source: tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at@ a86666

Action_Thermostats Add_AtomRandomPerturbation Add_FitFragmentPartialChargesAction Add_RotateAroundBondAction Add_SelectAtomByNameAction Added_ParseSaveFragmentResults AddingActions_SaveParseParticleParameters Adding_Graph_to_ChangeBondActions Adding_MD_integration_tests Adding_ParticleName_to_Atom Adding_StructOpt_integration_tests AtomFragments Automaking_mpqc_open AutomationFragmentation_failures Candidate_v1.5.4 Candidate_v1.6.0 Candidate_v1.6.1 ChangeBugEmailaddress ChangingTestPorts ChemicalSpaceEvaluator CombiningParticlePotentialParsing Combining_Subpackages Debian_Package_split Debian_package_split_molecuildergui_only Disabling_MemDebug Docu_Python_wait EmpiricalPotential_contain_HomologyGraph EmpiricalPotential_contain_HomologyGraph_documentation Enable_parallel_make_install Enhance_userguide Enhanced_StructuralOptimization Enhanced_StructuralOptimization_continued Example_ManyWaysToTranslateAtom Exclude_Hydrogens_annealWithBondGraph FitPartialCharges_GlobalError Fix_BoundInBox_CenterInBox_MoleculeActions Fix_ChargeSampling_PBC Fix_ChronosMutex Fix_FitPartialCharges Fix_FitPotential_needs_atomicnumbers Fix_ForceAnnealing Fix_IndependentFragmentGrids Fix_ParseParticles Fix_ParseParticles_split_forward_backward_Actions Fix_PopActions Fix_QtFragmentList_sorted_selection Fix_Restrictedkeyset_FragmentMolecule Fix_StatusMsg Fix_StepWorldTime_single_argument Fix_Verbose_Codepatterns Fix_fitting_potentials Fixes ForceAnnealing_goodresults ForceAnnealing_oldresults ForceAnnealing_tocheck ForceAnnealing_with_BondGraph ForceAnnealing_with_BondGraph_continued ForceAnnealing_with_BondGraph_continued_betteresults ForceAnnealing_with_BondGraph_contraction-expansion FragmentAction_writes_AtomFragments FragmentMolecule_checks_bonddegrees GeometryObjects Gui_Fixes Gui_displays_atomic_force_velocity ImplicitCharges IndependentFragmentGrids IndependentFragmentGrids_IndividualZeroInstances IndependentFragmentGrids_IntegrationTest IndependentFragmentGrids_Sole_NN_Calculation JobMarket_RobustOnKillsSegFaults JobMarket_StableWorkerPool JobMarket_unresolvable_hostname_fix MoreRobust_FragmentAutomation ODR_violation_mpqc_open PartialCharges_OrthogonalSummation PdbParser_setsAtomName PythonUI_with_named_parameters QtGui_reactivate_TimeChanged_changes Recreated_GuiChecks Rewrite_FitPartialCharges RotateToPrincipalAxisSystem_UndoRedo SaturateAtoms_findBestMatching SaturateAtoms_singleDegree StoppableMakroAction Subpackage_CodePatterns Subpackage_JobMarket Subpackage_LinearAlgebra Subpackage_levmar Subpackage_mpqc_open Subpackage_vmg Switchable_LogView ThirdParty_MPQC_rebuilt_buildsystem TrajectoryDependenant_MaxOrder TremoloParser_IncreasedPrecision TremoloParser_MultipleTimesteps TremoloParser_setsAtomName Ubuntu_1604_changes stable
Last change on this file since a86666 was e2925fd, checked in by Frederik Heber <heber@…>, 12 years ago

Split long-range calculations into two parts to overcome E-N-potential problems.

The general problem is that smeared-out nuclei charges cannot interact with
electron charge densities as they always overlap, hence we always make a large
error. The idea then is - as the potential energy is symmetric both
densities - to flip from N-E to E-N, i.\,e. to take the electron potential and
evaluate at nuclei positions instead of smeared-out nuclei charges with
eletronic charge distribution. However, then we need to make two calculations
for the four contributions: E-E, E-N and N-N, N-E (=E-N).

  • new enums SampleParticles_t eventually tells InterfaceVMGJob whether to sample the nuclei charges onto the grid or not.
  • TreatGrid_t tells InterfaceVMGJob whether to actually add the electronic charge onto the grid (this was added but is actually not required anymore).
  • FragmentationAutomationAction::performCall() now creates twice as many long-range jobs. This requires two variables in VMGData for storing integrated long-range energy: electron_long, nuclei_long, as both calculations are combined into a single VMGData instance per fragment.
  • Summation of long-range contributions is split into three instead of formerly two parts: electron (E-E), nuclei (N-N), and mixed (E-N). This allows to easierly check their cancellation. This needs new member in fusion map and name in printKeyNames.
  • naturally, the enums have to be passed a long way: VMGFragmentController, VMGJob, VMGData.
  • VMGData now has serialization version 1 due to new entry.
  • we enhanced documentation in FragmentationLongRangeResults::operator()() of how and what is summed per level.
  • FIX: InterfaceVMGJob::ImportRightHandSide() subtracted grid instead of adding it. Now, we set correct sign of electron charge distribution in MPQC.
  • TESTFIX: Regression test AnalyseFragmentResults now has short- and long-range part. Long-range part is only diff'ed when the compiled code has the capabilities.
  • Property mode set to 100644
File size: 5.0 KB
RevLine 
[55e1bc]1#
2# MoleCuilder - creates and alters molecular systems
3# Copyright (C) 2013 University of Bonn
4#
5# This program is free software: you can redistribute it and/or modify
6# it under the terms of the GNU General Public License as published by
7# the Free Software Foundation, either version 3 of the License, or
8# (at your option) any later version.
9#
10# This program is distributed in the hope that it will be useful,
11# but WITHOUT ANY WARRANTY; without even the implied warranty of
12# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13# GNU General Public License for more details.
14#
15# You should have received a copy of the GNU General Public License
16# along with this program. If not, see <http://www.gnu.org/licenses/>.
17#
18### fragment the molecule and check the number of configs
[6ff62c]19#
[e2925fd]20# BondFragmentShortRangeResults.dat is created like this:
21# ./molecuilder -i pre/alkane-3.pdb --change-box 20,0,20,0,0,20 --set-parser-parameters mpqc --parser-parameters "theory=CLHF;basis=6-31G;" --set-boundary-conditions Ignore Ignore Ignore --update-molecules --select-all-atoms --fragment-molecule BondFragment --DoSaturate 1 --ExcludeHydrogen 1 --distance 2. --order 6 --fragment-automation --DoLongrange 0 --server-address 127.0.0.1 --server-port 1026 --fragment-resultfile BondFragmentShortRangeResults.dat
[55e1bc]22
[e2925fd]23AT_SETUP([Fragmentation - Analyse short-range fragmentation results])
[55e1bc]24AT_KEYWORDS([fragmentation analyse-fragment-results])
25
[e2925fd]26file=BondFragmentShortRangeResults.dat
[55e1bc]27AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
28AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
29AT_CHECK([../../molecuilder --analyse-fragment-results --fragment-resultfile $file], 0, [ignore], [ignore])
[e2925fd]30AT_CHECK([output=BondFragment_Energy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
31AT_CHECK([output=BondFragment_Forces.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
32AT_CHECK([output=BondFragment_Times.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
33AT_CHECK([output=BondFragment_Eigenvalues.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
34AT_CHECK([output=BondFragment_Eigenhistogram.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/ShortRange/$output], 0, [ignore], [ignore])
35
36AT_CLEANUP
37
38#
39# BondFragmentLongRangeResults.dat is created like this:
40# ./molecuilder -i pre/alkane-3.pdb --change-box 20,0,20,0,0,20 --set-parser-parameters mpqc --parser-parameters "theory=CLHF;basis=6-31G;" --set-boundary-conditions Ignore Ignore Ignore --update-molecules --select-all-atoms --fragment-molecule BondFragment --DoSaturate 1 --ExcludeHydrogen 1 --distance 2. --order 6 --fragment-automation --DoLongrange 1 --DoValenceOnly 0 --grid-level 4 --near-field-cells 3 --server-address 127.0.0.1 --server-port 1026 --server-address 127.0.0.1 --server-port 1026 --fragment-resultfile BondFragmentLongRangeResults.dat
41
42AT_SETUP([Fragmentation - Analyse long-range fragmentation results])
43AT_KEYWORDS([fragmentation analyse-fragment-results])
44
45file=BondFragmentLongRangeResults.dat
46AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/$file $file], 0)
47AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
48AT_CHECK([../../molecuilder -i ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/pre/alkane-3.pdb --analyse-fragment-results --fragment-resultfile $file], 0, [ignore], [stderr])
49AT_CHECK([output=BondFragment_Energy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/$output], 0, [ignore], [ignore])
50AT_CHECK([output=BondFragment_Forces.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/$output], 0, [ignore], [ignore])
51AT_CHECK([output=BondFragment_Times.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/$output], 0, [ignore], [ignore])
52AT_CHECK([output=BondFragment_Eigenvalues.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/$output], 0, [ignore], [ignore])
53AT_CHECK([output=BondFragment_Eigenhistogram.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/$output], 0, [ignore], [ignore])
54AT_CHECK([grep "File contains long-range information" stderr], 0, [ignore], [ignore], [
55 AT_CHECK([output=BondFragment_LongRangeEnergy.dat; diff $output ${abs_top_srcdir}/tests/regression/Fragmentation/AnalyseFragmentationResults/post/LongRange/$output], 0, [ignore], [ignore])
56 ])
[55e1bc]57
58AT_CLEANUP
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