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./usr/share/doc/gromacs/html/doxygen/html-full/todo.xhtml
'html2text' not available in path. Installing the 'html2text' package may produce better output.
    
Offset 76, 16 lines modifiedOffset 76, 16 lines modified
76 <dt>Member·<a·class="el"·href="classAtomProperties.xhtml#a076037cf4e1ac19d1dbab8bd405895e1">AtomProperties::atomNumberFromElement</a>··(const·char·*element)</dt>76 <dt>Member·<a·class="el"·href="classAtomProperties.xhtml#a076037cf4e1ac19d1dbab8bd405895e1">AtomProperties::atomNumberFromElement</a>··(const·char·*element)</dt>
77 <dd><a·class="anchor"·id="_todo000212"></a>This·should·be·made·const·once·the·lazy·implementation·is·done·properly·for·the·class.··</dd>77 <dd><a·class="anchor"·id="_todo000212"></a>This·should·be·made·const·once·the·lazy·implementation·is·done·properly·for·the·class.··</dd>
78 <dt>Member·<a·class="el"·href="classAtomProperties.xhtml#aa128b4b7662a21b904b8642eead5bfdd">AtomProperties::elementFromAtomNumber</a>··(int·atomNumber)</dt>78 <dt>Member·<a·class="el"·href="classAtomProperties.xhtml#aa128b4b7662a21b904b8642eead5bfdd">AtomProperties::elementFromAtomNumber</a>··(int·atomNumber)</dt>
79 <dd><a·class="anchor"·id="_todo000211"></a>This·should·be·made·const·once·the·lazy·implementation·is·done·properly·for·the·class.··</dd>79 <dd><a·class="anchor"·id="_todo000211"></a>This·should·be·made·const·once·the·lazy·implementation·is·done·properly·for·the·class.··</dd>
80 <dt>Class·<a·class="el"·href="structBondedInteractionList.xhtml">BondedInteractionList</a>··</dt>80 <dt>Class·<a·class="el"·href="structBondedInteractionList.xhtml">BondedInteractionList</a>··</dt>
81 <dd><a·class="anchor"·id="_todo000048"></a>This·should·be·merged·with·<a·class="el"·href="structBondedInteraction.xhtml"·title="Information·about·single·bonded·interaction.">BondedInteraction</a>.··</dd>81 <dd><a·class="anchor"·id="_todo000048"></a>This·should·be·merged·with·<a·class="el"·href="structBondedInteraction.xhtml"·title="Information·about·single·bonded·interaction.">BondedInteraction</a>.··</dd>
82 <dt>File·<a·class="el"·href="boxdeformation_8cpp.xhtml">boxdeformation.cpp</a>··</dt>82 <dt>File·<a·class="el"·href="boxdeformation_8cpp.xhtml">boxdeformation.cpp</a>··</dt>
 83 <dd><p·class="startdd"><a·class="anchor"·id="_todo000078"></a>The·.mdp·specification·should·have·a·boolean·for·this·module.</p>
83 <dd><p·class="startdd"><a·class="anchor"·id="_todo000079"></a>grompp·should·set·up·fields·in·the·tpr·file·that·carry·the·information·about·the·original·box,·then·the·deform·module·would·can·be·build·alongside·the·update·module,·rather·than·need·to·be·set·up[·...·truncated·by·diffoscope;·len:·31,·SHA:·a32a9b5ab7b26482853043350da758d04dc106bbae914b30910014039e02c87b·...·]</p>84 <p·class="enddd"><a·class="anchor"·id="_todo000079"></a>grompp·should·set·up·fields·in·the·tpr·file·that·carry·the·information·about·the·original·box,·then·the·deform·module·would·can·be·build·alongside·the·update·module,·rather·than·need·to·be·set·up·befor[·...·truncated·by·diffoscope;·len:·26,·SHA:·421d8e1e7cbd3a6d4bb9043fed77c0e1b31ce0a2431f0d067268694a13f4dca0·...·]</p>
84 <p·class="enddd"><a·class="anchor"·id="_todo000078"></a>The·.mdp·specification·should·have·a·boolean·for·this·module.·</p> 
85 </dd>85 </dd>
86 <dt>Member·<a·class="el"·href="gpu__utils_8h.xhtml#a7211e54946ef7b5f5ac17a321fc03b9b">buildSupportsNonbondedOnGpu</a>··(std::string·*error)</dt>86 <dt>Member·<a·class="el"·href="gpu__utils_8h.xhtml#a7211e54946ef7b5f5ac17a321fc03b9b">buildSupportsNonbondedOnGpu</a>··(std::string·*error)</dt>
87 <dd><a·class="anchor"·id="_todo000057"></a>Move·this·to·NB·module·once·it·exists.··</dd>87 <dd><a·class="anchor"·id="_todo000057"></a>Move·this·to·NB·module·once·it·exists.··</dd>
88 <dt>Member·<a·class="el"·href="pme__gpu__constants_8h.xhtml#a295a71bb82bf73b07e0d215e454e46df">c_skipNeutralAtoms</a>··</dt>88 <dt>Member·<a·class="el"·href="pme__gpu__constants_8h.xhtml#a295a71bb82bf73b07e0d215e454e46df">c_skipNeutralAtoms</a>··</dt>
89 <dd><a·class="anchor"·id="_todo000039"></a>Estimate·performance·differences.··</dd>89 <dd><a·class="anchor"·id="_todo000039"></a>Estimate·performance·differences.··</dd>
90 <dt>Member·<a·class="el"·href="pme__gpu__constants_8h.xhtml#afae4fdf525a12645d708b29293436df0">c_usePadding</a>··</dt>90 <dt>Member·<a·class="el"·href="pme__gpu__constants_8h.xhtml#afae4fdf525a12645d708b29293436df0">c_usePadding</a>··</dt>
91 <dd><a·class="anchor"·id="_todo000038"></a>Estimate·performance·differences··</dd>91 <dd><a·class="anchor"·id="_todo000038"></a>Estimate·performance·differences··</dd>
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94 <dt>Member·<a·class="el"·href="pme__gpu__internal_8cpp.xhtml#a1d116c3487f18ead5ae5bc36bda98a37">checkDeviceBuffer</a>··(DeviceBuffer&lt;·T·&gt;·buffer,·int·requiredSize)</dt>94 <dt>Member·<a·class="el"·href="pme__gpu__internal_8cpp.xhtml#a1d116c3487f18ead5ae5bc36bda98a37">checkDeviceBuffer</a>··(DeviceBuffer&lt;·T·&gt;·buffer,·int·requiredSize)</dt>
95 <dd><a·class="anchor"·id="_todo000040"></a>Split·and·move·this·function·to·gpu_utils.·</dd>95 <dd><a·class="anchor"·id="_todo000040"></a>Split·and·move·this·function·to·gpu_utils.·</dd>
96 <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>96 <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>
97 <dd><a·class="anchor"·id="_todo000049"></a>Remove·once·constructor/destructor·takes·care·of·all·of·this.··</dd>97 <dd><a·class="anchor"·id="_todo000049"></a>Remove·once·constructor/destructor·takes·care·of·all·of·this.··</dd>
98 <dt>File·<a·class="el"·href="clustsize_8cpp.xhtml">clustsize.cpp</a>··</dt>98 <dt>File·<a·class="el"·href="clustsize_8cpp.xhtml">clustsize.cpp</a>··</dt>
99 <dd><a·class="anchor"·id="_todo000218"></a>These·will·be·superseded·by·tests·of·the·new·style·analysis·modules.·</dd>99 <dd><a·class="anchor"·id="_todo000218"></a>These·will·be·superseded·by·tests·of·the·new·style·analysis·modules.·</dd>
100 <dt>File·<a·class="el"·href="compiler_8cpp.xhtml">compiler.cpp</a>··</dt>100 <dt>File·<a·class="el"·href="compiler_8cpp.xhtml">compiler.cpp</a>··</dt>
101 <dd><p·class="startdd"><a·class="anchor"·id="_todo000183"></a>·Better·error·handling·and·memory·management·in·error·situations.·At·least,·the·main·compilation·function·leaves·the·selection·collection·in·a·bad·state·if·an·error·occurs.</p> 
102 <p·class="enddd"><a·class="anchor"·id="_todo000184"></a>·The·memory·usage·could·still·be·optimized.·Use·of·memory·pooling·could·still·be·extended,·and·a·lot·of·redundant·gmin/gmax·data·could·be·eliminated·for·complex·arithmetic·expressions.·</p>101 <dd><p·class="startdd"><a·class="anchor"·id="_todo000184"></a>·The·memory·usage·could·still·be·optimized.·Use·of·memory·pooling·could·still·be·extended,·and·a·lot·of·redundant·gmin/gmax·data·could·be·eliminated·for·complex·arithmetic·expressions.</p>
 102 <p·class="enddd"><a·class="anchor"·id="_todo000183"></a>·Better·error·handling·and·memory·management·in·error·situations.·At·least,·the·main·compilation·function·leaves·the·selection·collection·in·a·bad·state·if·an·error·occurs.·</p>
103 </dd>103 </dd>
104 <dt>File·<a·class="el"·href="tests_2constr_8cpp.xhtml">constr.cpp</a>··</dt>104 <dt>File·<a·class="el"·href="tests_2constr_8cpp.xhtml">constr.cpp</a>··</dt>
105 <dd><p·class="startdd"><a·class="anchor"·id="_todo000095"></a>Better·tests·for·virial·are·needed.·</p>105 <dd><p·class="startdd"><a·class="anchor"·id="_todo000095"></a>Better·tests·for·virial·are·needed.·</p>
106 <p·class="interdd">Tests·for·bigger·systems·to·test·threads·synchronization,·reduction,·etc.·on·the·GPU.·</p>106 <p·class="interdd">Tests·for·bigger·systems·to·test·threads·synchronization,·reduction,·etc.·on·the·GPU.·</p>
107 <p·class="interdd">Tests·for·algorithms·for·derivatives.·</p>107 <p·class="interdd">Tests·for·algorithms·for·derivatives.·</p>
108 <p·class="enddd">Free-energy·perturbation·tests·</p>108 <p·class="enddd">Free-energy·perturbation·tests·</p>
109 </dd>109 </dd>
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214 <dt>Member·<a·class="el"·href="namespacegmx.xhtml#a14ac652392d2a98ce5a3b3a3ca809206">gmx::getPageSize</a>··()</dt>214 <dt>Member·<a·class="el"·href="namespacegmx.xhtml#a14ac652392d2a98ce5a3b3a3ca809206">gmx::getPageSize</a>··()</dt>
215 <dd><a·class="anchor"·id="_todo000221"></a>Move·this·function·into·<a·class="el"·href="sysinfo_8cpp.xhtml"·title="Implements·functions·from·sysinfo.h.">sysinfo.cpp</a>·where·other·OS-specific·code/includes·live··</dd>215 <dd><a·class="anchor"·id="_todo000221"></a>Move·this·function·into·<a·class="el"·href="sysinfo_8cpp.xhtml"·title="Implements·functions·from·sysinfo.h.">sysinfo.cpp</a>·where·other·OS-specific·code/includes·live··</dd>
216 <dt>Member·<a·class="el"·href="classgmx_1_1GpuTaskAssignments.xhtml#a414447baa42eb2d6deabe6fe4bd64ff3">gmx::GpuTaskAssignments::initNonbondedDevice</a>··(const·t_commrec·*cr)·const</dt>216 <dt>Member·<a·class="el"·href="classgmx_1_1GpuTaskAssignments.xhtml#a414447baa42eb2d6deabe6fe4bd64ff3">gmx::GpuTaskAssignments::initNonbondedDevice</a>··(const·t_commrec·*cr)·const</dt>
217 <dd><a·class="anchor"·id="_todo000209"></a>This·also·sets·up·DLB·for·device·sharing,·where·appropriate,·but·that·responsbility·should·move·elsewhere.··</dd>217 <dd><a·class="anchor"·id="_todo000209"></a>This·also·sets·up·DLB·for·device·sharing,·where·appropriate,·but·that·responsbility·should·move·elsewhere.··</dd>
218 <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>·&amp;mdlog,·bool·printHostName,·bool·useGpuForBonded,·PmeRunMode·pmeRunMode,·bool·useGpuForUpdate)</dt>218 <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>·&amp;mdlog,·bool·printHostName,·bool·useGpuForBonded,·PmeRunMode·pmeRunMode,·bool·useGpuForUpdate)</dt>
219 <dd><a·class="anchor"·id="_todo000208"></a>It·could·be·useful·to·report·also·whether·any·nodes·differed,·and·in·what·way.·</dd>219 <dd><a·class="anchor"·id="_todo000208"></a>It·could·be·useful·to·report·also·whether·any·nodes·differed,·and·in·what·way.·</dd>
220 <dt>Class·<a·class="el"·href="classgmx_1_1GpuTaskAssignmentsBuilder.xhtml">gmx::GpuTaskAssignmentsBuilder</a>··</dt>220 <dt>Class·<a·class="el"·href="classgmx_1_1GpuTaskAssignmentsBuilder.xhtml">gmx::GpuTaskAssignmentsBuilder</a>··</dt>
 221 <dd><p·class="startdd"><a·class="anchor"·id="_todo000207"></a>Later·we·might·need·the·concept·of·computeTasksOnThisRank,·from·which·we·construct·gpuTasksOnThisRank.</p>
221 <dd><p·class="startdd"><a·class="anchor"·id="_todo000206"></a>Later,·this·might·become·a·loop·over·all·registered·modules·relevant·to·the·mdp·inputs,·to·find·those·that·have·such·tasks.</p>222 <p·class="enddd"><a·class="anchor"·id="_todo000206"></a>Later,·this·might·become·a·loop·over·all·registered·modules·relevant·to·the·mdp·inputs,·to·find·those·that·have·such·tasks.·</p>
222 <p·class="enddd"><a·class="anchor"·id="_todo000207"></a>Later·we·might·need·the·concept·of·computeTasksOnThisRank,·from·which·we·construct·gpuTasksOnThisRank.·</p> 
223 </dd>223 </dd>
224 <dt>Member·<a·class="el"·href="classgmx_1_1GromacsException.xhtml#a1bd116912e67c096ae949ddae85afe06">gmx::GromacsException::prependContext</a>··(const·std::string·&amp;context)</dt>224 <dt>Member·<a·class="el"·href="classgmx_1_1GromacsException.xhtml#a1bd116912e67c096ae949ddae85afe06">gmx::GromacsException::prependContext</a>··(const·std::string·&amp;context)</dt>
225 <dd><a·class="anchor"·id="_todo000227"></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>225 <dd><a·class="anchor"·id="_todo000227"></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>
226 <dt>Member·<a·class="el"·href="classgmx_1_1HelpWriterContext.xhtml#a6bec872f46ecd34601df72141fca3739">gmx::HelpWriterContext::setReplacement</a>··(const·std::string·&amp;search,·const·std::string·&amp;replace)</dt>226 <dt>Member·<a·class="el"·href="classgmx_1_1HelpWriterContext.xhtml#a6bec872f46ecd34601df72141fca3739">gmx::HelpWriterContext::setReplacement</a>··(const·std::string·&amp;search,·const·std::string·&amp;replace)</dt>
227 <dd><a·class="anchor"·id="_todo000168"></a>·Improve·semantics·if·the·same·<code>search</code>·item·is·set·multiple·times.··</dd>227 <dd><a·class="anchor"·id="_todo000168"></a>·Improve·semantics·if·the·same·<code>search</code>·item·is·set·multiple·times.··</dd>
228 <dt>Class·<a·class="el"·href="classgmx_1_1HostAllocationPolicy.xhtml">gmx::HostAllocationPolicy</a>··</dt>228 <dt>Class·<a·class="el"·href="classgmx_1_1HostAllocationPolicy.xhtml">gmx::HostAllocationPolicy</a>··</dt>
229 <dd><a·class="anchor"·id="_todo000059"></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>229 <dd><a·class="anchor"·id="_todo000059"></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>
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374 <dd><a·class="anchor"·id="_todo000220"></a>This·should·throw·upon·error·but·currently·does·not.··</dd>374 <dd><a·class="anchor"·id="_todo000220"></a>This·should·throw·upon·error·but·currently·does·not.··</dd>
375 <dt>Class·<a·class="el"·href="classgmx_1_1TrajectoryAnalysisSettings.xhtml">gmx::TrajectoryAnalysisSettings</a>··</dt>375 <dt>Class·<a·class="el"·href="classgmx_1_1TrajectoryAnalysisSettings.xhtml">gmx::TrajectoryAnalysisSettings</a>··</dt>
376 <dd><a·class="anchor"·id="_todo000216"></a>·Remove·plain·flags·from·the·public·interface.·</dd>376 <dd><a·class="anchor"·id="_todo000216"></a>·Remove·plain·flags·from·the·public·interface.·</dd>
377 <dt>Class·<a·class="el"·href="classgmx_1_1TrajectoryFrame.xhtml">gmx::TrajectoryFrame</a>··</dt>377 <dt>Class·<a·class="el"·href="classgmx_1_1TrajectoryFrame.xhtml">gmx::TrajectoryFrame</a>··</dt>
378 <dd><p·class="startdd"><a·class="anchor"·id="_todo000214"></a>Eventually·t_trxframe·should·be·replaced·by·a·class·such·as·this.·Currently·we·need·to·introduce·BoxMatrix·so·that·we·can·have·a·normal·C++·getter·that·returns·the·contents·of·a·box·matrix,·since·you·cannot·use·a·real[DIM][DIM]·as·a·function·return·type.</p>378 <dd><p·class="startdd"><a·class="anchor"·id="_todo000214"></a>Eventually·t_trxframe·should·be·replaced·by·a·class·such·as·this.·Currently·we·need·to·introduce·BoxMatrix·so·that·we·can·have·a·normal·C++·getter·that·returns·the·contents·of·a·box·matrix,·since·you·cannot·use·a·real[DIM][DIM]·as·a·function·return·type.</p>
379 <p·class="enddd"><a·class="anchor"·id="_todo000215"></a>Consider·a·std::optional·work-alike·type·for·expressing·that·a·field·may·or·may·not·have·content.··</p>379 <p·class="enddd"><a·class="anchor"·id="_todo000215"></a>Consider·a·std::optional·work-alike·type·for·expressing·that·a·field·may·or·may·not·have·content.··</p>
380 </dd>380 </dd>
381 <dt>Member·<a·class="el"·href="group__module__utility.xhtml#ga33e34477bae2bbb86c4d9af1823e3fd0">GMX_UNUSED_VALUE</a>··(value)</dt> 
382 <dd><a·class="anchor"·id="_todo000223"></a>Deprecated·-·use·gmx_unused··</dd> 
383 <dt>Class·<a·class="el"·href="classGpuParallel3dFft.xhtml">GpuParallel3dFft</a>··</dt> 
384 <dd><a·class="anchor"·id="_todo000036"></a>Make·this·class·actually·parallel·over·multiple·GPUs··</dd> 
385 <dt>File·<a·class="el"·href="handlerestart_8cpp.xhtml">handlerestart.cpp</a>··</dt> 
386 <dd><a·class="anchor"·id="_todo000133"></a>Clean·up·the·error-prone·logic·here.·Add·doxygen.·</dd> 
387 <dt>Member·<a·class="el"·href="manage__threading_8h.xhtml#ac33f2fc3d292ac10c5bfd0f1b2f0e4c8">init_bonded_threading</a>··(FILE·*fplog,·int·nenergrp)</dt> 
388 <dd><a·class="anchor"·id="_todo000072"></a>Avoid·explicit·pointers·by·using·Impl··</dd> 
389 <dt>File·<a·class="el"·href="tests_2invertmatrix_8cpp.xhtml">invertmatrix.cpp</a>··</dt> 
390 <dd><a·class="anchor"·id="_todo000076"></a>Test·error·conditions·when·they·throw·exceptions·</dd> 
391 <dt>File·<a·class="el"·href="leapfrogtestdata_8h.xhtml">leapfrogtestdata.h</a>··</dt> 
392 <dd><p·class="startdd"><a·class="anchor"·id="_todo000100"></a>Add·anisotropic·Parrinello-Rahman·and·other·pressure·coupling·schemes·</p> 
393 <p·class="interdd">Add·PBC·handling·test.·</p> 
394 <p·class="enddd">Reference·values·tests.·</p> 
395 </dd> 
396 <dt>File·<a·class="el"·href="legacyenergy_8cpp.xhtml">legacyenergy.cpp</a>··</dt> 
397 <dd><a·class="anchor"·id="_todo000030"></a>These·will·be·superseded·by·tests·of·the·energyanalysis·modules.·</dd> 
398 <dt>Module·<a·class="el"·href="group__module__modularsimulator.xhtml">module_modularsimulator</a>··</dt> 
399 <dd><a·class="anchor"·id="_todo000158"></a>Can·we·link·to·<code>docs/doxygen/lib/modularsimulator.md</code>?·</dd> 
400 <dt>Member·<a·class="el"·href="gpu__common_8h.xhtml#a698b6896c99fc213ac9ab38b8faac04f">Nbnxm::gpu_try_finish_task</a>··(gmx_nbnxn_gpu_t·*nb,·const·<a·class="el"·href="classgmx_1_1StepWorkload.xhtml"·title="Describes·work·done·on·this·domain·that·may·change·per-step.">gmx::StepWorkload</a>·&amp;stepWork,·const·AtomLocality·aloc,·real·*e_lj,·real·*e_el,·gmx::ArrayRef&lt;·gmx::RVec·&gt;·shiftForces,·GpuTaskCompletion·completionKind,·gmx_wallcycle·*wcycle)</dt> 
401 <dd><a·class="anchor"·id="_todo000163"></a>Move·into·shared·source·file·with·gmx_compile_cpp_as_cuda··</dd> 
402 <dt>Member·<a·class="el"·href="classNbnxm_1_1Grid.xhtml#a58ada6a17d7e2871e65099282736e32c">Nbnxm::Grid::cxy_ind</a>··()·const</dt> 
403 <dd><a·class="anchor"·id="_todo000165"></a>Needs·a·useful·name.··</dd> 
404 <dt>Member·<a·class="el"·href="classNbnxm_1_1Grid.xhtml#ae8c91c06759a34caa88b92b47a012d21">Nbnxm::Grid::cxy_na</a>··()·const</dt> 
405 <dd><a·class="anchor"·id="_todo000164"></a>Needs·a·useful·name.··</dd> 
406 <dt>Class·<a·class="el"·href="structgmx__gpu__info__t.xhtml">gmx_gpu_info_t</a>··</dt>381 <dt>Class·<a·class="el"·href="structgmx__gpu__info__t.xhtml">gmx_gpu_info_t</a>··</dt>
407 <dd><a·class="anchor"·id="_todo000065"></a>Use·a·std::vector··</dd>382 <dd><a·class="anchor"·id="_todo000065"></a>Use·a·std::vector··</dd>
408 <dt>Class·<a·class="el"·href="structgmx__hw__opt__t.xhtml">gmx_hw_opt_t</a>··</dt>383 <dt>Class·<a·class="el"·href="structgmx__hw__opt__t.xhtml">gmx_hw_opt_t</a>··</dt>
409 <dd><a·class="anchor"·id="_todo000066"></a>During·mdrunner(),·if·the·user·has·left·any·of·these·values·at·their·defaults·(which·tends·to·mean·"choose·automatically"),·then·those·values·are·over-written·with·the·result·of·such·automation.·This·creates·problems·for·the·subsequent·code·in·knowing·what·was·done,·why,·and·reporting·correctly·to·the·user.·Find·a·way·to·improve·this.··</dd>384 <dd><a·class="anchor"·id="_todo000066"></a>During·mdrunner(),·if·the·user·has·left·any·of·these·values·at·their·defaults·(which·tends·to·mean·"choose·automatically"),·then·those·values·are·over-written·with·the·result·of·such·automation.·This·creates·problems·for·the·subsequent·code·in·knowing·what·was·done,·why,·and·reporting·correctly·to·the·user.·Find·a·way·to·improve·this.··</dd>
410 <dt>Class·<a·class="el"·href="structgmx__multisim__t.xhtml">gmx_multisim_t</a>··</dt>385 <dt>Class·<a·class="el"·href="structgmx__multisim__t.xhtml">gmx_multisim_t</a>··</dt>
411 <dd><a·class="anchor"·id="_todo000136"></a>Change·this·to·class··</dd>386 <dd><a·class="anchor"·id="_todo000136"></a>Change·this·to·class··</dd>
412 <dt>Member·<a·class="el"·href="pme_8h.xhtml#ad5f423fc236c4c689352980cfe4a3706">gmx_pme_init</a>··(const·t_commrec·*cr,·const·<a·class="el"·href="structNumPmeDomains.xhtml"·title="Struct·for·passing·around·the·number·of·PME·domains.">NumPmeDomains</a>·&amp;numPmeDomains,·const·t_inputrec·*ir,·gmx_bool·bFreeEnergy_q,·gmx_bool·bFreeEnergy_lj,·gmx_bool·bReproducible,·real·ewaldcoeff_q,·real·ewaldcoeff_lj,·int·nthread,·PmeRunMode·runMode,·<a·class="el"·href="structPmeGpu.xhtml"·title="The·main·PME·GPU·host·structure,·included·in·the·PME·CPU·structure·by·pointer.">PmeGpu</a>·*pmeGpu,·const·<a·class="el"·href="structgmx__device__info__t.xhtml"·title="OpenCL·device·information.">gmx_device_info_t</a>·*gpuInfo,·PmeGpuProgramHandle·pmeGpuProgram,·const·<a·class="el"·href="classgmx_1_1MDLogger.xhtml"·title="Declares·a·logging·interface.">gmx::MDLogger</a>·&amp;mdlog)</dt>387 <dt>Member·<a·class="el"·href="pme_8h.xhtml#ad5f423fc236c4c689352980cfe4a3706">gmx_pme_init</a>··(const·t_commrec·*cr,·const·<a·class="el"·href="structNumPmeDomains.xhtml"·title="Struct·for·passing·around·the·number·of·PME·domains.">NumPmeDomains</a>·&amp;numPmeDomains,·const·t_inputrec·*ir,·gmx_bool·bFreeEnergy_q,·gmx_bool·bFreeEnergy_lj,·gmx_bool·bReproducible,·real·ewaldcoeff_q,·real·ewaldcoeff_lj,·int·nthread,·PmeRunMode·runMode,·<a·class="el"·href="structPmeGpu.xhtml"·title="The·main·PME·GPU·host·structure,·included·in·the·PME·CPU·structure·by·pointer.">PmeGpu</a>·*pmeGpu,·const·<a·class="el"·href="structgmx__device__info__t.xhtml"·title="OpenCL·device·information.">gmx_device_info_t</a>·*gpuInfo,·PmeGpuProgramHandle·pmeGpuProgram,·const·<a·class="el"·href="classgmx_1_1MDLogger.xhtml"·title="Declares·a·logging·interface.">gmx::MDLogger</a>·&amp;mdlog)</dt>
413 <dd><a·class="anchor"·id="_todo000032"></a>We·should·evolve·something·like·a·<code>GpuManager</code>·that·holds·<code><a·class="el"·href="structgmx__device__info__t.xhtml"·title="OpenCL·device·information.">gmx_device_info_t</a></code>·*·and·<code>PmeGpuProgramHandle</code>·and·perhaps·other·related·things·whose·lifetime·can/should·exceed·that·of·a·task·(or·perhaps·task·manager).·See·Redmine·#2522.··</dd>388 <dd><a·class="anchor"·id="_todo000032"></a>We·should·evolve·something·like·a·<code>GpuManager</code>·that·holds·<code><a·class="el"·href="structgmx__device__info__t.xhtml"·title="OpenCL·device·information.">gmx_device_info_t</a></code>·*·and·<code>PmeGpuProgramHandle</code>·and·perhaps·other·related·things·whose·lifetime·can/should·exceed·that·of·a·task·(or·perhaps·task·manager).·See·Redmine·#2522.··</dd>
 389 <dt>Member·<a·class="el"·href="group__module__utility.xhtml#ga33e34477bae2bbb86c4d9af1823e3fd0">GMX_UNUSED_VALUE</a>··(value)</dt>
 390 <dd><a·class="anchor"·id="_todo000223"></a>Deprecated·-·use·gmx_unused··</dd>
414 <dt>File·<a·class="el"·href="gpu__testutils_8h.xhtml">gpu_testutils.h</a>··</dt>391 <dt>File·<a·class="el"·href="gpu__testutils_8h.xhtml">gpu_testutils.h</a>··</dt>
415 <dd><a·class="anchor"·id="_todo000056"></a>This·should·eventually·go·to·src/testutils·</dd>392 <dd><a·class="anchor"·id="_todo000056"></a>This·should·eventually·go·to·src/testutils·</dd>
 393 <dt>Class·<a·class="el"·href="classGpuParallel3dFft.xhtml">GpuParallel3dFft</a>··</dt>
 394 <dd><a·class="anchor"·id="_todo000036"></a>Make·this·class·actually·parallel·over·multiple·GPUs··</dd>
416 <dt>File·<a·class="el"·href="awh_2grid_8h.xhtml">grid.h</a>··</dt>395 <dt>File·<a·class="el"·href="awh_2grid_8h.xhtml">grid.h</a>··</dt>
417 <dd><a·class="anchor"·id="_todo000015"></a>:·Replace·this·by·a·more·generic·grid·class·once·that·is·available.·</dd>396 <dd><a·class="anchor"·id="_todo000015"></a>:·Replace·this·by·a·more·generic·grid·class·once·that·is·available.·</dd>
418 <dt>File·<a·class="el"·href="programs_2mdrun_2tests_2grompp_8cpp.xhtml">grompp.cpp</a>··</dt>397 <dt>File·<a·class="el"·href="programs_2mdrun_2tests_2grompp_8cpp.xhtml">grompp.cpp</a>··</dt>
419 <dd><a·class="anchor"·id="_todo000240"></a>Refactor·SimulationRunner·to·split·off·SimulationPreparer,·so·that·integration·tests·of·grompp·can·stand·apart·from·tests·of·mdrun.·</dd>398 <dd><a·class="anchor"·id="_todo000240"></a>Refactor·SimulationRunner·to·split·off·SimulationPreparer,·so·that·integration·tests·of·grompp·can·stand·apart·from·tests·of·mdrun.·</dd>
 399 <dt>File·<a·class="el"·href="handlerestart_8cpp.xhtml">handlerestart.cpp</a>··</dt>
 400 <dd><a·class="anchor"·id="_todo000133"></a>Clean·up·the·error-prone·logic·here.·Add·doxygen.·</dd>
420 <dt>File·<a·class="el"·href="handlerestart_8h.xhtml">handlerestart.h</a>··</dt>401 <dt>File·<a·class="el"·href="handlerestart_8h.xhtml">handlerestart.h</a>··</dt>
421 <dd><a·class="anchor"·id="_todo000135"></a>There·may·be·other·code·in·<a·class="el"·href="runner_8cpp.xhtml"·title="Implements·the·MD·runner·routine·calling·all·integrators.">runner.cpp</a>·etc.·that·can·usefully·live·here·</dd>402 <dd><a·class="anchor"·id="_todo000135"></a>There·may·be·other·code·in·<a·class="el"·href="runner_8cpp.xhtml"·title="Implements·the·MD·runner·routine·calling·all·integrators.">runner.cpp</a>·etc.·that·can·usefully·live·here·</dd>
422 <dt>Class·<a·class="el"·href="classhistory__t.xhtml">history_t</a>··</dt>403 <dt>Class·<a·class="el"·href="classhistory__t.xhtml">history_t</a>··</dt>
423 <dd><a·class="anchor"·id="_todo000138"></a>Rename·this·with·a·more·descriptive·name.··</dd>404 <dd><a·class="anchor"·id="_todo000138"></a>Rename·this·with·a·more·descriptive·name.··</dd>
424 <dt>File·<a·class="el"·href="hostallocator_8h.xhtml">hostallocator.h</a>··</dt>405 <dt>File·<a·class="el"·href="hostallocator_8h.xhtml">hostallocator.h</a>··</dt>
425 <dd><a·class="anchor"·id="_todo000058"></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>406 <dd><a·class="anchor"·id="_todo000058"></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>
426 <dt>File·<a·class="el"·href="tests_2indexutil_8cpp.xhtml">indexutil.cpp</a>··</dt>407 <dt>File·<a·class="el"·href="tests_2indexutil_8cpp.xhtml">indexutil.cpp</a>··</dt>
427 <dd><a·class="anchor"·id="_todo000203"></a>·Tests·for·other·functions,·at·least·the·set·operations.·</dd>408 <dd><a·class="anchor"·id="_todo000203"></a>·Tests·for·other·functions,·at·least·the·set·operations.·</dd>
 409 <dt>Member·<a·class="el"·href="manage__threading_8h.xhtml#ac33f2fc3d292ac10c5bfd0f1b2f0e4c8">init_bonded_threading</a>··(FILE·*fplog,·int·nenergrp)</dt>
 410 <dd><a·class="anchor"·id="_todo000072"></a>Avoid·explicit·pointers·by·using·Impl··</dd>
 411 <dt>File·<a·class="el"·href="tests_2invertmatrix_8cpp.xhtml">invertmatrix.cpp</a>··</dt>
 412 <dd><a·class="anchor"·id="_todo000076"></a>Test·error·conditions·when·they·throw·exceptions·</dd>
428 <dt>File·<a·class="el"·href="iserializer_8h.xhtml">iserializer.h</a>··</dt>413 <dt>File·<a·class="el"·href="iserializer_8h.xhtml">iserializer.h</a>··</dt>
429 <dd><a·class="anchor"·id="_todo000229"></a>Generalize·and·transfer·serialization·functionality·used·in·mrc·density·file·header·serialization·to·here.·</dd>414 <dd><a·class="anchor"·id="_todo000229"></a>Generalize·and·transfer·serialization·functionality·used·in·mrc·density·file·header·serialization·to·here.·</dd>
430 <dt>File·<a·class="el"·href="leapfrog_8cpp.xhtml">leapfrog.cpp</a>··</dt>415 <dt>File·<a·class="el"·href="leapfrog_8cpp.xhtml">leapfrog.cpp</a>··</dt>
431 <dd><p·class="startdd"><a·class="anchor"·id="_todo000099"></a>Add·tests·for·integrators·with·pressure·control.·</p>416 <dd><p·class="startdd"><a·class="anchor"·id="_todo000099"></a>Add·tests·for·integrators·with·pressure·control.·</p>
432 <p·class="enddd">Add·PBC·handling·test.·</p>417 <p·class="enddd">Add·PBC·handling·test.·</p>
433 </dd>418 </dd>
 419 <dt>File·<a·class="el"·href="leapfrogtestdata_8h.xhtml">leapfrogtestdata.h</a>··</dt>
 420 <dd><p·class="startdd"><a·class="anchor"·id="_todo000100"></a>Add·anisotropic·Parrinello-Rahman·and·other·pressure·coupling·schemes·</p>
 421 <p·class="interdd">Add·PBC·handling·test.·</p>
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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>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>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·&amp;module)</dt>96 <dt>Member·<a·class="el"·href="classgmx_1_1AbstractAnalysisData.xhtml#a90b99e3f700dbb8992a2d65a6b2a6de5">gmx::AbstractAnalysisData::addColumnModule</a>··(int·col,·int·span,·const·AnalysisDataModulePointer·&amp;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>
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="_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_1AbstractAn[·...·truncated·by·diffoscope;·len:·152,·SHA:·6ebbdc2ec1fc0b0a624288debca515967d2a0023d363bf81d33be7d735642a3d·...·]</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> 
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>113 <dd><p·class="startdd"><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·tha[·...·truncated·by·diffoscope;·len:·275,·SHA:·440e0e8105e5a2157dc7353c549099f6836703b229364c7ad151f6d2d0b0790a·...·]</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&lt;·T·&gt;</a>··</dt>116 <dt>Class·<a·class="el"·href="classgmx_1_1ArrayRef.xhtml">gmx::ArrayRef&lt;·T·&gt;</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>·&amp;gpu_info,·const·std::vector&lt;·int·&gt;·&amp;compatibleGpus,·const·std::vector&lt;·int·&gt;·&amp;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>·&amp;gpu_info,·const·std::vector&lt;·int·&gt;·&amp;compatibleGpus,·const·std::vector&lt;·int·&gt;·&amp;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>
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="_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·constr[·...·truncated·by·diffoscope;·len:·46,·SHA:·40fa0cfd2ba00e21ce08dd09694136582c96f113b3cecd52783e33aa55256738·...·]·</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&lt;·T·&gt;</a>··</dt>132 <dt>Class·<a·class="el"·href="classgmx_1_1compat_1_1not__null.xhtml">gmx::compat::not_null&lt;·T·&gt;</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>·&amp;top,·const·<a·class="el"·href="structt__mdatoms.xhtml"·title="Declares·mdatom·data·structure.">t_mdatoms</a>·&amp;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>·&amp;top,·const·<a·class="el"·href="structt__mdatoms.xhtml"·title="Declares·mdatom·data·structure.">t_mdatoms</a>·&amp;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&lt;·variable·&gt;::elementSetup</a>··()·override</dt>136 <dt>Member·<a·class="el"·href="classgmx_1_1ConstraintsElement.xhtml#a49afd5b53ba3b039418a0ea819f716b2">gmx::ConstraintsElement&lt;·variable·&gt;::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 modifiedOffset 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>·&amp;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>·&amp;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>
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="_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·&amp;context)</dt>164 <dt>Member·<a·class="el"·href="classgmx_1_1GromacsException.xhtml#a1bd116912e67c096ae949ddae85afe06">gmx::GromacsException::prependContext</a>··(const·std::string·&amp;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·&amp;search,·const·std::string·&amp;replace)</dt>166 <dt>Member·<a·class="el"·href="classgmx_1_1HelpWriterContext.xhtml#a6bec872f46ecd34601df72141fca3739">gmx::HelpWriterContext::setReplacement</a>··(const·std::string·&amp;search,·const·std::string·&amp;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 modifiedOffset 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>
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="_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·diff,·onl[·...·truncated·by·diffoscope;·len:·66,·SHA:·d5e10fa5f395dbea0a719351b7cbe6e4d6de9c88f5d39f72e1c8c10a98e6ce6c·...·]</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&lt;·IRestraintPotential·&gt;·restraint,·const·std::string·&amp;name)</dt>190 <dt>Member·<a·class="el"·href="classgmx_1_1Mdrunner.xhtml#ac0067c523a99846930228d5e58762ed6">gmx::Mdrunner::addPotential</a>··(std::shared_ptr&lt;·IRestraintPotential·&gt;·restraint,·const·std::string·&amp;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·&amp;name,·const·<a·class="el"·href="classgmx_1_1Selection.xhtml"·title="Provides·access·to·a·single·selection.">Selection</a>·&amp;sel,·const·gmx_mtop_t·*mtop)</dt>192 <dt>Member·<a·class="el"·href="namespacegmx.xhtml#a516559bb0e35192a8b312c0c15b28daa">gmx::openTNG</a>··(const·std::string·&amp;name,·const·<a·class="el"·href="classgmx_1_1Selection.xhtml"·title="Provides·access·to·a·single·selection.">Selection</a>·&amp;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 modifiedOffset 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·&amp;filename)</dt>226 <dt>Member·<a·class="el"·href="classgmx_1_1TopologyInformation.xhtml#a5f16e5f1f376a4df101ff36d9f859a48">gmx::TopologyInformation::fillFromInputFile</a>··(const·std::string·&amp;filename)</dt>
227 <dd><a·class="anchor"·id="_todo000155"></a>This·should·throw·upon·error·but·currently·does·not.··</dd>227 <dd><a·class="anchor"·id="_todo000155"></a>This·should·throw·upon·error·but·currently·does·not.··</dd>
228 <dt>Class·<a·class="el"·href="classgmx_1_1TrajectoryAnalysisSettings.xhtml">gmx::TrajectoryAnalysisSettings</a>··</dt>228 <dt>Class·<a·class="el"·href="classgmx_1_1TrajectoryAnalysisSettings.xhtml">gmx::TrajectoryAnalysisSettings</a>··</dt>
229 <dd><a·class="anchor"·id="_todo000153"></a>·Remove·plain·flags·from·the·public·interface.·</dd>229 <dd><a·class="anchor"·id="_todo000153"></a>·Remove·plain·flags·from·the·public·interface.·</dd>
 230 <dt>Member·<a·class="el"·href="group__module__utility.xhtml#ga33e34477bae2bbb86c4d9af1823e3fd0">GMX_UNUSED_VALUE</a>··(value)</dt>
 231 <dd><a·class="anchor"·id="_todo000158"></a>Deprecated·-·use·gmx_unused··</dd>
 232 <dt>Member·<a·class="el"·href="manage__threading_8h.xhtml#ac33f2fc3d292ac10c5bfd0f1b2f0e4c8">init_bonded_threading</a>··(FILE·*fplog,·int·nenergrp)</dt>
 233 <dd><a·class="anchor"·id="_todo000061"></a>Avoid·explicit·pointers·by·using·Impl··</dd>
 234 <dt>Module·<a·class="el"·href="group__module__modularsimulator.xhtml">module_modularsimulator</a>··</dt>
 235 <dd><a·class="anchor"·id="_todo000115"></a>Can·we·link·to·<code>docs/doxygen/lib/modularsimulator.md</code>?·</dd>
 236 <dt>Member·<a·class="el"·href="pme_8h.xhtml#a1774a9bd62826af411a6e75debb069a1">pme_gpu_reinit_computation</a>··(const·gmx_pme_t·*pme,·gmx_wallcycle·*wcycle)</dt>
 237 <dd><a·class="anchor"·id="_todo000030"></a>Rename·this·function·to·<em>clear</em>·&ndash;·it·clearly·only·does·output·resetting·and·we·should·be·clear·about·what·the·function·does..·</dd>
 238 <dt>Member·<a·class="el"·href="pme_8h.xhtml#a9faddde52f5a636410141f52cc95d3e1">pme_gpu_task_enabled</a>··(const·gmx_pme_t·*pme)</dt>
 239 <dd><a·class="anchor"·id="_todo000029"></a>This·is·a·rather·static·data·that·should·be·managed·by·the·hardware·assignment·manager.·For·now,·it·is·synonymous·with·the·active·PME·codepath·(in·the·absence·of·dynamic·switching).·</dd>
 240 <dt>File·<a·class="el"·href="pme__gpu__types__host_8h.xhtml">pme_gpu_types_host.h</a>··</dt>
 241 <dd><a·class="anchor"·id="_todo000034"></a>Some·renaming/refactoring,·which·does·not·impair·the·performance:·&ndash;·bringing·the·function·names·up·to·guidelines·&ndash;·PmeGpuSettings·-&gt;·PmeGpuTasks·&ndash;·refining·GPU·notation·application·(#2053)·&ndash;·renaming·coefficients·to·charges·(?)·</dd>
 242 <dt>Member·<a·class="el"·href="classPreprocessingAtomTypes.xhtml#a50a6f8b3da52aa9a5f806f9309e2d0fb">PreprocessingAtomTypes::atomTypeFromName</a>··(const·std::string·&amp;str)·const</dt>
 243 <dd><a·class="anchor"·id="_todo000038"></a>The·code·should·be·changed·to·instead·use·a·<a·class="el"·href="namespacegmx_1_1compat.xhtml"·title="Compatibility·aliases·for·standard·library·features.">gmx::compat</a>·version·of·std::optional·to·return·an·iterator·to·the·element·being·searched,·or·an·empty·optional·construct·if·the·entry·has·not·been·found.·</dd>
 244 <dt>Member·<a·class="el"·href="classPreprocessingBondAtomType.xhtml#a47b01acdc202b43fae0fcc286955abb2">PreprocessingBondAtomType::bondAtomTypeFromName</a>··(const·std::string·&amp;str)·const</dt>
 245 <dd><a·class="anchor"·id="_todo000039"></a>The·code·should·be·changed·to·instead·use·a·<a·class="el"·href="namespacegmx_1_1compat.xhtml"·title="Compatibility·aliases·for·standard·library·features.">gmx::compat</a>·version·of·std::optional·to·return·a·handle·to·the·element·being·searched,·or·an·empty·optional·construct·if·the·entry·has·not·been·found.·</dd>
 246 <dt>Member·<a·class="el"·href="smalloc_8h.xhtml#ab3d98b1efa6c2b42d2c0d216eafafec5">set_over_alloc_dd</a>··(gmx_bool·set)</dt>
 247 <dd><a·class="anchor"·id="_todo000165"></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>
 248 <dt>File·<a·class="el"·href="simulationsignal_8h.xhtml">simulationsignal.h</a>··</dt>
 249 <dd><a·class="anchor"·id="_todo000079"></a>Move·this·to·mdrunutility·module·alongside·gathering·multi-simulation·communication·infrastructure·there.·</dd>
 250 <dt>File·<a·class="el"·href="update__constrain__cuda_8h.xhtml">update_constrain_cuda.h</a>··</dt>
 251 <dd><a·class="anchor"·id="_todo000080"></a>Change·"cuda"·suffix·to·"gpu"·</dd>
230 <dt>Class·<a·class="el"·href="structgmx__gpu__info__t.xhtml">gmx_gpu_info_t</a>··</dt>252 <dt>Class·<a·class="el"·href="structgmx__gpu__info__t.xhtml">gmx_gpu_info_t</a>··</dt>
231 <dd><a·class="anchor"·id="_todo000057"></a>Use·a·std::vector··</dd>253 <dd><a·class="anchor"·id="_todo000057"></a>Use·a·std::vector··</dd>
232 <dt>Class·<a·class="el"·href="structgmx__multisim__t.xhtml">gmx_multisim_t</a>··</dt>254 <dt>Class·<a·class="el"·href="structgmx__multisim__t.xhtml">gmx_multisim_t</a>··</dt>
233 <dd><a·class="anchor"·id="_todo000094"></a>Change·this·to·class··</dd>255 <dd><a·class="anchor"·id="_todo000094"></a>Change·this·to·class··</dd>
234 <dt>Member·<a·class="el"·href="pme_8h.xhtml#ad5f423fc236c4c689352980cfe4a3706">gmx_pme_init</a>··(const·t_commrec·*cr,·const·<a·class="el"·href="structNumPmeDomains.xhtml"·title="Struct·for·passing·around·the·number·of·PME·domains.">NumPmeDomains</a>·&amp;numPmeDomains,·const·t_inputrec·*ir,·gmx_bool·bFreeEnergy_q,·gmx_bool·bFreeEnergy_lj,·gmx_bool·bReproducible,·real·ewaldcoeff_q,·real·ewaldcoeff_lj,·int·nthread,·PmeRunMode·runMode,·PmeGpu·*pmeGpu,·const·gmx_device_info_t·*gpuInfo,·PmeGpuProgramHandle·pmeGpuProgram,·const·<a·class="el"·href="classgmx_1_1MDLogger.xhtml"·title="Declares·a·logging·interface.">gmx::MDLogger</a>·&amp;mdlog)</dt>256 <dt>Member·<a·class="el"·href="pme_8h.xhtml#ad5f423fc236c4c689352980cfe4a3706">gmx_pme_init</a>··(const·t_commrec·*cr,·const·<a·class="el"·href="structNumPmeDomains.xhtml"·title="Struct·for·passing·around·the·number·of·PME·domains.">NumPmeDomains</a>·&amp;numPmeDomains,·const·t_inputrec·*ir,·gmx_bool·bFreeEnergy_q,·gmx_bool·bFreeEnergy_lj,·gmx_bool·bReproducible,·real·ewaldcoeff_q,·real·ewaldcoeff_lj,·int·nthread,·PmeRunMode·runMode,·PmeGpu·*pmeGpu,·const·gmx_device_info_t·*gpuInfo,·PmeGpuProgramHandle·pmeGpuProgram,·const·<a·class="el"·href="classgmx_1_1MDLogger.xhtml"·title="Declares·a·logging·interface.">gmx::MDLogger</a>·&amp;mdlog)</dt>
235 <dd><a·class="anchor"·id="_todo000027"></a>We·should·evolve·something·like·a·<code>GpuManager</code>·that·holds·<code>gmx_device_info_t</code>·*·and·<code>PmeGpuProgramHandle</code>·and·perhaps·other·related·things·whose·lifetime·can/should·exceed·that·of·a·task·(or·perhaps·task·manager).·See·Redmine·#2522.··</dd>257 <dd><a·class="anchor"·id="_todo000027"></a>We·should·evolve·something·like·a·<code>GpuManager</code>·that·holds·<code>gmx_device_info_t</code>·*·and·<code>PmeGpuProgramHandle</code>·and·perhaps·other·related·things·whose·lifetime·can/should·exceed·that·of·a·task·(or·perhaps·task·manager).·See·Redmine·#2522.··</dd>
236 <dt>Member·<a·class="el"·href="group__module__utility.xhtml#ga33e34477bae2bbb86c4d9af1823e3fd0">GMX_UNUSED_VALUE</a>··(value)</dt> 
237 <dd><a·class="anchor"·id="_todo000158"></a>Deprecated·-·use·gmx_unused··</dd> 
238 <dt>File·<a·class="el"·href="gpu__testutils_8h.xhtml">gpu_testutils.h</a>··</dt>258 <dt>File·<a·class="el"·href="gpu__testutils_8h.xhtml">gpu_testutils.h</a>··</dt>
239 <dd><a·class="anchor"·id="_todo000048"></a>This·should·eventually·go·to·src/testutils·</dd>259 <dd><a·class="anchor"·id="_todo000048"></a>This·should·eventually·go·to·src/testutils·</dd>
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./usr/share/doc/gromacs/html/reference-manual/preface.html
'html2text' not available in path. Installing the 'html2text' package may produce better output.
    
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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·–·2024:</p>68 <p>©·2001·–·2025:</p>
69 <blockquote>69 <blockquote>
70 <div><p>The·GROMACS·development·teams·at·the·Royal·Institute·of·Technology·and70 <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·due73 <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·improve74 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,
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./usr/share/doc/gromacs/html/searchindex.js
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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,
916 ········"2024":·[144,·174],917 ········"2025":·[144,·155],
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,
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