Changeset 7a51be for src/Actions

Timestamp:

Feb 11, 2011, 9:37:26 PM (14 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:

f649de

Parents:

170ba6

Message:

new function FormatParserStorage::get to obtain specialized FormatParser instance.

• used in FillVoidWithMoleculeAction and FillWithMoleculeAction.
• both Actions also now use MoleculeByOrder descriptor to obtain last molecule.
• FillBoxWithMolecule() now returns void.
• implemented FillVoidWithMoleculeAction::performUndo().
• TEST: Filling/FillWithMolecule - added undo test.
• TESTFIX: Filling/FillVoidWithMolecule - due to loading of filler molecule with parser, water.data had to be adapted in its ATOMDATA line to match test.data. Otherwise, resulting file will have non-matching ATOMDATA although being otherwise consistent. (This is a workaround to ticket #141).

Location:

src/Actions/MoleculeAction

Files:

• FillVoidWithMoleculeAction.cpp (modified) (2 diffs)
• FillWithMoleculeAction.cpp (modified) (4 diffs)
• FillWithMoleculeAction.def (modified) (1 diff)

src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp

@@ -23 +23 @@
 #include "bondgraph.hpp"
 #include "boundary.hpp"
+#include "CodePatterns/Verbose.hpp"
 #include "config.hpp"
+#include "Descriptors/MoleculeIdDescriptor.hpp"
+#include "Descriptors/MoleculeOrderDescriptor.hpp"
 #include "molecule.hpp"
-#include "CodePatterns/Verbose.hpp"
+#include "Parser/FormatParserStorage.hpp"
 #include "World.hpp"
 
-#include "Descriptors/MoleculeIdDescriptor.hpp"
-#include "Parser/MpqcParser.hpp"
-#include "Parser/PcpParser.hpp"
-#include "Parser/PdbParser.hpp"
-#include "Parser/TremoloParser.hpp"
-#include "Parser/XyzParser.hpp"
-#include "Parser/FormatParserStorage.hpp"
 
 #include <algorithm>
@@ -70 +66 @@
   ifstream input;
   input.open(params.fillername.string().c_str());
-  switch (FormatParserStorage::getInstance().getTypeFromSuffix(FilenameSuffix)) {
-    case mpqc:
-      {
-        MpqcParser mpqcparser;
-        mpqcparser.load(&input);
-        break;
-      }
-    case pcp:
-      {
-        PcpParser pcpparser;
-        pcpparser.load(&input);
-        break;
-      }
-    case pdb:
-      {
-        PdbParser pdbparser;
-        pdbparser.load(&input);
-        break;
-      }
-    case tremolo:
-      {
-        TremoloParser tremoloparser;
-        tremoloparser.load(&input);
-        break;
-      }
-    case xyz:
-      {
-        XyzParser xyzparser;
-        xyzparser.load(&input);
-        break;
-      }
-    default:
-      DoeLog(0) && (eLog()<< Verbose(0) << "Could not parse filler molecule from " << params.fillername << "." << endl);
-      break;
-  }
+  ParserTypes type = FormatParserStorage::getInstance().getTypeFromSuffix(FilenameSuffix);
+  FormatParser &parser = FormatParserStorage::getInstance().get(type);
+  parser.load(&input);
 
   // search the filler molecule that has been just parsed
-  molecule *filler = NULL;
-  for (World::MoleculeIterator iter = World::getInstance().getMoleculeIter();
-      iter != World::getInstance().moleculeEnd();
-      ++iter)
-    filler = *iter; // get last molecule
+  molecule *filler = World::getInstance().getMolecule(MoleculeByOrder(-1)); // get last molecule
   filler->SetNameFromFilename(params.fillername.string().c_str());
   World::getInstance().getConfig()->BG->ConstructBondGraph(filler);

src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

@@ -23 +23 @@
 #include "bondgraph.hpp"
 #include "boundary.hpp"
+#include "CodePatterns/Verbose.hpp"
 #include "config.hpp"
+#include "Descriptors/MoleculeIdDescriptor.hpp"
+#include "Descriptors/MoleculeOrderDescriptor.hpp"
 #include "molecule.hpp"
-#include "CodePatterns/Verbose.hpp"
+#include "Parser/FormatParserStorage.hpp"
 #include "World.hpp"
 
@@ -53 +56 @@
       << ", DoRotate " << params.DoRotate << "." << endl);
   // construct water molecule
-  molecule *filler = World::getInstance().createMolecule();
-  if (!filler->AddXYZFile(params.fillername.string())) {
-    DoeLog(0) && (eLog()<< Verbose(0) << "Could not parse filler molecule from " << params.fillername << "." << endl);
-  }
+  std::vector<molecule *> presentmolecules = World::getInstance().getAllMolecules();
+//  DoLog(0) && (Log() << Verbose(0) << presentmolecules.size() << " molecules initially are present." << std::endl);
+  std::string FilenameSuffix = params.fillername.string().substr(params.fillername.string().find_last_of('.')+1, params.fillername.string().length());
+  ifstream input;
+  input.open(params.fillername.string().c_str());
+  ParserTypes type = FormatParserStorage::getInstance().getTypeFromSuffix(FilenameSuffix);
+  FormatParser &parser = FormatParserStorage::getInstance().get(type);
+  parser.load(&input);
+
+  // search the filler molecule that has been just parsed
+  molecule *filler = World::getInstance().getMolecule(MoleculeByOrder(-1)); // get last molecule
   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::getInstance().getConfig()->BG->ConstructBondGraph(filler);
-//    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
+
   // call routine
   double distance[NDIM];
   for (int i=0;i<NDIM;i++)
     distance[i] = params.distances[i];
-  Filling = FillBoxWithMolecule(
+  FillBoxWithMolecule(
       World::getInstance().getMolecules(),
       filler, *(World::getInstance().getConfig()),
@@ -89 +85 @@
       params.RandMoleculeDisplacement,
       params.DoRotate);
-  if (Filling != NULL) {
-    Filling->ActiveFlag = false;
-    World::getInstance().getMolecules()->insert(Filling);
-  }
   for (molecule::iterator iter = filler->begin(); !filler->empty(); iter = filler->begin()) {
     atom *Walker = *iter;
@@ -100 +92 @@
   World::getInstance().destroyMolecule(filler);
 
-  return Action::success;
+  // generate list of newly created molecules
+  // (we can in general remove more quickly from a list than a vector)
+  std::vector<molecule *> fillermolecules = World::getInstance().getAllMolecules();
+//  DoLog(0) && (Log() << Verbose(0) << fillermolecules.size() << " molecules are present." << std::endl);
+  std::list<molecule *> fillermolecules_list;
+  std::copy( fillermolecules.begin(),  fillermolecules.end(), std::back_inserter( fillermolecules_list ));
+//  DoLog(0) && (Log() << Verbose(0) << fillermolecules_list.size() << " molecules have been copied." << std::endl);
+  for (std::vector<molecule *>::const_iterator iter = presentmolecules.begin();
+      iter != presentmolecules.end();
+      ++iter) {
+    fillermolecules_list.remove(*iter);
+  }
+//  DoLog(0) && (Log() << Verbose(0) << fillermolecules_list.size() << " molecules left after removal." << std::endl);
+  fillermolecules.clear();
+  std::copy(fillermolecules_list.begin(), fillermolecules_list.end(), std::back_inserter( fillermolecules ));
+
+//  DoLog(0) && (Log() << Verbose(0) << fillermolecules.size() << " molecules have been inserted." << std::endl);
+
+  return Action::state_ptr(new MoleculeFillWithMoleculeState(fillermolecules,params));
 }
 
 Action::state_ptr MoleculeFillWithMoleculeAction::performUndo(Action::state_ptr _state) {
-//  MoleculeFillWithMoleculeState *state = assert_cast<MoleculeFillWithMoleculeState*>(_state.get());
+  MoleculeFillWithMoleculeState *state = assert_cast<MoleculeFillWithMoleculeState*>(_state.get());
 
-//  string newName = state->mol->getName();
-//  state->mol->setName(state->lastName);
+  MoleculeListClass *MolList = World::getInstance().getMolecules();
 
-  return Action::failure;
+  BOOST_FOREACH(molecule *_mol, state->fillermolecules) {
+    MolList->erase(_mol);
+    if ((_mol != NULL) && (!(World::getInstance().getAllMolecules(MoleculeById(_mol->getId()))).empty())) {
+      for(molecule::iterator iter = _mol->begin();
+          !_mol->empty();
+          iter = _mol->begin()) {
+        atom *Walker = *iter;
+        _mol->erase(iter);
+        World::getInstance().destroyAtom(Walker);
+      }
+      World::getInstance().destroyMolecule(_mol);
+    }
+  }
+
+  // as molecules and atoms from state are removed, we have to create a new one
+  std::vector<molecule *> fillermolecules;
+  return Action::state_ptr(new MoleculeFillWithMoleculeState(fillermolecules,state->params));
 }
 
 Action::state_ptr MoleculeFillWithMoleculeAction::performRedo(Action::state_ptr _state){
-  // Undo and redo have to do the same for this action
-  return performUndo(_state);
+  //MoleculeFillWithMoleculeState *state = assert_cast<MoleculeFillWithMoleculeState*>(_state.get());
+
+  return Action::failure;
+  //return Action::state_ptr(_state);
 }
 
 bool MoleculeFillWithMoleculeAction::canUndo() {
-  return false;
+  return true;
 }
 
 bool MoleculeFillWithMoleculeAction::shouldUndo() {
-  return false;
+  return true;
 }
 /** =========== end of function ====================== */

src/Actions/MoleculeAction/FillWithMoleculeAction.def

@@ -19 +19 @@
 #define paramreferences (fillername)(distances)(boundary)(RandAtomDisplacement)(RandMoleculeDisplacement)(MaxDistance)(DoRotate)
 
-#undef statetypes
-#undef statereferences
+#define statetypes (std::vector<molecule *>)
+#define statereferences (fillermolecules)
 
 // some defines for all the names, you may use ACTION, STATE and PARAMS