Changeset 98c428 for src/Actions/MoleculeAction

Timestamp:

Feb 22, 2012, 11:27:55 AM (13 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:

44f53e

Parents:

3dfd9c

git-author:

Frederik Heber <heber@…> (01/12/12 14:23:39)

git-committer:

Frederik Heber <heber@…> (02/22/12 11:27:55)

Message:

FormatParserStorage has now two convenience functions ::load().

• this way one doesn't have to find out the suffix anymore.

Location:

src/Actions/MoleculeAction

Files:

• FillVoidWithMoleculeAction.cpp (modified) (1 diff)
• FillWithMoleculeAction.cpp (modified) (1 diff)
• FillWithMoleculeAction.def (modified) (1 diff)

src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp

@@ -73 +73 @@
   // search the filler molecule that has been just parsed
   molecule *filler = World::getInstance().getMolecule(MoleculeByOrder(-1)); // get last molecule
+  ASSERT(filler != NULL,
+      "MoleculeFillVoidWithMoleculeAction::performCall() - no last molecule found, nothing parsed?.");
   filler->SetNameFromFilename(params.fillername.string().c_str());
   World::AtomComposite Set = filler->getAtomSet();

src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

@@ -60 +60 @@
   std::string FilenameSuffix = params.fillername.string().substr(params.fillername.string().find_last_of('.')+1, params.fillername.string().length());
   ifstream input;
+  LOG(0, "STATUS: Loading filler molecule " << params.fillername.string().c_str()
+      << " of suffix " << FilenameSuffix << ".");
   input.open(params.fillername.string().c_str());
-  ParserTypes type = FormatParserStorage::getInstance().getTypeFromSuffix(FilenameSuffix);
-  FormatParserInterface &parser = FormatParserStorage::getInstance().get(type);
-  parser.load(&input);
+  FormatParserStorage::getInstance().load(input, FilenameSuffix);
+  input.close();
 
   // search the filler molecule that has been just parsed
   molecule *filler = World::getInstance().getMolecule(MoleculeByOrder(-1)); // get last molecule
+  ASSERT(filler != NULL,
+      "MoleculeFillWithMoleculeAction::performCall() - no last molecule found, nothing parsed?.");
   filler->SetNameFromFilename(params.fillername.string().c_str());
-//    molecule *Filling = NULL;
-//    atom *first = NULL, *second = NULL, *third = NULL;
-//    first = World::getInstance().createAtom();
-//    first->type = World::getInstance().getPeriode()->FindElement(1);
-//    first->x = Vector(0.441, -0.143, 0.);
-//    filler->AddAtom(first);
-//    second = World::getInstance().createAtom();
-//    second->type = World::getInstance().getPeriode()->FindElement(1);
-//    second->x = Vector(-0.464, 1.137, 0.0);
-//    filler->AddAtom(second);
-//    third = World::getInstance().createAtom();
-//    third->type = World::getInstance().getPeriode()->FindElement(8);
-//    third->x = Vector(-0.464, 0.177, 0.);
-//    filler->AddAtom(third);
-//    filler->AddBond(first, third, 1);
-//    filler->AddBond(second, third, 1);
   World::AtomComposite Set = filler->getAtomSet();
+  LOG(1, "INFO: The filler molecules has " << Set.size() << " atoms.");
   World::getInstance().getBondGraph()->CreateAdjacency(Set);
-//    filler->SetNameFromFilename("water");
+
   // TODO: Remove the erasure of molecule when saving does not depend on them anymore.
   World::getInstance().getMolecules()->erase(filler); // remove it, Parser adds it automatically

src/Actions/MoleculeAction/FillWithMoleculeAction.def

@@ -7 +7 @@
 
 // all includes and forward declarations necessary for non-integral types below
+#include <boost/filesystem/path.hpp>
 #include "LinearAlgebra/Vector.hpp"
 class MoleculeListClass;