Changeset 2a0eb0 for tests/regression/Fragmentation

Timestamp:

Dec 3, 2012, 9:49:06 AM (12 years ago)

Author:

Frederik Heber <heber@…>

Branches:

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

Children:

3501d2

Parents:

34e74fd

git-author:

Frederik Heber <heber@…> (09/19/12 09:47:16)

git-committer:

Frederik Heber <heber@…> (12/03/12 09:49:06)

Message:

FragmentationAction now works on selected atoms, split into molecules.

• i.e. we still call Fragmentation on a specific molecule but fragmentMolecule() receives a vector of ids to use in its AtomMask. This is however not yet implemented.
• TESTFIX: added --select-molecules-atoms to all fragmentation calls.

Location:

tests/regression/Fragmentation

Files:

• FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at (modified) (1 diff)
• FragmentMolecule/testsuite-fragmentation-fragment-molecule.at (modified) (1 diff)

tests/regression/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at

@@ -42 +42 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/FragmentMolecule-MaxOrder/pre/test.conf $file], 0)
 AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i $file  -v 1 --select-molecule-by-id 0 -f ./BondFragment --distance 1.55 --order 2 --output-types "pcp"], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i $file  -v 1 --select-molecule-by-id 0 -f ./BondFragment --distance 1.55 --order 2 --output-types "pcp"], 2, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i $file -I -v 1 --select-molecule-by-id 0 --select-molecules-atoms -f ./BondFragment --distance 1.55 --order 2 --output-types "pcp"], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i $file -I -v 1 --select-molecule-by-id 0 --select-molecules-atoms -f ./BondFragment --distance 1.55 --order 2 --output-types "pcp"], 2, [ignore], [ignore])
 
 AT_CLEANUP

tests/regression/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at

@@ -41 +41 @@
 AT_CHECK([/bin/cp -f ${abs_top_srcdir}/tests/regression/Fragmentation/FragmentMolecule/pre/test.conf $file], 0)
 AT_CHECK([chmod u+w $file], 0, [ignore], [ignore])
-AT_CHECK([../../molecuilder -i $file  -v 1 -I --select-molecule-by-id 0 -f ./BondFragment --distance 1.55 --order 2 --output-types "pcp"], 0, [ignore], [ignore])
+AT_CHECK([../../molecuilder -i $file -I -v 1 --select-molecule-by-id 0 --select-molecules-atoms -f ./BondFragment --distance 1.55 --order 2 --output-types "pcp"], 0, [ignore], [ignore])
 #AT_CHECK([diff BondFragment0.conf ${abs_top_srcdir}/tests/regression/Fragmentation/FragmentMolecule/post/BondFragment0.conf], 0, [ignore], [ignore])
 #AT_CHECK([diff BondFragment1.conf ${abs_top_srcdir}/tests/regression/Fragmentation/FragmentMolecule/post/BondFragment1.conf], 0, [ignore], [ignore])