Changeset 35b698 for src/Actions/MoleculeAction

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@…>

Location:

src/Actions/MoleculeAction

Files:

• FillWithMoleculeAction.cpp (modified) (1 diff)
• LinearInterpolationofTrajectoriesAction.cpp (modified) (1 diff)
• SaveAdjacencyAction.cpp (modified) (1 diff)
• SaveBondsAction.cpp (modified) (1 diff)

src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

@@ -102 +102 @@
       World::getInstance().getMolecules()->insert(Filling);
     }
+    for (molecule::iterator iter = filler->begin(); !filler->empty(); iter = filler->begin()) {
+      atom *Walker = *iter;
+      filler->erase(iter);
+      World::getInstance().destroyAtom(Walker);
+    }
     World::getInstance().destroyMolecule(filler);
 

src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp

@@ -69 +69 @@
     if (IdMapping)
       DoLog(1) && (Log() << Verbose(1) << "Using Identity for the permutation map." << endl);
-    char outputname[MAXSTRINGSIZE];
-    strcpy(outputname, filename.c_str());
-    // TODO: LinearInterpolationBetweenConfiguration should use stream, not the filename directly! (better for unit test)
-    if (!mol->LinearInterpolationBetweenConfiguration(start, end, outputname, *(World::getInstance().getConfig()), IdMapping))
-      DoLog(2) && (Log() << Verbose(2) << "Could not store " << outputname << " files." << endl);
+    if (!mol->LinearInterpolationBetweenConfiguration(start, end, filename, *(World::getInstance().getConfig()), IdMapping))
+      DoLog(2) && (Log() << Verbose(2) << "Could not store " << filename << " files." << endl);
     else
       DoLog(2) && (Log() << Verbose(2) << "Steps created and " << filename << " files stored." << endl);

src/Actions/MoleculeAction/SaveAdjacencyAction.cpp

@@ -65 +65 @@
     World::getInstance().getConfig()->BG->ConstructBondGraph(mol);
     // TODO: sollte stream nicht filename benutzen, besser fuer unit test
-    char outputname[MAXSTRINGSIZE];
-    strcpy(outputname, filename.c_str());
-    mol->StoreAdjacencyToFile(NULL, outputname);
+    mol->StoreAdjacencyToFile(filename);
     delete dialog;
     return Action::success;

src/Actions/MoleculeAction/SaveBondsAction.cpp

@@ -64 +64 @@
     DoLog(0) && (Log() << Verbose(0) << "Storing bonds to path " << filename << "." << endl);
     World::getInstance().getConfig()->BG->ConstructBondGraph(mol);
-    // TODO: sollte stream, nicht filenamen direkt nutzen, beser fuer unit tests
-    char outputname[MAXSTRINGSIZE];
-    strcpy(outputname, filename.c_str());
-    mol->StoreBondsToFile(NULL, outputname);
+    // TODO: sollte stream, nicht filenamen direkt nutzen, besser fuer unit tests
+    mol->StoreBondsToFile(filename);
     delete dialog;
     return Action::success;