source: tests/regression/Fragmentation/FitParticleCharges/testsuite-fragmentation-fit-particle-charges.at@ 57ba6f

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 Candidate_v1.7.0 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 57ba6f was c4a323, checked in by Frederik Heber <heber@…>, 12 years ago

Added FitParticleChargesAction for fitting partial nuclei charges to electrostatic potential.

  • right now just fits to first found potential of specified homology.
  • checks HomologyGraph::value_t::containsGrids whether grids have actually been stored.
  • added regression test to FitParticleCharges.
  • Property mode set to 100644
File size: 2.4 KB
Line 
1#
2# MoleCuilder - creates and alters molecular systems
3# Copyright (C) 2013 Frederik Heber
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### fit particle charges
19
20# the potential has been generated by:
21# ./molecuilder -i pre/water.pdb --center-in-box "8,0,8,0,0,8" --select-all-atoms --fragment-molecule BondFragment --distance 2 --order 1 --fragment-automation --server-address 127.0.0.1 --server-port 1026 --DoLongrange 1 --grid 4 --DoPrintDebug 1 --DoValenceOnly 0 --analyse-fragment-results --store-grids 1 --save-homologies homology_grid_4_full.dat
22
23AT_SETUP([Fragmentation - Fit particle charges to water])
24AT_KEYWORDS([fragmentation parse-homologies fit-particle-charges])
25AT_SKIP_IF([../../molecuilder --help --actionname fit-particle-charges; if test $? -eq 5; then /bin/true; else /bin/false; fi])
26
27# homology file created with water.pdb and as follows:
28# molecuilder -i water.pdb --select-all-atoms --fragment-molecule --distance 2 --order 1 --fragment-automation --server-address 127.0.0.1 --server-port 1026 --DoLongrange 1 --grid 5 --store-grids 1 --analyse-fragment-results --save-homologies homology_grid.dat
29file=homology_grid.dat
30AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/FitParticleCharges/pre/$file $file], 0)
31AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
32AT_CHECK([../../molecuilder --parse-homologies $file --fit-particle-charges --potential-file water.particles --fragment-charges 8 1 1 --radius 1.5], 0, [stdout], [ignore])
33# check that L_2 error is below 1e-6
34AT_CHECK([grep "L2-Norm" stdout | awk '{if ($6 > 1e1) exit 1}'], 0, [ignore], [ignore])
35AT_CHECK([grep "L1-Norm" stdout | awk '{if ($6 > 1e0) exit 1}'], 0, [ignore], [ignore])
36AT_CHECK([grep "We have fitted the following charges ( -0.73.*; 0.36.*; 0.36.*; )." stdout], 0, [ignore], [ignore])
37
38AT_CLEANUP
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