·needed·a·plain·C-style·<a·class="el"·href="structt__mdatoms.xhtml"·title="Declares·mdatom·data·structure.">t_mdatoms</a>,·so·this·type·combines·that·with·the·memory·management·needed·for·efficient·PME·on·GPU·transfers.·The·mdatoms_·member·should·be·removed.··</dd> | 185 | <dd><a·class="anchor"·id="_todo000075"></a>The·group-scheme·kernels·needed·a·plain·C-style·<a·class="el"·href="structt__mdatoms.xhtml"·title="Declares·mdatom·data·structure.">t_mdatoms</a>,·so·this·type·combines·that·with·the·memory·management·needed·for·efficient·PME·on·GPU·transfers.·The·mdatoms_·member·should·be·removed.··</dd> |
| 186 | <dt>Class·<a·class="el"·href="classgmx_1_1Mdrunner.xhtml">gmx::Mdrunner</a>··</dt> | 186 | <dt>Class·<a·class="el"·href="classgmx_1_1Mdrunner.xhtml">gmx::Mdrunner</a>··</dt> |
| 187 | <dd><p·class="startdd"><a·class="anchor"·id="_todo000089"></a>Preparing·logging·and·MPI·contexts·could·probably·be·a·higher-level·responsibility,·so·that·an·<a·class="el"·href="classgmx_1_1Mdrunner.xhtml"·title="Runner·object·for·supporting·setup·and·execution·of·mdrun.">Mdrunner</a>·would·get·made·without·needing·to·re-initialize·these·components·(as·currently·happens·always·for·the·master·rank,·and·differently·for·the·spawned·ranks·with·thread-MPI).</p> | ||
| 188 | <p·class=" | 187 | <dd><p·class="startdd"><a·class="anchor"·id="_todo000088"></a>Most·of·the·attributes·should·be·declared·by·specific·modules·as·command-line·options.·Accordingly,·they·do·not·conform·to·the·naming·scheme,·because·that·would·make·for·a·lot·of·noise·in·the·dif[·...·truncated·by·diffoscope;·len:·71,·SHA:·368c9a60eecc4b2cf5c793500e6e27546fcd326a5be1ead2bc81ec1153b3b949·...·]</p> |
| 188 | <p·class="enddd"><a·class="anchor"·id="_todo000089"></a>Preparing·logging·and·MPI·contexts·could·probably·be·a·higher-level·responsibility,·so·that·an·<a·class="el"·href="classgmx_1_1Mdrunner.xhtml"·title="Runner·object·for·supporting·setup·and·execution·of·mdrun.">Mdrunner</a>·would·get·made·without·needing·to·re-initialize·these·components·(as·currently·happens·always·for·the·master·rank,·and·differently·for·the·spawned·ranks·with·thread-MPI).·</p> | ||
| 189 | </dd> | 189 | </dd> |
| 190 | <dt>Member·<a·class="el"·href="classgmx_1_1Mdrunner.xhtml#ac0067c523a99846930228d5e58762ed6">gmx::Mdrunner::addPotential</a>··(std::shared_ptr<·IRestraintPotential·>·restraint,·const·std::string·&name)</dt> | 190 | <dt>Member·<a·class="el"·href="classgmx_1_1Mdrunner.xhtml#ac0067c523a99846930228d5e58762ed6">gmx::Mdrunner::addPotential</a>··(std::shared_ptr<·IRestraintPotential·>·restraint,·const·std::string·&name)</dt> |
| 191 | <dd><a·class="anchor"·id="_todo000090"></a><a·class="el"·href="classgmx_1_1Mdrunner.xhtml"·title="Runner·object·for·supporting·setup·and·execution·of·mdrun.">Mdrunner</a>·should·fetch·such·resources·from·the·<a·class="el"·href="classgmx_1_1SimulationContext.xhtml"·title="Simulation·environment·and·configuration.">SimulationContext</a>·rather·than·offering·this·public·interface.··</dd> | 191 | <dd><a·class="anchor"·id="_todo000090"></a><a·class="el"·href="classgmx_1_1Mdrunner.xhtml"·title="Runner·object·for·supporting·setup·and·execution·of·mdrun.">Mdrunner</a>·should·fetch·such·resources·from·the·<a·class="el"·href="classgmx_1_1SimulationContext.xhtml"·title="Simulation·environment·and·configuration.">SimulationContext</a>·rather·than·offering·this·public·interface.··</dd> |
| 192 | <dt>Member·<a·class="el"·href="namespacegmx.xhtml#a516559bb0e35192a8b312c0c15b28daa">gmx::openTNG</a>··(const·std::string·&name,·const·<a·class="el"·href="classgmx_1_1Selection.xhtml"·title="Provides·access·to·a·single·selection.">Selection</a>·&sel,·const·gmx_mtop_t·*mtop)</dt> | 192 | <dt>Member·<a·class="el"·href="namespacegmx.xhtml#a516559bb0e35192a8b312c0c15b28daa">gmx::openTNG</a>··(const·std::string·&name,·const·<a·class="el"·href="classgmx_1_1Selection.xhtml"·title="Provides·access·to·a·single·selection.">Selection</a>·&sel,·const·gmx_mtop_t·*mtop)</dt> |
| 193 | <dd><a·class="anchor"·id="_todo000017"></a>Those·should·be·methods·in·a·replacement·for·t_trxstatus·instead.··</dd> | 193 | <dd><a·class="anchor"·id="_todo000017"></a>Those·should·be·methods·in·a·replacement·for·t_trxstatus·instead.··</dd> |
| 194 | <dt>Member·<a·class="el"·href="namespacegmx.xhtml#a3f775199bddf83f286ee8172f7dda987">gmx::OptionFlag</a>··</dt> | 194 | <dt>Member·<a·class="el"·href="namespacegmx.xhtml#a3f775199bddf83f286ee8172f7dda987">gmx::OptionFlag</a>··</dt> |
| 195 | <dd><a·class="anchor"·id="_todo000129"></a>·The·flags·related·to·default·values·are·confusing,·consider·reorganizing·them.··</dd> | 195 | <dd><a·class="anchor"·id="_todo000129"></a>·The·flags·related·to·default·values·are·confusing,·consider·reorganizing·them.··</dd> |
| Offset 223, 76 lines modified | Offset 223, 76 lines modified | ||
| 223 | <dd><a·class="anchor"·id="_todo000178"></a>Eliminate·this·limitation·of·TinyXML2.·See·e.g.·<a·href="https://github.com/leethomason/tinyxml2/issues/432">https://github.com/leethomason/tinyxml2/issues/432</a>··</dd> | 223 | <dd><a·class="anchor"·id="_todo000178"></a>Eliminate·this·limitation·of·TinyXML2.·See·e.g.·<a·href="https://github.com/leethomason/tinyxml2/issues/432">https://github.com/leethomason/tinyxml2/issues/432</a>··</dd> |
| 224 | <dt>Member·<a·class="el"·href="classgmx_1_1TextWriter.xhtml#a87a974330d5791f7410e6b20e516d5ae">gmx::TextWriter::wrapperSettings</a>··()</dt> | 224 | <dt>Member·<a·class="el"·href="classgmx_1_1TextWriter.xhtml#a87a974330d5791f7410e6b20e516d5ae">gmx::TextWriter::wrapperSettings</a>··()</dt> |
| 225 | <dd><a·class="anchor"·id="_todo000167"></a>·Wrapping·is·not·currently·implemented·for·code·that·writes·partial·lines·with·<a·class="el"·href="classgmx_1_1TextWriter.xhtml#a7a6aceff08f3a9bb9c5514892ea3dc3e"·title="Writes·a·string·to·the·stream.">writeString()</a>.··</dd> | 225 | <dd><a·class="anchor"·id="_todo000167"></a>·Wrapping·is·not·currently·implemented·for·code·that·writes·partial·lines·with·<a·class="el"·href="classgmx_1_1TextWriter.xhtml#a7a6aceff08f3a9bb9c5514892ea3dc3e"·title="Writes·a·string·to·the·stream.">writeString()</a>.··</dd> |
| 226 | <dt>Member·<a·class="el"·href="classgmx_1_1TopologyInformation.xhtml#a5f16e5f1f376a4df101ff36d9f859a48">gmx::TopologyInformation::fillFromInputFile</a>··(const·std::string·&filename)</dt> | 226 | <dt>Member·<a·class="el"·href="classgmx_1_1TopologyInformation.xhtml#a5f16e5f1f376a4df101ff36d9f859a48">gmx::TopologyInformation::fillFromInputFile</a>··(const·std::string·&filename)</dt> |
| Max diff block lines reached; 14451/39276 bytes (36.79%) of diff not shown. | |||
| Offset 3, 29 lines modified | Offset 3, 14 lines modified | ||
| 3 | Gromacs· 2020.6-Debian-2020.6-2 | 3 | Gromacs· 2020.6-Debian-2020.6-2 |
| 4 | Todo·List | 4 | Todo·List |
| 5 | ··Member·AtomProperties::atomNumberFromElement·(const·char·*element) | ||
| 6 | ······This·should·be·made·const·once·the·lazy·implementation·is·done·properly | ||
| 7 | ······for·the·class. | ||
| 8 | ··Member·AtomProperties::elementFromAtomNumber·(int·atomNumber) | ||
| 9 | ······This·should·be·made·const·once·the·lazy·implementation·is·done·properly | ||
| 10 | ······for·the·class. | ||
| 11 | ··Class·BondedInteractionList | ||
| 12 | ······This·should·be·merged·with·BondedInteraction. | ||
| 13 | ··Member·buildSupportsNonbondedOnGpu·(std::string·*error) | ||
| 14 | ······Move·this·to·NB·module·once·it·exists. | ||
| 15 | ··Member·clearModificationBlock·(MoleculePatchDatabase·*globalPatches) | ||
| 16 | ······Remove·once·constructor/destructor·takes·care·of·all·of·this. | ||
| 17 | ··Member·copyPreprocessResidues·(const·PreprocessResidue·&s,·PreprocessResidue | ||
| 18 | ··*d,·t_symtab·*symtab) | ||
| 19 | ······Remove·once·copy·can·be·done·directly. | ||
| 20 | ··Member·ddSendrecv·(const·gmx_domdec_t·*dd,·int·ddDimensionIndex,·int | 5 | ··Member·ddSendrecv·(const·gmx_domdec_t·*dd,·int·ddDimensionIndex,·int |
| 21 | ··direction,·T·*sendBuffer,·int·numElementsToSend,·T·*receiveBuffer,·int | 6 | ··direction,·T·*sendBuffer,·int·numElementsToSend,·T·*receiveBuffer,·int |
| 22 | ··numElementsToReceive) | 7 | ··numElementsToReceive) |
| 23 | ······This·function·template·is·deprecated,·new·calls·should·be·made·to·the | 8 | ······This·function·template·is·deprecated,·new·calls·should·be·made·to·the |
| 24 | ······version·taking·ArrayRef·parameters·and·this·function·template·removed | 9 | ······version·taking·ArrayRef·parameters·and·this·function·template·removed |
| 25 | ······when·unused. | 10 | ······when·unused. |
| 26 | ··Member·df_history_t | 11 | ··Member·df_history_t |
| Offset 33, 34 lines modified | Offset 18, 49 lines modified | ||
| 33 | ··Member·DIR_SEPARATOR | 18 | ··Member·DIR_SEPARATOR |
| 34 | ······Get·rid·of·this·(Redmine·#950).·It·is·not·necessary·for·constructing | 19 | ······Get·rid·of·this·(Redmine·#950).·It·is·not·necessary·for·constructing |
| 35 | ······paths·on·the·systems·that·it·currently·supports,·and·is·not·reliable·in | 20 | ······paths·on·the·systems·that·it·currently·supports,·and·is·not·reliable·in |
| 36 | ······parsing·input·paths·either,·since·Windows·needs·to·accept·both·instead·of | 21 | ······parsing·input·paths·either,·since·Windows·needs·to·accept·both·instead·of |
| 37 | ······only·DIR_SEPARATOR.·At·the·very·least,·we·should·refactor·the·clients·of | 22 | ······only·DIR_SEPARATOR.·At·the·very·least,·we·should·refactor·the·clients·of |
| 38 | ······this·header·so·that·they·operate·upon·path·objects·rather·than·raw·path | 23 | ······this·header·so·that·they·operate·upon·path·objects·rather·than·raw·path |
| 39 | ······strings. | 24 | ······strings. |
| 40 | ··File·domdec_network.h | ||
| 41 | ······Wrap·the·raw·dd_bcast·in·md.cpp·into·a·higher-level·function·in·the | ||
| 42 | ······domdec·module,·then·this·file·can·be·module-internal. | ||
| 43 | ··Member·fit_acf·(int·ncorr,·int·fitfn,·const·gmx_output_env_t·*oenv,·gmx_bool | 25 | ··Member·fit_acf·(int·ncorr,·int·fitfn,·const·gmx_output_env_t·*oenv,·gmx_bool |
| 44 | ··bVerbose,·real·tbeginfit,·real·tendfit,·real·dt,·real·c1[],·real·*fit) | 26 | ··bVerbose,·real·tbeginfit,·real·tendfit,·real·dt,·real·c1[],·real·*fit) |
| 45 | ······check·parameters | 27 | ······check·parameters |
| 28 | ··Member·AtomProperties::atomNumberFromElement·(const·char·*element) | ||
| 29 | ······This·should·be·made·const·once·the·lazy·implementation·is·done·properly | ||
| 30 | ······for·the·class. | ||
| 31 | ··Member·AtomProperties::elementFromAtomNumber·(int·atomNumber) | ||
| 32 | ······This·should·be·made·const·once·the·lazy·implementation·is·done·properly | ||
| 33 | ······for·the·class. | ||
| 34 | ··Class·BondedInteractionList | ||
| 35 | ······This·should·be·merged·with·BondedInteraction. | ||
| 36 | ··Member·buildSupportsNonbondedOnGpu·(std::string·*error) | ||
| 37 | ······Move·this·to·NB·module·once·it·exists. | ||
| 38 | ··Member·clearModificationBlock·(MoleculePatchDatabase·*globalPatches) | ||
| 39 | ······Remove·once·constructor/destructor·takes·care·of·all·of·this. | ||
| 40 | ··Member·copyPreprocessResidues·(const·PreprocessResidue·&s,·PreprocessResidue | ||
| 41 | ··*d,·t_symtab·*symtab) | ||
| 42 | ······Remove·once·copy·can·be·done·directly. | ||
| 43 | ··File·domdec_network.h | ||
| 44 | ······Wrap·the·raw·dd_bcast·in·md.cpp·into·a·higher-level·function·in·the | ||
| 45 | ······domdec·module,·then·this·file·can·be·module-internal. | ||
| 46 | ··Class·gmx::AbstractAnalysisArrayData | 46 | ··Class·gmx::AbstractAnalysisArrayData |
| 47 | ·······Add·support·for·multiple·data·sets. | 47 | ·······Add·support·for·multiple·data·sets. |
| 48 | ··Class·gmx::AbstractAnalysisData | 48 | ··Class·gmx::AbstractAnalysisData |
| 49 | ·······Improve·the·exception-handling·semantics.·In·most·cases,·it·doesn't·make | 49 | ·······Improve·the·exception-handling·semantics.·In·most·cases,·it·doesn't·make |
| 50 | ······much·sense·to·continue·data·processing·after·one·module·fails,·but·having | 50 | ······much·sense·to·continue·data·processing·after·one·module·fails,·but·having |
| 51 | ······the·alternative·would·not·hurt. | 51 | ······the·alternative·would·not·hurt. |
| 52 | ··Member·gmx::AbstractAnalysisData::addColumnModule·(int·col,·int·span,·const | 52 | ··Member·gmx::AbstractAnalysisData::addColumnModule·(int·col,·int·span,·const |
| 53 | ··AnalysisDataModulePointer·&module) | 53 | ··AnalysisDataModulePointer·&module) |
| 54 | ·······Generalize·this·method·to·multiple·data·sets·(e.g.,·for·adding·modules | ||
| 55 | ······that·only·process·a·single·data·set). | ||
| 56 | ·······This·method·doesn't·currently·work·in·all·cases·with·multipoint·data·or | 54 | ·······This·method·doesn't·currently·work·in·all·cases·with·multipoint·data·or |
| 57 | ······with·multiple·data·sets.·In·particular,·if·the·added·module·requests | 55 | ······with·multiple·data·sets.·In·particular,·if·the·added·module·requests |
| 58 | ······storage·and·uses·getDataFrame(),·it·will·behave·unpredictably·(most | 56 | ······storage·and·uses·getDataFrame(),·it·will·behave·unpredictably·(most |
| 59 | ······likely·asserts). | 57 | ······likely·asserts). |
| 58 | ·······Generalize·this·method·to·multiple·data·sets·(e.g.,·for·adding·modules | ||
| 59 | ······that·only·process·a·single·data·set). | ||
| 60 | ··Member·gmx::AbstractAnalysisData::applyModule·(IAnalysisDataModule·*module) | 60 | ··Member·gmx::AbstractAnalysisData::applyModule·(IAnalysisDataModule·*module) |
| 61 | ·······Currently,·this·method·may·not·work·correctly·if·module·requests·storage | 61 | ·······Currently,·this·method·may·not·work·correctly·if·module·requests·storage |
| 62 | ······(addModule()·has·the·same·problem·if·called·after·data·is·started). | 62 | ······(addModule()·has·the·same·problem·if·called·after·data·is·started). |
| 63 | ··Member·gmx::AbstractOptionStorage::processSet·()=0 | 63 | ··Member·gmx::AbstractOptionStorage::processSet·()=0 |
| 64 | ·······Improve·the·call·semantics. | 64 | ·······Improve·the·call·semantics. |
| 65 | ··Class·gmx::AnalysisData | 65 | ··Class·gmx::AnalysisData |
| 66 | ·······Parallel·implementation·is·not·complete. | 66 | ·······Parallel·implementation·is·not·complete. |
| Offset 68, 19 lines modified | Offset 68, 19 lines modified | ||
| 68 | ······Use·a·proper·enum. | 68 | ······Use·a·proper·enum. |
| 69 | ··Class·gmx::AnalysisDataStorage | 69 | ··Class·gmx::AnalysisDataStorage |
| 70 | ·······Proper·multi-threaded·implementation. | 70 | ·······Proper·multi-threaded·implementation. |
| 71 | ··Class·gmx::AnalysisNeighborhood | 71 | ··Class·gmx::AnalysisNeighborhood |
| 72 | ·······Generalize·the·exclusion·machinery·to·make·it·easier·to·use·for·other | 72 | ·······Generalize·the·exclusion·machinery·to·make·it·easier·to·use·for·other |
| 73 | ······cases·than·atom-atom·exclusions·from·the·topology. | 73 | ······cases·than·atom-atom·exclusions·from·the·topology. |
| 74 | ··Class·gmx::AnalysisNeighborhoodSearch | 74 | ··Class·gmx::AnalysisNeighborhoodSearch |
| 75 | ·······Consider·removing·minimumDistance(),·as·nearestPoint()·already·returns | ||
| 76 | ······the·distance. | ||
| 75 | ·······Make·it·such·that·reset()·is·not·necessary·to·call·in·code·that | 77 | ·······Make·it·such·that·reset()·is·not·necessary·to·call·in·code·that |
| 76 | ······repeatedly·assigns·the·result·of·AnalysisNeighborhood::initSearch()·to | 78 | ······repeatedly·assigns·the·result·of·AnalysisNeighborhood::initSearch()·to |
| 77 | ······the·same·variable·(see·sm_distance.cpp). | 79 | ······the·same·variable·(see·sm_distance.cpp). |
| 78 | ·······Consider·removing·minimumDistance(),·as·nearestPoint()·already·returns | ||
| 79 | ······the·distance. | ||
| 80 | ··Class·gmx::ArrayRef<_T_> | 80 | ··Class·gmx::ArrayRef<_T_> |
| 81 | ·······This·class·is·not·complete.·There·are·likely·also·methods·missing·(not | 81 | ·······This·class·is·not·complete.·There·are·likely·also·methods·missing·(not |
| 82 | ······required·for·current·usage). | 82 | ······required·for·current·usage). |
| 83 | ··Class·gmx::Awh | 83 | ··Class·gmx::Awh |
| 84 | ······Update·parameter·reading·and·checkpointing,·when·general·C++·framework·is | 84 | ······Update·parameter·reading·and·checkpointing,·when·general·C++·framework·is |
| 85 | ······ready. | 85 | ······ready. |
| 86 | ··Member·gmx::BoxMatrix | 86 | ··Member·gmx::BoxMatrix |
| Offset 97, 22 lines modified | Offset 97, 22 lines modified | ||
| 97 | ······compatible·GPUs·can·be·different·on·each·node,·so·this·routine·ought·to | 97 | ······compatible·GPUs·can·be·different·on·each·node,·so·this·routine·ought·to |
| 98 | ······do·communication·to·determine·whether·all·ranks·are·able·to·proceed. | 98 | ······do·communication·to·determine·whether·all·ranks·are·able·to·proceed. |
| 99 | ······Currently·this·relies·on·the·MPI·runtime·to·kill·the·other·processes | 99 | ······Currently·this·relies·on·the·MPI·runtime·to·kill·the·other·processes |
| 100 | ······because·GROMACS·lacks·the·appropriate·infrastructure·to·do·a·good·job·of | 100 | ······because·GROMACS·lacks·the·appropriate·infrastructure·to·do·a·good·job·of |
| 101 | ······coordinating·error·messages·and·behaviour·across·MPMD·ranks·and·multiple | 101 | ······coordinating·error·messages·and·behaviour·across·MPMD·ranks·and·multiple |
| 102 | ······simulations. | 102 | ······simulations. |
| 103 | ··Class·gmx::ClfftInitializer | 103 | ··Class·gmx::ClfftInitializer |
| 104 | ······Consider·making·a·composite·object·that·also·handles·on-demand | ||
| 105 | ······compilation,·managing·lifetime·of·PME·FFT·kernel·programs·to·avoid | ||
| 106 | ······exhausting·resources·and/or·recompiling·kernels·previously·used.·See | ||
| 107 | ······Redmine·#2535. | ||
| 108 | ······Consider·implementing·an·appropriate·flavor·of·the·nifty·counter·idiom·so | 104 | ······Consider·implementing·an·appropriate·flavor·of·the·nifty·counter·idiom·so |
| 109 | ······that·both·static·initialization·and·deinitialization·can·work·in·a·fast, | 105 | ······that·both·static·initialization·and·deinitialization·can·work·in·a·fast, |
| 110 | ······leak-free,·and·thread-safe·way·without·imposing·constraints·on·the | 106 | ······leak-free,·and·thread-safe·way·without·imposing·constraints·on·the |
| 111 | ······calling·code.·See·Redmine·#2535. | 107 | ······calling·code.·See·Redmine·#2535. |
| 108 | ······Consider·making·a·composite·object·that·also·handles·on-demand | ||
| 109 | ······compilation,·managing·lifetime·of·PME·FFT·kernel·programs·to·avoid | ||
| 110 | ······exhausting·resources·and/or·recompiling·kernels·previously·used.·See | ||
| 111 | ······Redmine·#2535. | ||
| 112 | ··Class·gmx::compat::not_null<_T_> | 112 | ··Class·gmx::compat::not_null<_T_> |
| Max diff block lines reached; 10780/17501 bytes (61.60%) of diff not shown. | |||
| Offset 71, 16 lines modified | Offset 71, 14 lines modified | ||
| 71 | <dd><a·class="anchor"·id="_todo000119"></a>This·should·be·made·const·once·the·lazy·implementation·is·done·properly·for·the·class.··</dd> | 71 | <dd><a·class="anchor"·id="_todo000119"></a>This·should·be·made·const·once·the·lazy·implementation·is·done·properly·for·the·class.··</dd> |
| 72 | <dt>Member·<a·class="el"·href="classAtomProperties.xhtml#aa128b4b7662a21b904b8642eead5bfdd">AtomProperties::elementFromAtomNumber</a>··(int·atomNumber)</dt> | 72 | <dt>Member·<a·class="el"·href="classAtomProperties.xhtml#aa128b4b7662a21b904b8642eead5bfdd">AtomProperties::elementFromAtomNumber</a>··(int·atomNumber)</dt> |
| 73 | <dd><a·class="anchor"·id="_todo000118"></a>This·should·be·made·const·once·the·lazy·implementation·is·done·properly·for·the·class.··</dd> | 73 | <dd><a·class="anchor"·id="_todo000118"></a>This·should·be·made·const·once·the·lazy·implementation·is·done·properly·for·the·class.··</dd> |
| 74 | <dt>Member·<a·class="el"·href="hackblock_8h.xhtml#aebf7055bd2787b678b68cd10b985e280">clearModificationBlock</a>··(MoleculePatchDatabase·*globalPatches)</dt> | 74 | <dt>Member·<a·class="el"·href="hackblock_8h.xhtml#aebf7055bd2787b678b68cd10b985e280">clearModificationBlock</a>··(MoleculePatchDatabase·*globalPatches)</dt> |
| 75 | <dd><a·class="anchor"·id="_todo000031"></a>Remove·once·constructor/destructor·takes·care·of·all·of·this.··</dd> | 75 | <dd><a·class="anchor"·id="_todo000031"></a>Remove·once·constructor/destructor·takes·care·of·all·of·this.··</dd> |
| 76 | <dt>Member·<a·class="el"·href="hackblock_8h.xhtml#aecbab27ca8905331266d9ea02f925137">copyPreprocessResidues</a>··(const·PreprocessResidue·&s,·PreprocessResidue·*d,·t_symtab·*symtab)</dt> | 76 | <dt>Member·<a·class="el"·href="hackblock_8h.xhtml#aecbab27ca8905331266d9ea02f925137">copyPreprocessResidues</a>··(const·PreprocessResidue·&s,·PreprocessResidue·*d,·t_symtab·*symtab)</dt> |
| 77 | <dd><a·class="anchor"·id="_todo000032"></a>Remove·once·copy·can·be·done·directly.··</dd> | 77 | <dd><a·class="anchor"·id="_todo000032"></a>Remove·once·copy·can·be·done·directly.··</dd> |
| 78 | <dt>Member·<a·class="el"·href="state_8h.xhtml#aa4de64296c013fbd01f41b25c64a774c">df_history_t</a>··</dt> | ||
| 79 | <dd><a·class="anchor"·id="_todo000072"></a>Split·out·into·microstate·and·observables·history.··</dd> | ||
| 80 | <dt>Class·<a·class="el"·href="classgmx_1_1AbstractAnalysisArrayData.xhtml">gmx::AbstractAnalysisArrayData</a>··</dt> | 78 | <dt>Class·<a·class="el"·href="classgmx_1_1AbstractAnalysisArrayData.xhtml">gmx::AbstractAnalysisArrayData</a>··</dt> |
| 81 | <dd><a·class="anchor"·id="_todo000006"></a>·Add·support·for·multiple·data·sets.·</dd> | 79 | <dd><a·class="anchor"·id="_todo000006"></a>·Add·support·for·multiple·data·sets.·</dd> |
| 82 | <dt>Class·<a·class="el"·href="classgmx_1_1AbstractAnalysisData.xhtml">gmx::AbstractAnalysisData</a>··</dt> | 80 | <dt>Class·<a·class="el"·href="classgmx_1_1AbstractAnalysisData.xhtml">gmx::AbstractAnalysisData</a>··</dt> |
| 83 | <dd><a·class="anchor"·id="_todo000001"></a>·Improve·the·exception-handling·semantics.·In·most·cases,·it·doesn't·make·much·sense·to·continue·data·processing·after·one·module·fails,·but·having·the·alternative·would·not·hurt.·</dd> | 81 | <dd><a·class="anchor"·id="_todo000001"></a>·Improve·the·exception-handling·semantics.·In·most·cases,·it·doesn't·make·much·sense·to·continue·data·processing·after·one·module·fails,·but·having·the·alternative·would·not·hurt.·</dd> |
| 84 | <dt>Member·<a·class="el"·href="classgmx_1_1AbstractAnalysisData.xhtml#a90b99e3f700dbb8992a2d65a6b2a6de5">gmx::AbstractAnalysisData::addColumnModule</a>··(int·col,·int·span,·const·AnalysisDataModulePointer·&module)</dt> | 82 | <dt>Member·<a·class="el"·href="classgmx_1_1AbstractAnalysisData.xhtml#a90b99e3f700dbb8992a2d65a6b2a6de5">gmx::AbstractAnalysisData::addColumnModule</a>··(int·col,·int·span,·const·AnalysisDataModulePointer·&module)</dt> |
| 85 | <dd><p·class="startdd"><a·class="anchor"·id="_todo000002"></a>·This·method·doesn't·currently·work·in·all·cases·with·multipoint·data·or·with·multiple·data·sets.·In·particular,·if·the·added·module·requests·storage·and·uses·<a·class="el"·href="classgmx_1_1AbstractAnalysisData.xhtml#a0443667626b1e371ff9eef6143383c31"·title="Access·stored·data.">getDataFrame()</a>,·it·will·behave·unpredictably·(most·likely·asserts).</p> | 83 | <dd><p·class="startdd"><a·class="anchor"·id="_todo000002"></a>·This·method·doesn't·currently·work·in·all·cases·with·multipoint·data·or·with·multiple·data·sets.·In·particular,·if·the·added·module·requests·storage·and·uses·<a·class="el"·href="classgmx_1_1AbstractAnalysisData.xhtml#a0443667626b1e371ff9eef6143383c31"·title="Access·stored·data.">getDataFrame()</a>,·it·will·behave·unpredictably·(most·likely·asserts).</p> |
| 86 | <p·class="enddd"><a·class="anchor"·id="_todo000003"></a>·Generalize·this·method·to·multiple·data·sets·(e.g.,·for·adding·modules·that·only·process·a·single·data·set).·</p> | 84 | <p·class="enddd"><a·class="anchor"·id="_todo000003"></a>·Generalize·this·method·to·multiple·data·sets·(e.g.,·for·adding·modules·that·only·process·a·single·data·set).·</p> |
| Offset 95, 22 lines modified | Offset 93, 18 lines modified | ||
| 95 | <dd><a·class="anchor"·id="_todo000107"></a>·Generalize·the·exclusion·machinery·to·make·it·easier·to·use·for·other·cases·than·atom-atom·exclusions·from·the·topology.·</dd> | 93 | <dd><a·class="anchor"·id="_todo000107"></a>·Generalize·the·exclusion·machinery·to·make·it·easier·to·use·for·other·cases·than·atom-atom·exclusions·from·the·topology.·</dd> |
| 96 | <dt>Class·<a·class="el"·href="classgmx_1_1AnalysisNeighborhoodSearch.xhtml">gmx::AnalysisNeighborhoodSearch</a>··</dt> | 94 | <dt>Class·<a·class="el"·href="classgmx_1_1AnalysisNeighborhoodSearch.xhtml">gmx::AnalysisNeighborhoodSearch</a>··</dt> |
| 97 | <dd><p·class="startdd"><a·class="anchor"·id="_todo000108"></a>·Make·it·such·that·<a·class="el"·href="classgmx_1_1AnalysisNeighborhoodSearch.xhtml#a5e749843e759e164b790eee1d8004489"·title="Clears·this·search.">reset()</a>·is·not·necessary·to·call·in·code·that·repeatedly·assigns·the·result·of·<a·class="el"·href="classgmx_1_1AnalysisNeighborhood.xhtml#ac11ba1b44a1c777677276f6ec664a82d"·title="Initializes·neighborhood·search·for·a·set·of·positions.">AnalysisNeighborhood::initSearch()</a>·to·the·same·variable·(see·sm_distance.cpp).</p> | 95 | <dd><p·class="startdd"><a·class="anchor"·id="_todo000108"></a>·Make·it·such·that·<a·class="el"·href="classgmx_1_1AnalysisNeighborhoodSearch.xhtml#a5e749843e759e164b790eee1d8004489"·title="Clears·this·search.">reset()</a>·is·not·necessary·to·call·in·code·that·repeatedly·assigns·the·result·of·<a·class="el"·href="classgmx_1_1AnalysisNeighborhood.xhtml#ac11ba1b44a1c777677276f6ec664a82d"·title="Initializes·neighborhood·search·for·a·set·of·positions.">AnalysisNeighborhood::initSearch()</a>·to·the·same·variable·(see·sm_distance.cpp).</p> |
| 98 | <p·class="enddd"><a·class="anchor"·id="_todo000109"></a>·Consider·removing·<a·class="el"·href="classgmx_1_1AnalysisNeighborhoodSearch.xhtml#a94cca278a9cee6a8ce84254bbecb9b90"·title="Calculates·the·minimum·distance·from·the·reference·points.">minimumDistance()</a>,·as·<a·class="el"·href="classgmx_1_1AnalysisNeighborhoodSearch.xhtml#a90f03798a665eb91af207b01331f7424"·title="Finds·the·closest·reference·point.">nearestPoint()</a>·already·returns·the·distance.·</p> | 96 | <p·class="enddd"><a·class="anchor"·id="_todo000109"></a>·Consider·removing·<a·class="el"·href="classgmx_1_1AnalysisNeighborhoodSearch.xhtml#a94cca278a9cee6a8ce84254bbecb9b90"·title="Calculates·the·minimum·distance·from·the·reference·points.">minimumDistance()</a>,·as·<a·class="el"·href="classgmx_1_1AnalysisNeighborhoodSearch.xhtml#a90f03798a665eb91af207b01331f7424"·title="Finds·the·closest·reference·point.">nearestPoint()</a>·already·returns·the·distance.·</p> |
| 99 | </dd> | 97 | </dd> |
| 100 | <dt>Class·<a·class="el"·href="classgmx_1_1ArrayRef.xhtml">gmx::ArrayRef<·T·></a>··</dt> | 98 | <dt>Class·<a·class="el"·href="classgmx_1_1ArrayRef.xhtml">gmx::ArrayRef<·T·></a>··</dt> |
| 101 | <dd><a·class="anchor"·id="_todo000125"></a>·This·class·is·not·complete.·There·are·likely·also·methods·missing·(not·required·for·current·usage).·</dd> | 99 | <dd><a·class="anchor"·id="_todo000125"></a>·This·class·is·not·complete.·There·are·likely·also·methods·missing·(not·required·for·current·usage).·</dd> |
| 102 | <dt>Member·<a·class="el"·href="namespacegmx.xhtml#ad95d30be525ee425b837e73681541507">gmx::BoxMatrix</a>··</dt> | ||
| 103 | <dd><a·class="anchor"·id="_todo000120"></a>Implement·a·full·replacement·for·C-style·real[DIM][DIM]··</dd> | ||
| 104 | <dt>Member·<a·class="el"·href="namespacegmx.xhtml#a36a614356b557457126513747fbb559f">gmx::checkUserGpuIds</a>··(const·<a·class="el"·href="structgmx__gpu__info__t.xhtml"·title="Information·about·GPU·devices·on·this·physical·node.">gmx_gpu_info_t</a>·&gpu_info,·const·std::vector<·int·>·&compatibleGpus,·const·std::vector<·int·>·&gpuIds)</dt> | 100 | <dt>Member·<a·class="el"·href="namespacegmx.xhtml#a36a614356b557457126513747fbb559f">gmx::checkUserGpuIds</a>··(const·<a·class="el"·href="structgmx__gpu__info__t.xhtml"·title="Information·about·GPU·devices·on·this·physical·node.">gmx_gpu_info_t</a>·&gpu_info,·const·std::vector<·int·>·&compatibleGpus,·const·std::vector<·int·>·&gpuIds)</dt> |
| 105 | <dd><a·class="anchor"·id="_todo000117"></a>Note·that·the·selected·GPUs·can·be·different·on·each·rank,·and·the·IDs·of·compatible·GPUs·can·be·different·on·each·node,·so·this·routine·ought·to·do·communication·to·determine·whether·all·ranks·are·able·to·proceed.·Currently·this·relies·on·the·MPI·runtime·to·kill·the·other·processes·because·GROMACS·lacks·the·appropriate·infrastructure·to·do·a·good·job·of·coordinating·error·messages·and·behaviour·across·MPMD·ranks·and·multiple·simulations.·</dd> | 101 | <dd><a·class="anchor"·id="_todo000117"></a>Note·that·the·selected·GPUs·can·be·different·on·each·rank,·and·the·IDs·of·compatible·GPUs·can·be·different·on·each·node,·so·this·routine·ought·to·do·communication·to·determine·whether·all·ranks·are·able·to·proceed.·Currently·this·relies·on·the·MPI·runtime·to·kill·the·other·processes·because·GROMACS·lacks·the·appropriate·infrastructure·to·do·a·good·job·of·coordinating·error·messages·and·behaviour·across·MPMD·ranks·and·multiple·simulations.·</dd> |
| 106 | <dt>Member·<a·class="el"·href="namespacegmx.xhtml#a3b3ecc36ead08ea2c31b70f0b85b30d6">gmx::CoordinateFileFlags</a>··</dt> | 102 | <dt>Member·<a·class="el"·href="namespacegmx.xhtml#a3b3ecc36ead08ea2c31b70f0b85b30d6">gmx::CoordinateFileFlags</a>··</dt> |
| 107 | <dd><a·class="anchor"·id="_todo000013"></a>Use·std::bitset<16>·for·the·entries.·</dd> | 103 | <dd><a·class="anchor"·id="_todo000013"></a>Use·std::bitset<16>·for·the·entries.·</dd> |
| 108 | <dt>Member·<a·class="el"·href="namespacegmx.xhtml#a1759b36b1eaccfd0a3b3b82f87d3e111">gmx::cshake</a>··(const·int·iatom[],·int·ncon,·int·*nnit,·int·maxnit,·const·real·constraint_distance_squared[],·real·positions[],·const·real·initial_displacements[],·const·real·half_of_reduced_mass[],·real·omega,·const·real·invmass[],·const·real·distance_squared_tolerance[],·real·scaled_lagrange_multiplier[],·int·*nerror)</dt> | ||
| 109 | <dd><a·class="anchor"·id="_todo000061"></a>Make·SHAKE·use·better·data·structures,·in·particular·for·iatom.··</dd> | ||
| 110 | <dt>Member·<a·class="el"·href="structgmx_1_1DataFileInfo.xhtml#a539535c0a378efd8cc95d7124fcfdec5">gmx::DataFileInfo::bFromDefaultDir</a>··</dt> | 104 | <dt>Member·<a·class="el"·href="structgmx_1_1DataFileInfo.xhtml#a539535c0a378efd8cc95d7124fcfdec5">gmx::DataFileInfo::bFromDefaultDir</a>··</dt> |
| 111 | <dd><a·class="anchor"·id="_todo000127"></a>·Consider·replacing·with·an·enum·that·identifies·the·source·(current·dir,·GMXLIB,·default).··</dd> | 105 | <dd><a·class="anchor"·id="_todo000127"></a>·Consider·replacing·with·an·enum·that·identifies·the·source·(current·dir,·GMXLIB,·default).··</dd> |
| 112 | <dt>Class·<a·class="el"·href="structgmx_1_1detail_1_1PaddingTraits.xhtml">gmx::detail::PaddingTraits<·T·></a>··</dt> | 106 | <dt>Class·<a·class="el"·href="structgmx_1_1detail_1_1PaddingTraits.xhtml">gmx::detail::PaddingTraits<·T·></a>··</dt> |
| 113 | <dd><a·class="anchor"·id="_todo000049"></a>Consider·explicitly·tying·these·types·to·the·SimdTrait·types.·That·would·require·depending·on·the·SIMD·module,·or·extracting·the·traits·from·it.·This·would·also·permit·maxSimdWidthOfBaseType·to·be·set·more·efficiently,·e.g.·as·a·metaprogramming·max·over·the·maximum·width·from·different·implementations.··</dd> | 107 | <dd><a·class="anchor"·id="_todo000049"></a>Consider·explicitly·tying·these·types·to·the·SimdTrait·types.·That·would·require·depending·on·the·SIMD·module,·or·extracting·the·traits·from·it.·This·would·also·permit·maxSimdWidthOfBaseType·to·be·set·more·efficiently,·e.g.·as·a·metaprogramming·max·over·the·maximum·width·from·different·implementations.··</dd> |
| 114 | <dt>Class·<a·class="el"·href="classgmx_1_1ExceptionInitializer.xhtml">gmx::ExceptionInitializer</a>··</dt> | 108 | <dt>Class·<a·class="el"·href="classgmx_1_1ExceptionInitializer.xhtml">gmx::ExceptionInitializer</a>··</dt> |
| 115 | <dd><a·class="anchor"·id="_todo000129"></a>·With·the·exception·of·the·reason·string,·information·added·with·this·class·is·not·currently·accessible·through·any·public·API,·except·for·calling·<a·class="el"·href="group__module__utility.xhtml#gac6287dc8a550a2d54429e44994e00e58"·title="Formats·a·standard·fatal·error·message·for·reporting·an·exception.">printFatalErrorMessage()</a>,·<a·class="el"·href="group__module__utility.xhtml#gac7703ad35b606758d2d12edc0a3d5217"·title="Formats·an·error·message·for·reporting·an·exception.">formatExceptionMessageToString()</a>·or·<a·class="el"·href="group__module__utility.xhtml#gac5e6f6ec944fb2484d6f273c9a0ff495"·title="Formats·an·error·message·for·reporting·an·exception.">formatExceptionMessageToFile()</a>.·This·is·not·implemented·as·there·is·not·yet·need·for·it,·and·it·is·not·clear·what·would·be·the·best·alternative·for·the·access.·It·should·be·possible·to·refactor·the·internal·implementation·to·suit·the·needs·of·such·external·access·without·requiring·changes·in·code·that·throws·these·exceptions.·</dd> | 109 | <dd><a·class="anchor"·id="_todo000129"></a>·With·the·exception·of·the·reason·string,·information·added·with·this·class·is·not·currently·accessible·through·any·public·API,·except·for·calling·<a·class="el"·href="group__module__utility.xhtml#gac6287dc8a550a2d54429e44994e00e58"·title="Formats·a·standard·fatal·error·message·for·reporting·an·exception.">printFatalErrorMessage()</a>,·<a·class="el"·href="group__module__utility.xhtml#gac7703ad35b606758d2d12edc0a3d5217"·title="Formats·an·error·message·for·reporting·an·exception.">formatExceptionMessageToString()</a>·or·<a·class="el"·href="group__module__utility.xhtml#gac5e6f6ec944fb2484d6f273c9a0ff495"·title="Formats·an·error·message·for·reporting·an·exception.">formatExceptionMessageToFile()</a>.·This·is·not·implemented·as·there·is·not·yet·need·for·it,·and·it·is·not·clear·what·would·be·the·best·alternative·for·the·access.·It·should·be·possible·to·refactor·the·internal·implementation·to·suit·the·needs·of·such·external·access·without·requiring·changes·in·code·that·throws·these·exceptions.·</dd> |
| 116 | <dt>Member·<a·class="el"·href="classgmx_1_1FileNameOption.xhtml#aa182da8a00d4ff7556615cedc38a8de2">gmx::FileNameOption::libraryFile</a>··(bool·bLibrary=true)</dt> | 110 | <dt>Member·<a·class="el"·href="classgmx_1_1FileNameOption.xhtml#aa182da8a00d4ff7556615cedc38a8de2">gmx::FileNameOption::libraryFile</a>··(bool·bLibrary=true)</dt> |
| Offset 121, 44 lines modified | Offset 115, 50 lines modified | ||
| 121 | <dd><a·class="anchor"·id="_todo000124"></a>Move·this·function·into·sysinfo.cpp·where·other·OS-specific·code/includes·live··</dd> | 115 | <dd><a·class="anchor"·id="_todo000124"></a>Move·this·function·into·sysinfo.cpp·where·other·OS-specific·code/includes·live··</dd> |
| 122 | <dt>Member·<a·class="el"·href="classgmx_1_1GromacsException.xhtml#a1bd116912e67c096ae949ddae85afe06">gmx::GromacsException::prependContext</a>··(const·std::string·&context)</dt> | 116 | <dt>Member·<a·class="el"·href="classgmx_1_1GromacsException.xhtml#a1bd116912e67c096ae949ddae85afe06">gmx::GromacsException::prependContext</a>··(const·std::string·&context)</dt> |
| 123 | <dd><a·class="anchor"·id="_todo000130"></a>·The·added·information·is·currently·not·accessible·through·<a·class="el"·href="classgmx_1_1GromacsException.xhtml#a1c47abcf4fd5758615b74b11dcff50d5"·title="Returns·the·reason·string·for·the·exception.">what()</a>,·nor·through·any·other·means·except·for·calling·<a·class="el"·href="group__module__utility.xhtml#gac6287dc8a550a2d54429e44994e00e58"·title="Formats·a·standard·fatal·error·message·for·reporting·an·exception.">printFatalErrorMessage()</a>,·<a·class="el"·href="group__module__utility.xhtml#gac7703ad35b606758d2d12edc0a3d5217"·title="Formats·an·error·message·for·reporting·an·exception.">formatExceptionMessageToString()</a>·or·<a·class="el"·href="group__module__utility.xhtml#gac5e6f6ec944fb2484d6f273c9a0ff495"·title="Formats·an·error·message·for·reporting·an·exception.">formatExceptionMessageToFile()</a>.·See·<a·class="el"·href="classgmx_1_1ExceptionInitializer.xhtml"·title="Provides·information·for·Gromacs·exception·constructors.">ExceptionInitializer</a>·for·more·discussion.··</dd> | 117 | <dd><a·class="anchor"·id="_todo000130"></a>·The·added·information·is·currently·not·accessible·through·<a·class="el"·href="classgmx_1_1GromacsException.xhtml#a1c47abcf4fd5758615b74b11dcff50d5"·title="Returns·the·reason·string·for·the·exception.">what()</a>,·nor·through·any·other·means·except·for·calling·<a·class="el"·href="group__module__utility.xhtml#gac6287dc8a550a2d54429e44994e00e58"·title="Formats·a·standard·fatal·error·message·for·reporting·an·exception.">printFatalErrorMessage()</a>,·<a·class="el"·href="group__module__utility.xhtml#gac7703ad35b606758d2d12edc0a3d5217"·title="Formats·an·error·message·for·reporting·an·exception.">formatExceptionMessageToString()</a>·or·<a·class="el"·href="group__module__utility.xhtml#gac5e6f6ec944fb2484d6f273c9a0ff495"·title="Formats·an·error·message·for·reporting·an·exception.">formatExceptionMessageToFile()</a>.·See·<a·class="el"·href="classgmx_1_1ExceptionInitializer.xhtml"·title="Provides·information·for·Gromacs·exception·constructors.">ExceptionInitializer</a>·for·more·discussion.··</dd> |
| 124 | <dt>Class·<a·class="el"·href="classgmx_1_1IRestraintPotential.xhtml">gmx::IRestraintPotential</a>··</dt> | 118 | <dt>Class·<a·class="el"·href="classgmx_1_1IRestraintPotential.xhtml">gmx::IRestraintPotential</a>··</dt> |
| 125 | <dd><a·class="anchor"·id="_todo000104"></a>Template·headers·can·help·to·build·compatible·calculation·methods·with·different·input·requirements.·For·reference,·see·<a·href="https://github.com/kassonlab/sample_restraint">https://github.com/kassonlab/sample_restraint</a>·</dd> | 119 | <dd><a·class="anchor"·id="_todo000104"></a>Template·headers·can·help·to·build·compatible·calculation·methods·with·different·input·requirements.·For·reference,·see·<a·href="https://github.com/kassonlab/sample_restraint">https://github.com/kassonlab/sample_restraint</a>·</dd> |
| 126 | <dt>Member·<a·class="el"·href="classgmx_1_1IRestraintPotential.xhtml#abd785aca4a7790377720f445e8263ffb">gmx::IRestraintPotential::evaluate</a>··(Vector·r1,·Vector·r2,·double·t)=0</dt> | 120 | <dt>Member·<a·class="el"·href="classgmx_1_1IRestraintPotential.xhtml#abd785aca4a7790377720f445e8263ffb">gmx::IRestraintPotential::evaluate</a>··(Vector·r1,·Vector·r2,·double·t)=0</dt> |
| 127 | <dd><a·class="anchor"·id="_todo000105"></a>The·virtual·function·call·should·be·replaced·by·a·(table·of)·function·objects·retrieved·before·the·run.··</dd> | 121 | <dd><a·class="anchor"·id="_todo000105"></a>The·virtual·function·call·should·be·replaced·by·a·(table·of)·function·objects·retrieved·before·the·run.··</dd> |
| 128 | <dt>Member·<a·class="el"·href="namespacegmx.xhtml#a516559bb0e35192a8b312c0c15b28daa">gmx::openTNG</a>··(const·std::string·&name,·const·<a·class="el"·href="classgmx_1_1Selection.xhtml"·title="Provides·access·to·a·single·selection.">Selection</a>·&sel,·const·gmx_mtop_t·*mtop)</dt> | ||
| 129 | <dd><a·class="anchor"·id="_todo000012"></a>Those·should·be·methods·in·a·replacement·for·t_trxstatus·instead.··</dd> | ||
| 130 | <dt>Member·<a·class="el"·href="namespacegmx.xhtml#a6e94dc41a08ab7544a47d42216d8c1e5">gmx::reportGpuUsage</a>··(const·MDLogger·&mdlog,·ArrayRef<·const·GpuTaskAssignment·>·gpuTaskAssignmentOnRanksOfThisNode,·size_t·numGpuTasksOnThisNode,·size_t·numPpRanks,·bool·printHostName,·bool·useGpuForBonded,·PmeRunMode·pmeRunMode,·bool·useGpuForUpdate)</dt> | 122 | <dt>Member·<a·class="el"·href="namespacegmx.xhtml#a6e94dc41a08ab7544a47d42216d8c1e5">gmx::reportGpuUsage</a>··(const·MDLogger·&mdlog,·ArrayRef<·const·GpuTaskAssignment·>·gpuTaskAssignmentOnRanksOfThisNode,·size_t·numGpuTasksOnThisNode,·size_t·numPpRanks,·bool·printHostName,·bool·useGpuForBonded,·PmeRunMode·pmeRunMode,·bool·useGpuForUpdate)</dt> |
| 131 | <dd><a·class="anchor"·id="_todo000114"></a>It·could·be·useful·to·report·also·whether·any·nodes·differed,·and·in·what·way.·</dd> | 123 | <dd><a·class="anchor"·id="_todo000114"></a>It·could·be·useful·to·report·also·whether·any·nodes·differed,·and·in·what·way.·</dd> |
| 132 | <dt>Member·<a·class="el"·href="classgmx_1_1Selection.xhtml#aa7007210627e2b003a1ee0d54c02908a">gmx::Selection::setEvaluateVelocities</a>··(bool·bEnabled)</dt> | 124 | <dt>Member·<a·class="el"·href="classgmx_1_1Selection.xhtml#aa7007210627e2b003a1ee0d54c02908a">gmx::Selection::setEvaluateVelocities</a>··(bool·bEnabled)</dt> |
| 133 | <dd><a·class="anchor"·id="_todo000111"></a>·Implement·it·such·that·in·the·above·case,·<a·class="el"·href="classgmx_1_1Selection.xhtml#aca14d361fb67d6d709f81eed5ea36770"·title="Returns·whether·velocities·are·available·for·this·selection.">hasVelocities()</a>·will·return·false·for·such·frames.·</dd> | 125 | <dd><a·class="anchor"·id="_todo000111"></a>·Implement·it·such·that·in·the·above·case,·<a·class="el"·href="classgmx_1_1Selection.xhtml#aca14d361fb67d6d709f81eed5ea36770"·title="Returns·whether·velocities·are·available·for·this·selection.">hasVelocities()</a>·will·return·false·for·such·frames.·</dd> |
| 134 | <dt>Class·<a·class="el"·href="classgmx_1_1SelectionOption.xhtml">gmx::SelectionOption</a>··</dt> | 126 | <dt>Class·<a·class="el"·href="classgmx_1_1SelectionOption.xhtml">gmx::SelectionOption</a>··</dt> |
| 135 | <dd><p·class="startdd"><a·class="anchor"·id="_todo000112"></a>·Support·for·specifying·that·an·option·accepts,·e.g.,·two·to·four·selections.·Currently,·only·a·fixed·count·or·any·number·of·selections·is·possible.</p> | 127 | <dd><p·class="startdd"><a·class="anchor"·id="_todo000112"></a>·Support·for·specifying·that·an·option·accepts,·e.g.,·two·to·four·selections.·Currently,·only·a·fixed·count·or·any·number·of·selections·is·possible.</p> |
| 136 | <p·class="enddd"></p> | 128 | <p·class="enddd"></p> |
| 137 | </dd> | 129 | </dd> |
| 138 | <dt>Class·<a·class="el"·href="classgmx_1_1TrajectoryAnalysisSettings.xhtml">gmx::TrajectoryAnalysisSettings</a>··</dt> | 130 | <dt>Class·<a·class="el"·href="classgmx_1_1TrajectoryAnalysisSettings.xhtml">gmx::TrajectoryAnalysisSettings</a>··</dt> |
| 139 | <dd><a·class="anchor"·id="_todo000121"></a>·Remove·plain·flags·from·the·public·interface.·</dd> | 131 | <dd><a·class="anchor"·id="_todo000121"></a>·Remove·plain·flags·from·the·public·interface.·</dd> |
| 140 | <dt>Class·<a·class="el"·href="structgmx__gpu__info__t.xhtml">gmx_gpu_info_t</a>··</dt> | ||
| 141 | <dd><a·class="anchor"·id="_todo000043"></a>Use·a·std::vector··</dd> | ||
| 142 | <dt>Member·<a·class="el"·href="group__module__utility.xhtml#ga33e34477bae2bbb86c4d9af1823e3fd0">GMX_UNUSED_VALUE</a>··(value)</dt> | 132 | <dt>Member·<a·class="el"·href="group__module__utility.xhtml#ga33e34477bae2bbb86c4d9af1823e3fd0">GMX_UNUSED_VALUE</a>··(value)</dt> |
| 143 | <dd><a·class="anchor"·id="_todo000126"></a>Deprecated·-·use·gmx_unused··</dd> | 133 | <dd><a·class="anchor"·id="_todo000126"></a>Deprecated·-·use·gmx_unused··</dd> |
| 134 | <dt>Module·<a·class="el"·href="group__module__modularsimulator.xhtml">module_modularsimulator</a>··</dt> | ||
| 135 | <dd><a·class="anchor"·id="_todo000089"></a>Can·we·link·to·<code>docs/doxygen/lib/modularsimulator.md</code>?·</dd> | ||
| 136 | <dt>Member·<a·class="el"·href="smalloc_8h.xhtml#ab3d98b1efa6c2b42d2c0d216eafafec5">set_over_alloc_dd</a>··(gmx_bool·set)</dt> | ||
| 137 | <dd><a·class="anchor"·id="_todo000132"></a>·This·is·mdrun-specific,·so·it·might·be·better·to·put·this·and·<a·class="el"·href="smalloc_8h.xhtml#af1533c63c1d40c5bb9bfaaa6d898369a"·title="Returns·new·allocation·count·for·domain·decomposition·allocations.">over_alloc_dd()</a>·much·higher·up.··</dd> | ||
| 138 | <dt>File·<a·class="el"·href="simulationsignal_8h.xhtml">simulationsignal.h</a>··</dt> | ||
| 139 | <dd><a·class="anchor"·id="_todo000063"></a>Move·this·to·mdrunutility·module·alongside·gathering·multi-simulation·communication·infrastructure·there.·</dd> | ||
| 140 | <dt>Member·<a·class="el"·href="state_8h.xhtml#aa4de64296c013fbd01f41b25c64a774c">df_history_t</a>··</dt> | ||
| 141 | <dd><a·class="anchor"·id="_todo000072"></a>Split·out·into·microstate·and·observables·history.··</dd> | ||
| 142 | <dt>Member·<a·class="el"·href="namespacegmx.xhtml#ad95d30be525ee425b837e73681541507">gmx::BoxMatrix</a>··</dt> | ||
| 143 | <dd><a·class="anchor"·id="_todo000120"></a>Implement·a·full·replacement·for·C-style·real[DIM][DIM]··</dd> | ||
| 144 | <dt>Member·<a·class="el"·href="namespacegmx.xhtml#a1759b36b1eaccfd0a3b3b82f87d3e111">gmx::cshake</a>··(const·int·iatom[],·int·ncon,·int·*nnit,·int·maxnit,·const·real·constraint_distance_squared[],·real·positions[],·const·real·initial_displacements[],·const·real·half_of_reduced_mass[],·real·omega,·const·real·invmass[],·const·real·distance_squared_tolerance[],·real·scaled_lagrange_multiplier[],·int·*nerror)</dt> | ||
| 145 | <dd><a·class="anchor"·id="_todo000061"></a>Make·SHAKE·use·better·data·structures,·in·particular·for·iatom.··</dd> | ||
| 146 | <dt>Member·<a·class="el"·href="namespacegmx.xhtml#a516559bb0e35192a8b312c0c15b28daa">gmx::openTNG</a>··(const·std::string·&name,·const·<a·class="el"·href="classgmx_1_1Selection.xhtml"·title="Provides·access·to·a·single·selection.">Selection</a>·&sel,·const·gmx_mtop_t·*mtop)</dt> | ||
| 147 | <dd><a·class="anchor"·id="_todo000012"></a>Those·should·be·methods·in·a·replacement·for·t_trxstatus·instead.··</dd> | ||
| 148 | <dt>Class·<a·class="el"·href="structgmx__gpu__info__t.xhtml">gmx_gpu_info_t</a>··</dt> | ||
| 149 | <dd><a·class="anchor"·id="_todo000043"></a>Use·a·std::vector··</dd> | ||
| 144 | <dt>File·<a·class="el"·href="hostallocator_8h.xhtml">hostallocator.h</a>··</dt> | 150 | <dt>File·<a·class="el"·href="hostallocator_8h.xhtml">hostallocator.h</a>··</dt> |
| 145 | <dd><a·class="anchor"·id="_todo000037"></a>This·should·not·be·in·the·public·API,·but·it·needs·to·be·for·the·moment·because·<a·class="el"·href="state_8h.xhtml"·title="This·file·contains·the·definition·of·the·microstate·of·the·simulated·system.">state.h</a>·is·in·that·API.·</dd> | 151 | <dd><a·class="anchor"·id="_todo000037"></a>This·should·not·be·in·the·public·API,·but·it·needs·to·be·for·the·moment·because·<a·class="el"·href="state_8h.xhtml"·title="This·file·contains·the·definition·of·the·microstate·of·the·simulated·system.">state.h</a>·is·in·that·API.·</dd> |
| 146 | <dt>Module·<a·class="el"·href="group__module__domdec.xhtml">module_domdec</a>··</dt> | 152 | <dt>Module·<a·class="el"·href="group__module__domdec.xhtml">module_domdec</a>··</dt> |
| 147 | <dd><a·class="anchor"·id="_todo000015"></a>Get·domdec·stuff·out·of·mdtypes/commrec.h·</dd> | 153 | <dd><a·class="anchor"·id="_todo000015"></a>Get·domdec·stuff·out·of·mdtypes/commrec.h·</dd> |
| 148 | <dt>Module·<a·class="el"·href="group__module__modularsimulator.xhtml">module_modularsimulator</a>··</dt> | ||
| 149 | <dd><a·class="anchor"·id="_todo000089"></a>Can·we·link·to·<code>docs/doxygen/lib/modularsimulator.md</code>?·</dd> | ||
| 150 | <dt>File·<a·class="el"·href="pbc__aiuc_8h.xhtml">pbc_aiuc.h</a>··</dt> | 154 | <dt>File·<a·class="el"·href="pbc__aiuc_8h.xhtml">pbc_aiuc.h</a>··</dt> |
| 151 | <dd><a·class="anchor"·id="_todo000101"></a>CPU,·GPU·and·SIMD·routines·essentially·do·the·same·operations·on·different·data-types.·Currently·this·leads·to·code·duplication,·which·has·to·be·resolved.·For·details,·see·Redmine·task·#2863·<a·href="https://redmine.gromacs.org/issues/2863">https://redmine.gromacs.org/issues/2863</a>·</dd> | 155 | <dd><a·class="anchor"·id="_todo000101"></a>CPU,·GPU·and·SIMD·routines·essentially·do·the·same·operations·on·different·data-types.·Currently·this·leads·to·code·duplication,·which·has·to·be·resolved.·For·details,·see·Redmine·task·#2863·<a·href="https://redmine.gromacs.org/issues/2863">https://redmine.gromacs.org/issues/2863</a>·</dd> |
| 152 | <dt>Member·<a·class="el"·href="pbc__aiuc_8h.xhtml#ad6672483b8f9d260ae582c4a63dafa6f">pbcDxAiuc</a>··(const·<a·class="el"·href="structPbcAiuc.xhtml"·title="Compact·and·ordered·version·of·the·PBC·matrix.">PbcAiuc</a>·&pbcAiuc,·const·rvec·&r1,·const·rvec·&r2,·rvec·dr)</dt> | 156 | <dt>Member·<a·class="el"·href="pbc__aiuc_8h.xhtml#ad6672483b8f9d260ae582c4a63dafa6f">pbcDxAiuc</a>··(const·<a·class="el"·href="structPbcAiuc.xhtml"·title="Compact·and·ordered·version·of·the·PBC·matrix.">PbcAiuc</a>·&pbcAiuc,·const·rvec·&r1,·const·rvec·&r2,·rvec·dr)</dt> |
| 153 | <dd><a·class="anchor"·id="_todo000102"></a>This·routine·operates·on·rvec·types·and·uses·<a·class="el"·href="structPbcAiuc.xhtml"·title="Compact·and·ordered·version·of·the·PBC·matrix.">PbcAiuc</a>·to·define·periodic·box,·but·essentially·does·the·same·thing·as·SIMD·and·GPU·version.·These·will·have·to·be·unified·in·future·to·avoid·code·duplication.·See·Redmine·task·#2863:·<a·href="https://redmine.gromacs.org/issues/2863">https://redmine.gromacs.org/issues/2863</a>·</dd> | 157 | <dd><a·class="anchor"·id="_todo000102"></a>This·routine·operates·on·rvec·types·and·uses·<a·class="el"·href="structPbcAiuc.xhtml"·title="Compact·and·ordered·version·of·the·PBC·matrix.">PbcAiuc</a>·to·define·periodic·box,·but·essentially·does·the·same·thing·as·SIMD·and·GPU·version.·These·will·have·to·be·unified·in·future·to·avoid·code·duplication.·See·Redmine·task·#2863:·<a·href="https://redmine.gromacs.org/issues/2863">https://redmine.gromacs.org/issues/2863</a>·</dd> |
| 154 | <dt>Member·<a·class="el"·href="smalloc_8h.xhtml#ab3d98b1efa6c2b42d2c0d216eafafec5">set_over_alloc_dd</a>··(gmx_bool·set)</dt> | ||
| 155 | <dd><a·class="anchor"·id="_todo000132"></a>·This·is·mdrun-specific,·so·it·might·be·better·to·put·this·and·<a·class="el"·href="smalloc_8h.xhtml#af1533c63c1d40c5bb9bfaaa6d898369a"·title="Returns·new·allocation·count·for·domain·decomposition·allocations.">over_alloc_dd()</a>·much·higher·up.··</dd> | ||
| 156 | <dt>File·<a·class="el"·href="simulationsignal_8h.xhtml">simulationsignal.h</a>··</dt> | ||
| 157 | <dd><a·class="anchor"·id="_todo000063"></a>Move·this·to·mdrunutility·module·alongside·gathering·multi-simulation·communication·infrastructure·there.·</dd> | ||
| 158 | <dt>File·<a·class="el"·href="string__view_8h.xhtml">string_view.h</a>··</dt> | 158 | <dt>File·<a·class="el"·href="string__view_8h.xhtml">string_view.h</a>··</dt> |
| 159 | <dd><a·class="anchor"·id="_todo000011"></a>Remove·when·requiring·C++17,·which·has·a·standardized·version·of·std::string_view.·</dd> | 159 | <dd><a·class="anchor"·id="_todo000011"></a>Remove·when·requiring·C++17,·which·has·a·standardized·version·of·std::string_view.·</dd> |
| 160 | <dt>Class·<a·class="el"·href="classt__state.xhtml">t_state</a>··</dt> | 160 | <dt>Class·<a·class="el"·href="classt__state.xhtml">t_state</a>··</dt> |
| 161 | <dd><a·class="anchor"·id="_todo000073"></a>Move·pure·observables·history·to·ObservablesHistory.·</dd> | 161 | <dd><a·class="anchor"·id="_todo000073"></a>Move·pure·observables·history·to·ObservablesHistory.·</dd> |
| 162 | </dl> | 162 | </dl> |
| 163 | </div></div><!--·contents·--> | 163 | </div></div><!--·contents·--> |
| 164 | </div><!--·PageDoc·--> | 164 | </div><!--·PageDoc·--> |
| Offset 14, 16 lines modified | Offset 14, 14 lines modified | ||
| 14 | ······This·should·be·made·const·once·the·lazy·implementation·is·done·properly | 14 | ······This·should·be·made·const·once·the·lazy·implementation·is·done·properly |
| 15 | ······for·the·class. | 15 | ······for·the·class. |
| 16 | ··Member·clearModificationBlock·(MoleculePatchDatabase·*globalPatches) | 16 | ··Member·clearModificationBlock·(MoleculePatchDatabase·*globalPatches) |
| 17 | ······Remove·once·constructor/destructor·takes·care·of·all·of·this. | 17 | ······Remove·once·constructor/destructor·takes·care·of·all·of·this. |
| 18 | ··Member·copyPreprocessResidues·(const·PreprocessResidue·&s,·PreprocessResidue | 18 | ··Member·copyPreprocessResidues·(const·PreprocessResidue·&s,·PreprocessResidue |
| 19 | ··*d,·t_symtab·*symtab) | 19 | ··*d,·t_symtab·*symtab) |
| 20 | ······Remove·once·copy·can·be·done·directly. | 20 | ······Remove·once·copy·can·be·done·directly. |
| 21 | ··Member·df_history_t | ||
| 22 | ······Split·out·into·microstate·and·observables·history. | ||
| 23 | ··Class·gmx::AbstractAnalysisArrayData | 21 | ··Class·gmx::AbstractAnalysisArrayData |
| 24 | ·······Add·support·for·multiple·data·sets. | 22 | ·······Add·support·for·multiple·data·sets. |
| 25 | ··Class·gmx::AbstractAnalysisData | 23 | ··Class·gmx::AbstractAnalysisData |
| 26 | ·······Improve·the·exception-handling·semantics.·In·most·cases,·it·doesn't·make | 24 | ·······Improve·the·exception-handling·semantics.·In·most·cases,·it·doesn't·make |
| 27 | ······much·sense·to·continue·data·processing·after·one·module·fails,·but·having | 25 | ······much·sense·to·continue·data·processing·after·one·module·fails,·but·having |
| 28 | ······the·alternative·would·not·hurt. | 26 | ······the·alternative·would·not·hurt. |
| 29 | ··Member·gmx::AbstractAnalysisData::addColumnModule·(int·col,·int·span,·const | 27 | ··Member·gmx::AbstractAnalysisData::addColumnModule·(int·col,·int·span,·const |
| Offset 49, 33 lines modified | Offset 47, 25 lines modified | ||
| 49 | ······repeatedly·assigns·the·result·of·AnalysisNeighborhood::initSearch()·to | 47 | ······repeatedly·assigns·the·result·of·AnalysisNeighborhood::initSearch()·to |
| 50 | ······the·same·variable·(see·sm_distance.cpp). | 48 | ······the·same·variable·(see·sm_distance.cpp). |
| 51 | ·······Consider·removing·minimumDistance(),·as·nearestPoint()·already·returns | 49 | ·······Consider·removing·minimumDistance(),·as·nearestPoint()·already·returns |
| 52 | ······the·distance. | 50 | ······the·distance. |
| 53 | ··Class·gmx::ArrayRef<_T_> | 51 | ··Class·gmx::ArrayRef<_T_> |
| 54 | ·······This·class·is·not·complete.·There·are·likely·also·methods·missing·(not | 52 | ·······This·class·is·not·complete.·There·are·likely·also·methods·missing·(not |
| 55 | ······required·for·current·usage). | 53 | ······required·for·current·usage). |
| 56 | ··Member·gmx::BoxMatrix | ||
| 57 | ······Implement·a·full·replacement·for·C-style·real[DIM][DIM] | ||
| 58 | ··Member·gmx::checkUserGpuIds·(const·gmx_gpu_info_t·&gpu_info,·const·std:: | 54 | ··Member·gmx::checkUserGpuIds·(const·gmx_gpu_info_t·&gpu_info,·const·std:: |
| 59 | ··vector<·int·>·&compatibleGpus,·const·std::vector<·int·>·&gpuIds) | 55 | ··vector<·int·>·&compatibleGpus,·const·std::vector<·int·>·&gpuIds) |
| 60 | ······Note·that·the·selected·GPUs·can·be·different·on·each·rank,·and·the·IDs·of | 56 | ······Note·that·the·selected·GPUs·can·be·different·on·each·rank,·and·the·IDs·of |
| 61 | ······compatible·GPUs·can·be·different·on·each·node,·so·this·routine·ought·to | 57 | ······compatible·GPUs·can·be·different·on·each·node,·so·this·routine·ought·to |
| 62 | ······do·communication·to·determine·whether·all·ranks·are·able·to·proceed. | 58 | ······do·communication·to·determine·whether·all·ranks·are·able·to·proceed. |
| 63 | ······Currently·this·relies·on·the·MPI·runtime·to·kill·the·other·processes | 59 | ······Currently·this·relies·on·the·MPI·runtime·to·kill·the·other·processes |
| 64 | ······because·GROMACS·lacks·the·appropriate·infrastructure·to·do·a·good·job·of | 60 | ······because·GROMACS·lacks·the·appropriate·infrastructure·to·do·a·good·job·of |
| 65 | ······coordinating·error·messages·and·behaviour·across·MPMD·ranks·and·multiple | 61 | ······coordinating·error·messages·and·behaviour·across·MPMD·ranks·and·multiple |
| 66 | ······simulations. | 62 | ······simulations. |
| 67 | ··Member·gmx::CoordinateFileFlags | 63 | ··Member·gmx::CoordinateFileFlags |
| 68 | ······Use·std::bitset<16>·for·the·entries. | 64 | ······Use·std::bitset<16>·for·the·entries. |
| 69 | ··Member·gmx::cshake·(const·int·iatom[],·int·ncon,·int·*nnit,·int·maxnit,·const | ||
| 70 | ··real·constraint_distance_squared[],·real·positions[],·const·real | ||
| 71 | ··initial_displacements[],·const·real·half_of_reduced_mass[],·real·omega,·const | ||
| 72 | ··real·invmass[],·const·real·distance_squared_tolerance[],·real | ||
| 73 | ··scaled_lagrange_multiplier[],·int·*nerror) | ||
| 74 | ······Make·SHAKE·use·better·data·structures,·in·particular·for·iatom. | ||
| 75 | ··Member·gmx::DataFileInfo::bFromDefaultDir | 65 | ··Member·gmx::DataFileInfo::bFromDefaultDir |
| 76 | ·······Consider·replacing·with·an·enum·that·identifies·the·source·(current·dir, | 66 | ·······Consider·replacing·with·an·enum·that·identifies·the·source·(current·dir, |
| 77 | ······GMXLIB,·default). | 67 | ······GMXLIB,·default). |
| 78 | ··Class·gmx::detail::PaddingTraits<_T_> | 68 | ··Class·gmx::detail::PaddingTraits<_T_> |
| 79 | ······Consider·explicitly·tying·these·types·to·the·SimdTrait·types.·That·would | 69 | ······Consider·explicitly·tying·these·types·to·the·SimdTrait·types.·That·would |
| 80 | ······require·depending·on·the·SIMD·module,·or·extracting·the·traits·from·it. | 70 | ······require·depending·on·the·SIMD·module,·or·extracting·the·traits·from·it. |
| 81 | ······This·would·also·permit·maxSimdWidthOfBaseType·to·be·set·more·efficiently, | 71 | ······This·would·also·permit·maxSimdWidthOfBaseType·to·be·set·more·efficiently, |
| Offset 110, 17 lines modified | Offset 100, 14 lines modified | ||
| 110 | ··Class·gmx::IRestraintPotential | 100 | ··Class·gmx::IRestraintPotential |
| 111 | ······Template·headers·can·help·to·build·compatible·calculation·methods·with | 101 | ······Template·headers·can·help·to·build·compatible·calculation·methods·with |
| 112 | ······different·input·requirements.·For·reference,·see·https://github.com/ | 102 | ······different·input·requirements.·For·reference,·see·https://github.com/ |
| 113 | ······kassonlab/sample_restraint | 103 | ······kassonlab/sample_restraint |
| 114 | ··Member·gmx::IRestraintPotential::evaluate·(Vector·r1,·Vector·r2,·double·t)=0 | 104 | ··Member·gmx::IRestraintPotential::evaluate·(Vector·r1,·Vector·r2,·double·t)=0 |
| 115 | ······The·virtual·function·call·should·be·replaced·by·a·(table·of)·function | 105 | ······The·virtual·function·call·should·be·replaced·by·a·(table·of)·function |
| 116 | ······objects·retrieved·before·the·run. | 106 | ······objects·retrieved·before·the·run. |
| 117 | ··Member·gmx::openTNG·(const·std::string·&name,·const·Selection·&sel,·const | ||
| 118 | ··gmx_mtop_t·*mtop) | ||
| 119 | ······Those·should·be·methods·in·a·replacement·for·t_trxstatus·instead. | ||
| 120 | ··Member·gmx::reportGpuUsage·(const·MDLogger·&mdlog,·ArrayRef<·const | 107 | ··Member·gmx::reportGpuUsage·(const·MDLogger·&mdlog,·ArrayRef<·const |
| 121 | ··GpuTaskAssignment·>·gpuTaskAssignmentOnRanksOfThisNode,·size_t | 108 | ··GpuTaskAssignment·>·gpuTaskAssignmentOnRanksOfThisNode,·size_t |
| 122 | ··numGpuTasksOnThisNode,·size_t·numPpRanks,·bool·printHostName,·bool | 109 | ··numGpuTasksOnThisNode,·size_t·numPpRanks,·bool·printHostName,·bool |
| 123 | ··useGpuForBonded,·PmeRunMode·pmeRunMode,·bool·useGpuForUpdate) | 110 | ··useGpuForBonded,·PmeRunMode·pmeRunMode,·bool·useGpuForUpdate) |
| 124 | ······It·could·be·useful·to·report·also·whether·any·nodes·differed,·and·in·what | 111 | ······It·could·be·useful·to·report·also·whether·any·nodes·differed,·and·in·what |
| 125 | ······way. | 112 | ······way. |
| 126 | ··Member·gmx::Selection::setEvaluateVelocities·(bool·bEnabled) | 113 | ··Member·gmx::Selection::setEvaluateVelocities·(bool·bEnabled) |
| Offset 128, 42 lines modified | Offset 115, 55 lines modified | ||
| 128 | ······false·for·such·frames. | 115 | ······false·for·such·frames. |
| 129 | ··Class·gmx::SelectionOption | 116 | ··Class·gmx::SelectionOption |
| 130 | ·······Support·for·specifying·that·an·option·accepts,·e.g.,·two·to·four | 117 | ·······Support·for·specifying·that·an·option·accepts,·e.g.,·two·to·four |
| 131 | ······selections.·Currently,·only·a·fixed·count·or·any·number·of·selections·is | 118 | ······selections.·Currently,·only·a·fixed·count·or·any·number·of·selections·is |
| 132 | ······possible. | 119 | ······possible. |
| 133 | ··Class·gmx::TrajectoryAnalysisSettings | 120 | ··Class·gmx::TrajectoryAnalysisSettings |
| 134 | ·······Remove·plain·flags·from·the·public·interface. | 121 | ·······Remove·plain·flags·from·the·public·interface. |
| 135 | ··Class·gmx_gpu_info_t | ||
| 136 | ······Use·a·std::vector | ||
| 137 | ··Member·GMX_UNUSED_VALUE·(value) | 122 | ··Member·GMX_UNUSED_VALUE·(value) |
| 138 | ······Deprecated·-·use·gmx_unused | 123 | ······Deprecated·-·use·gmx_unused |
| 124 | ··Module·module_modularsimulator | ||
| 125 | ······Can·we·link·to·docs/doxygen/lib/modularsimulator.md? | ||
| 126 | ··Member·set_over_alloc_dd·(gmx_bool·set) | ||
| 127 | ·······This·is·mdrun-specific,·so·it·might·be·better·to·put·this·and | ||
| 128 | ······over_alloc_dd()·much·higher·up. | ||
| 129 | ··File·simulationsignal.h | ||
| 130 | ······Move·this·to·mdrunutility·module·alongside·gathering·multi-simulation | ||
| 131 | ······communication·infrastructure·there. | ||
| 132 | ··Member·df_history_t | ||
| 133 | ······Split·out·into·microstate·and·observables·history. | ||
| 134 | ··Member·gmx::BoxMatrix | ||
| 135 | ······Implement·a·full·replacement·for·C-style·real[DIM][DIM] | ||
| 136 | ··Member·gmx::cshake·(const·int·iatom[],·int·ncon,·int·*nnit,·int·maxnit,·const | ||
| 137 | ··real·constraint_distance_squared[],·real·positions[],·const·real | ||
| 138 | ··initial_displacements[],·const·real·half_of_reduced_mass[],·real·omega,·const | ||
| 139 | ··real·invmass[],·const·real·distance_squared_tolerance[],·real | ||
| 140 | ··scaled_lagrange_multiplier[],·int·*nerror) | ||
| 141 | ······Make·SHAKE·use·better·data·structures,·in·particular·for·iatom. | ||
| 142 | ··Member·gmx::openTNG·(const·std::string·&name,·const·Selection·&sel,·const | ||
| 143 | ··gmx_mtop_t·*mtop) | ||
| 144 | ······Those·should·be·methods·in·a·replacement·for·t_trxstatus·instead. | ||
| 145 | ··Class·gmx_gpu_info_t | ||
| 146 | ······Use·a·std::vector | ||
| 139 | ··File·hostallocator.h | 147 | ··File·hostallocator.h |
| 140 | ······This·should·not·be·in·the·public·API,·but·it·needs·to·be·for·the·moment | 148 | ······This·should·not·be·in·the·public·API,·but·it·needs·to·be·for·the·moment |
| 141 | ······because·state.h·is·in·that·API. | 149 | ······because·state.h·is·in·that·API. |
| 142 | ··Module·module_domdec | 150 | ··Module·module_domdec |
| 143 | ······Get·domdec·stuff·out·of·mdtypes/commrec.h | 151 | ······Get·domdec·stuff·out·of·mdtypes/commrec.h |
| 144 | ··Module·module_modularsimulator | ||
| 145 | ······Can·we·link·to·docs/doxygen/lib/modularsimulator.md? | ||
| 146 | ··File·pbc_aiuc.h | 152 | ··File·pbc_aiuc.h |
| 147 | ······CPU,·GPU·and·SIMD·routines·essentially·do·the·same·operations·on | 153 | ······CPU,·GPU·and·SIMD·routines·essentially·do·the·same·operations·on |
| 148 | ······different·data-types.·Currently·this·leads·to·code·duplication,·which·has | 154 | ······different·data-types.·Currently·this·leads·to·code·duplication,·which·has |
| 149 | ······to·be·resolved.·For·details,·see·Redmine·task·#2863·https:// | 155 | ······to·be·resolved.·For·details,·see·Redmine·task·#2863·https:// |
| 150 | ······redmine.gromacs.org/issues/2863 | 156 | ······redmine.gromacs.org/issues/2863 |
| 151 | ··Member·pbcDxAiuc·(const·PbcAiuc·&pbcAiuc,·const·rvec·&r1,·const·rvec·&r2, | 157 | ··Member·pbcDxAiuc·(const·PbcAiuc·&pbcAiuc,·const·rvec·&r1,·const·rvec·&r2, |
| 152 | ··rvec·dr) | 158 | ··rvec·dr) |
| 153 | ······This·routine·operates·on·rvec·types·and·uses·PbcAiuc·to·define·periodic | 159 | ······This·routine·operates·on·rvec·types·and·uses·PbcAiuc·to·define·periodic |
| 154 | ······box,·but·essentially·does·the·same·thing·as·SIMD·and·GPU·version.·These | 160 | ······box,·but·essentially·does·the·same·thing·as·SIMD·and·GPU·version.·These |
| 155 | ······will·have·to·be·unified·in·future·to·avoid·code·duplication.·See·Redmine | 161 | ······will·have·to·be·unified·in·future·to·avoid·code·duplication.·See·Redmine |
| 156 | ······task·#2863:·https://redmine.gromacs.org/issues/2863 | 162 | ······task·#2863:·https://redmine.gromacs.org/issues/2863 |
| 157 | ··Member·set_over_alloc_dd·(gmx_bool·set) | ||
| 158 | ·······This·is·mdrun-specific,·so·it·might·be·better·to·put·this·and | ||
| 159 | ······over_alloc_dd()·much·higher·up. | ||
| 160 | ··File·simulationsignal.h | ||
| 161 | ······Move·this·to·mdrunutility·module·alongside·gathering·multi-simulation | ||
| 162 | ······communication·infrastructure·there. | ||
| Max diff block lines reached; 258/7183 bytes (3.59%) of diff not shown. | |||
| Offset 61, 15 lines modified | Offset 61, 15 lines modified | ||
| 61 | and·Artem·Zhmurov.</p> | 61 | and·Artem·Zhmurov.</p> |
| 62 | <p>Mark·Abraham,·Berk·Hess,·David·van·der·Spoel,·and·Erik·Lindahl.</p> | 62 | <p>Mark·Abraham,·Berk·Hess,·David·van·der·Spoel,·and·Erik·Lindahl.</p> |
| 63 | <p>©·1991·–·2000:</p> | 63 | <p>©·1991·–·2000:</p> |
| 64 | <blockquote> | 64 | <blockquote> |
| 65 | <div><p>Department·of·Biophysical·Chemistry,·University·of·Groningen. | 65 | <div><p>Department·of·Biophysical·Chemistry,·University·of·Groningen. |
| 66 | Nijenborgh·4,·9747·AG·Groningen,·The·Netherlands.</p> | 66 | Nijenborgh·4,·9747·AG·Groningen,·The·Netherlands.</p> |
| 67 | </div></blockquote> | 67 | </div></blockquote> |
| 68 | <p>©·2001·–·202 | 68 | <p>©·2001·–·2024:</p> |
| 69 | <blockquote> | 69 | <blockquote> |
| 70 | <div><p>The·GROMACS·development·teams·at·the·Royal·Institute·of·Technology·and | 70 | <div><p>The·GROMACS·development·teams·at·the·Royal·Institute·of·Technology·and |
| 71 | Uppsala·University,·Sweden.</p> | 71 | Uppsala·University,·Sweden.</p> |
| 72 | </div></blockquote> | 72 | </div></blockquote> |
| 73 | <p>This·manual·is·not·complete·and·has·no·pretension·to·be·so·due | 73 | <p>This·manual·is·not·complete·and·has·no·pretension·to·be·so·due |
| 74 | to·lack·of·time·of·the·contributors·–·our·first·priority·is·to·improve | 74 | to·lack·of·time·of·the·contributors·–·our·first·priority·is·to·improve |
| 75 | the·software.·It·is·worked·on·continuously, | 75 | the·software.·It·is·worked·on·continuously, |
| Offset 25, 15 lines modified | Offset 25, 15 lines modified | ||
| 25 | Meulenhoff,·Teemu·Murtola,·Szilárd·Páll,·Sander·Pronk,·Roland·Schulz,·Michael | 25 | Meulenhoff,·Teemu·Murtola,·Szilárd·Páll,·Sander·Pronk,·Roland·Schulz,·Michael |
| 26 | Shirts,·Alexey·Shvetsov,·Alfons·Sijbers,·Peter·Tieleman,·Teemu·Virolainen, | 26 | Shirts,·Alexey·Shvetsov,·Alfons·Sijbers,·Peter·Tieleman,·Teemu·Virolainen, |
| 27 | Christian·Wennberg,·Maarten·Wolf,·and·Artem·Zhmurov. | 27 | Christian·Wennberg,·Maarten·Wolf,·and·Artem·Zhmurov. |
| 28 | Mark·Abraham,·Berk·Hess,·David·van·der·Spoel,·and·Erik·Lindahl. | 28 | Mark·Abraham,·Berk·Hess,·David·van·der·Spoel,·and·Erik·Lindahl. |
| 29 | ©·1991·â·2000: | 29 | ©·1991·â·2000: |
| 30 | ·····Department·of·Biophysical·Chemistry,·University·of·Groningen. | 30 | ·····Department·of·Biophysical·Chemistry,·University·of·Groningen. |
| 31 | ·····Nijenborgh·4,·9747·AG·Groningen,·The·Netherlands. | 31 | ·····Nijenborgh·4,·9747·AG·Groningen,·The·Netherlands. |
| 32 | ©·2001·â·202 | 32 | ©·2001·â·2024: |
| 33 | ·····The·GROMACS·development·teams·at·the·Royal·Institute·of·Technology | 33 | ·····The·GROMACS·development·teams·at·the·Royal·Institute·of·Technology |
| 34 | ·····and·Uppsala·University,·Sweden. | 34 | ·····and·Uppsala·University,·Sweden. |
| 35 | This·manual·is·not·complete·and·has·no·pretension·to·be·so·due·to·lack·of·time | 35 | This·manual·is·not·complete·and·has·no·pretension·to·be·so·due·to·lack·of·time |
| 36 | of·the·contributors·â·our·first·priority·is·to·improve·the·software.·It·is | 36 | of·the·contributors·â·our·first·priority·is·to·improve·the·software.·It·is |
| 37 | worked·on·continuously,·which·in·some·cases·might·mean·the·information·is·not | 37 | worked·on·continuously,·which·in·some·cases·might·mean·the·information·is·not |
| 38 | entirely·correct. | 38 | entirely·correct. |
| 39 | Comments·on·form·and·content·are·welcome,·please·send·them·to·one·of·the | 39 | Comments·on·form·and·content·are·welcome,·please·send·them·to·one·of·the |
| Offset 909, 16 lines modified | Offset 909, 16 lines modified | ||
| 909 | ········"2015":·[144,·145], | 909 | ········"2015":·[144,·145], |
| 910 | ········"2016":·[1,·145,·160,·161,·167,·168,·169,·170,·171,·178,·182], | 910 | ········"2016":·[1,·145,·160,·161,·167,·168,·169,·170,·171,·178,·182], |
| 911 | ········"2017":·[36,·145,·157,·158,·160,·182,·194], | 911 | ········"2017":·[36,·145,·157,·158,·160,·182,·194], |
| 912 | ········"2018":·[1,·25,·159,·176,·182,·183,·184,·185,·186,·187,·189,·191,·193,·201,·226], | 912 | ········"2018":·[1,·25,·159,·176,·182,·183,·184,·185,·186,·187,·189,·191,·193,·201,·226], |
| 913 | ········"2019":·[2,·4,·28,·145,·171,·172,·173,·174,·191,·197,·198,·199,·200,·201,·226], | 913 | ········"2019":·[2,·4,·28,·145,·171,·172,·173,·174,·191,·197,·198,·199,·200,·201,·226], |
| 914 | ········"2020":·[2,·24,·26,·36,·144,·187,·206], | 914 | ········"2020":·[2,·24,·26,·36,·144,·187,·206], |
| 915 | ········"2021":·[198,·201,·202,·212], | 915 | ········"2021":·[198,·201,·202,·212], |
| 916 | ········"2024":·174, | ||
| 917 | ········"202 | 916 | ········"2024":·[144,·174], |
| 917 | ········"2025":·155, | ||
| 918 | ········"2026":·181, | 918 | ········"2026":·181, |
| 919 | ········"2027":·181, | 919 | ········"2027":·181, |
| 920 | ········"2028":·181, | 920 | ········"2028":·181, |
| 921 | ········"2029":·155, | 921 | ········"2029":·155, |
| 922 | ········"2031":·174, | 922 | ········"2031":·174, |
| 923 | ········"2032":·[45,·145,·174], | 923 | ········"2032":·[45,·145,·174], |
| 924 | ········"2033":·155, | 924 | ········"2033":·155, |
| Offset 134, 19 lines modified | Offset 134, 19 lines modified | ||
| 134 | -rw-r--r--···0·root·········(0)·root·········(0)·····1722·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gmxapi/gmxapi-config-version.cmake | 134 | -rw-r--r--···0·root·········(0)·root·········(0)·····1722·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gmxapi/gmxapi-config-version.cmake |
| 135 | -rw-r--r--···0·root·········(0)·root·········(0)·····1181·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gmxapi/gmxapi-config.cmake | 135 | -rw-r--r--···0·root·········(0)·root·········(0)·····1181·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gmxapi/gmxapi-config.cmake |
| 136 | -rw-r--r--···0·root·········(0)·root·········(0)······940·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gmxapi/gmxapi-release.cmake | 136 | -rw-r--r--···0·root·········(0)·root·········(0)······940·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gmxapi/gmxapi-release.cmake |
| 137 | -rw-r--r--···0·root·········(0)·root·········(0)·····3281·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gmxapi/gmxapi.cmake | 137 | -rw-r--r--···0·root·········(0)·root·········(0)·····3281·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gmxapi/gmxapi.cmake |
| 138 | drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gromacs/ | 138 | drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gromacs/ |
| 139 | -rw-r--r--···0·root·········(0)·root·········(0)·····2025·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gromacs/gromacs-config-version.cmake | 139 | -rw-r--r--···0·root·········(0)·root·········(0)·····2025·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gromacs/gromacs-config-version.cmake |
| 140 | -rw-r--r--···0·root·········(0)·root·········(0)·····6217·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gromacs/gromacs-config.cmake | 140 | -rw-r--r--···0·root·········(0)·root·········(0)·····6217·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gromacs/gromacs-config.cmake |
| 141 | -rw-r--r--···0·root·········(0)·root·········(0)·····231 | 141 | -rw-r--r--···0·root·········(0)·root·········(0)·····2312·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gromacs/gromacs-toolchain.cmake |
| 142 | -rw-r--r--···0·root·········(0)·root·········(0)······855·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gromacs/libgromacs-release.cmake | 142 | -rw-r--r--···0·root·········(0)·root·········(0)······855·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gromacs/libgromacs-release.cmake |
| 143 | -rw-r--r--···0·root·········(0)·root·········(0)·····3592·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gromacs/libgromacs.cmake | 143 | -rw-r--r--···0·root·········(0)·root·········(0)·····3592·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gromacs/libgromacs.cmake |
| 144 | drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gromacs_d/ | 144 | drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gromacs_d/ |
| 145 | -rw-r--r--···0·root·········(0)·root·········(0)·····231 | 145 | -rw-r--r--···0·root·········(0)·root·········(0)·····2312·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gromacs_d/gromacs-toolchain_d.cmake |
| 146 | -rw-r--r--···0·root·········(0)·root·········(0)·····2025·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gromacs_d/gromacs_d-config-version.cmake | 146 | -rw-r--r--···0·root·········(0)·root·········(0)·····2025·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gromacs_d/gromacs_d-config-version.cmake |
| 147 | -rw-r--r--···0·root·········(0)·root·········(0)·····6222·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gromacs_d/gromacs_d-config.cmake | 147 | -rw-r--r--···0·root·········(0)·root·········(0)·····6222·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gromacs_d/gromacs_d-config.cmake |
| 148 | -rw-r--r--···0·root·········(0)·root·········(0)······861·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gromacs_d/libgromacs-release.cmake | 148 | -rw-r--r--···0·root·········(0)·root·········(0)······861·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gromacs_d/libgromacs-release.cmake |
| 149 | -rw-r--r--···0·root·········(0)·root·········(0)·····3592·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gromacs_d/libgromacs.cmake | 149 | -rw-r--r--···0·root·········(0)·root·········(0)·····3592·2021-03-29·04:45:03.000000·./usr/share/gromacs/cmake/gromacs_d/libgromacs.cmake |
| 150 | drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-03-29·04:45:03.000000·./usr/share/gromacs/template/ | 150 | drwxr-xr-x···0·root·········(0)·root·········(0)········0·2021-03-29·04:45:03.000000·./usr/share/gromacs/template/ |
| 151 | -rw-r--r--···0·root·········(0)·root·········(0)·····1851·2021-03-04·14:49:48.000000·./usr/share/gromacs/template/CMakeLists.txt | 151 | -rw-r--r--···0·root·········(0)·root·········(0)·····1851·2021-03-04·14:49:48.000000·./usr/share/gromacs/template/CMakeLists.txt |
| 152 | -rw-r--r--···0·root·········(0)·root·········(0)·····1196·2021-03-04·14:49:48.000000·./usr/share/gromacs/template/Makefile.pkg | 152 | -rw-r--r--···0·root·········(0)·root·········(0)·····1196·2021-03-04·14:49:48.000000·./usr/share/gromacs/template/Makefile.pkg |
| Offset 30, 15 lines modified | Offset 30, 15 lines modified | ||
| 30 | #·official·version·at·http://www.gromacs.org. | 30 | #·official·version·at·http://www.gromacs.org. |
| 31 | # | 31 | # |
| 32 | #·To·help·us·fund·GROMACS·development,·we·humbly·ask·that·you·cite | 32 | #·To·help·us·fund·GROMACS·development,·we·humbly·ask·that·you·cite |
| 33 | #·the·research·papers·on·the·package.·Check·out·http://www.gromacs.org. | 33 | #·the·research·papers·on·the·package.·Check·out·http://www.gromacs.org. |
| 34 | #·Setting·CMAKE_SYSTEM_NAME·tells·CMake·we·are·cross·compiling. | 34 | #·Setting·CMAKE_SYSTEM_NAME·tells·CMake·we·are·cross·compiling. |
| 35 | SET(CMAKE_SYSTEM_NAME·"Linux") | 35 | SET(CMAKE_SYSTEM_NAME·"Linux") |
| 36 | SET(CMAKE_SYSTEM_VERSION·"6. | 36 | SET(CMAKE_SYSTEM_VERSION·"6.1.0-17-amd64") |
| 37 | SET(CMAKE_C_COMPILER··"/usr/bin/cc") | 37 | SET(CMAKE_C_COMPILER··"/usr/bin/cc") |
| 38 | SET(CMAKE_CXX_COMPILER·"/usr/bin/c++") | 38 | SET(CMAKE_CXX_COMPILER·"/usr/bin/c++") |
| 39 | SET(CMAKE_LINKER·"/usr/bin/ld") | 39 | SET(CMAKE_LINKER·"/usr/bin/ld") |
| 40 | #·The·following·are·only·relevant·in·Mac·OS·X·environments. | 40 | #·The·following·are·only·relevant·in·Mac·OS·X·environments. |
| 41 | SET(CMAKE_OSX_DEPLOYMENT_TARGET·""·CACHE·STRING·"OS·X·Deployment·target"·FORCE) | 41 | SET(CMAKE_OSX_DEPLOYMENT_TARGET·""·CACHE·STRING·"OS·X·Deployment·target"·FORCE) |
| 42 | SET(CMAKE_OSX_ARCHITECTURES·"") | 42 | SET(CMAKE_OSX_ARCHITECTURES·"") |
| 43 | #·Ref:·https://stackoverflow.com/questions/32414112/setting-sdk-on-cross-compilation-to-osx-in-cmake | 43 | #·Ref:·https://stackoverflow.com/questions/32414112/setting-sdk-on-cross-compilation-to-osx-in-cmake |
| Offset 30, 15 lines modified | Offset 30, 15 lines modified | ||
| 30 | #·official·version·at·http://www.gromacs.org. | 30 | #·official·version·at·http://www.gromacs.org. |
| 31 | # | 31 | # |
| 32 | #·To·help·us·fund·GROMACS·development,·we·humbly·ask·that·you·cite | 32 | #·To·help·us·fund·GROMACS·development,·we·humbly·ask·that·you·cite |
| 33 | #·the·research·papers·on·the·package.·Check·out·http://www.gromacs.org. | 33 | #·the·research·papers·on·the·package.·Check·out·http://www.gromacs.org. |
| 34 | #·Setting·CMAKE_SYSTEM_NAME·tells·CMake·we·are·cross·compiling. | 34 | #·Setting·CMAKE_SYSTEM_NAME·tells·CMake·we·are·cross·compiling. |
| 35 | SET(CMAKE_SYSTEM_NAME·"Linux") | 35 | SET(CMAKE_SYSTEM_NAME·"Linux") |
| 36 | SET(CMAKE_SYSTEM_VERSION·"6. | 36 | SET(CMAKE_SYSTEM_VERSION·"6.1.0-17-amd64") |
| 37 | SET(CMAKE_C_COMPILER··"/usr/bin/cc") | 37 | SET(CMAKE_C_COMPILER··"/usr/bin/cc") |
| 38 | SET(CMAKE_CXX_COMPILER·"/usr/bin/c++") | 38 | SET(CMAKE_CXX_COMPILER·"/usr/bin/c++") |
| 39 | SET(CMAKE_LINKER·"/usr/bin/ld") | 39 | SET(CMAKE_LINKER·"/usr/bin/ld") |
| 40 | #·The·following·are·only·relevant·in·Mac·OS·X·environments. | 40 | #·The·following·are·only·relevant·in·Mac·OS·X·environments. |
| 41 | SET(CMAKE_OSX_DEPLOYMENT_TARGET·""·CACHE·STRING·"OS·X·Deployment·target"·FORCE) | 41 | SET(CMAKE_OSX_DEPLOYMENT_TARGET·""·CACHE·STRING·"OS·X·Deployment·target"·FORCE) |
| 42 | SET(CMAKE_OSX_ARCHITECTURES·"") | 42 | SET(CMAKE_OSX_ARCHITECTURES·"") |
| 43 | #·Ref:·https://stackoverflow.com/questions/32414112/setting-sdk-on-cross-compilation-to-osx-in-cmake | 43 | #·Ref:·https://stackoverflow.com/questions/32414112/setting-sdk-on-cross-compilation-to-osx-in-cmake |