Changeset 35b698 for tests/regression/Domain/6/post/test-x.conf.xyz

Timestamp:

Jun 23, 2010, 3:52:50 PM (15 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:

d0fbec

Parents:

dc0d21

git-author:

Frederik Heber <heber@…> (06/23/10 15:20:35)

git-committer:

Frederik Heber <heber@…> (06/23/10 15:52:50)

Message:

BIG CHANGE: config::load and config::save in ParseCommandLineOptions() and main() replaced with FormatParser replacements.

Fragmentation:

• FragmentMolecule() - configuration is not needed anymore, but a path (including prefix)
• class molecule:
  • lots of changes from char * to std:string (due to above): LinearInterpolationBetweenConfiguration(), CheckOrderAtSite(), StoreBondsToFile(), StoreAdjacencyToFile(), CheckAdjacencyFileAgainstMolecule(), CheckAdjacencyFileAgainstMolecule_Init(), ParseOrderAtSiteFromFile(), StoreOrderAtSiteFile(), StoreForcesFile(), ScanAdaptiveFileIntoMap(), StoreForcesFile(), AddHydrogenCorrection(), OutputConfigForListOfFragments()
  • in all above functions, also stringstreams have been replaced by simple strings and file != NULL by file.good()
  • no more CalculateOrbitals(), shifted to class PcpParser
• FragmentationAction: argument of -f is now the prefix, molecule is obtained by molecule-by-id
• no more strcpy needed in: MoleculeLinearInterpolationofTrajectoriesAction, MoleculeSaveAdjacencyAction, MoleculeSaveBondsAction
• oldmenu::FragmentAtoms() - needs to ask for path with prefix now
• config: RetrieveConfigPathAndName() and configpath removed (replaced by above path with prefix)
• changes due to this removal: SaveConfig(), config::Load(), config::LoadOld()

• FIX: MoleculeFillWithMoleculeAction: filler atoms have to be removed before the system can be stored to file.
• FIX: PcpParser::load() - has to put the molecule also into World's MoleculeListClass (otherwise the name cannot be set right after loading)

• ParseCommandLineOptions()
  • new parameter BondGraphFileName and creation of bond graph is done in main()
  • no more config::load, just parser->load(), ConfigFileName is set extra and we always set configPresent to present.
  • FIX: filename is only set when no molecule was allocated before
  • FIX: case 't' and 'f' had wrong argc checks
• main()
  • FormatParserStorage is set with mpqc, pcp and xyz
  • BondGraph is constructed from new string BondGrapghFileName

• new Libparser.a
• all sources from PARSER subdir are compiled into libparser such that only ParserUnitTest is recompiled.

Testfixes:

• testsuite-fragmentation - changes to due to different -f calling syntax.
• most of the xyz files had to be replaced due to a single whitespace at the end of each entry: Domain/6, Simple_configuration/2, Simple_configuration/3, Simple_configuration/4, Simple_configuration/5, Simple_configuration/8
• in many cases were the number orbitals (and thus MaxMinStopStep) wrong: Filling/1, Simple_configuration/4, Simple_configuration/5

Signed-off-by: Frederik Heber <heber@…>

File:

• tests/regression/Domain/6/post/test-x.conf.xyz (modified) (1 diff)

tests/regression/Domain/6/post/test-x.conf.xyz

@@ -1 +1 @@
 22
         Created by molecuilder on Mon May 31 19:07:16 2010
-H       9.78209 2.64589 2.64589 
-C       27.2836 3.27519 3.53589 
-C       28.5328 4.15859 3.53589 
-C       29.7821 3.27519 3.53589 
-H       27.2836 2.64589 4.42589 
-H       9.78209 2.64589 4.42589 
-H       10.672  3.90454 3.53589 
-H       8.53279 4.78789 2.64589 
-H       27.2836 2.64589 2.64589 
-H       26.3936 3.90454 3.53589 
-H       28.5328 4.78789 4.42589 
-H       28.5328 4.78789 2.64589 
-H       30.672  3.90454 3.53589 
-H       29.7821 2.64589 4.42589 
-H       29.7821 2.64589 2.64589 
-H       8.53279 4.78789 4.42589 
-H       6.39363 3.90454 3.53589 
-H       7.28359 2.64589 2.64589 
-H       7.28359 2.64589 4.42589 
-C       9.78209 3.27519 3.53589 
-C       8.53279 4.15859 3.53589 
-C       7.28359 3.27519 3.53589 
+H       9.78209 2.64589 2.64589
+C       27.2836 3.27519 3.53589
+C       28.5328 4.15859 3.53589
+C       29.7821 3.27519 3.53589
+H       27.2836 2.64589 4.42589
+H       9.78209 2.64589 4.42589
+H       10.672  3.90454 3.53589
+H       8.53279 4.78789 2.64589
+H       27.2836 2.64589 2.64589
+H       26.3936 3.90454 3.53589
+H       28.5328 4.78789 4.42589
+H       28.5328 4.78789 2.64589
+H       30.672  3.90454 3.53589
+H       29.7821 2.64589 4.42589
+H       29.7821 2.64589 2.64589
+H       8.53279 4.78789 4.42589
+H       6.39363 3.90454 3.53589
+H       7.28359 2.64589 2.64589
+H       7.28359 2.64589 4.42589
+C       9.78209 3.27519 3.53589
+C       8.53279 4.15859 3.53589
+C       7.28359 3.27519 3.53589