Changeset 66fd49 for src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp

Timestamp:

Feb 3, 2011, 9:51:18 AM (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:

d6f886

Parents:

0b15bb

git-author:

Frederik Heber <heber@…> (12/30/10 20:52:17)

git-committer:

Frederik Heber <heber@…> (02/03/11 09:51:18)

Message:

Rewrite of FillVoidWithMoleculeAction.

FillVoidWithMoleculeAction:

• new parameter MinDistance and default value of 0.
• BUGFIX: filler is already created when parsing file, removed useless creation of it initially (also caused lots of confusion due to an "extra" molecule).
• Undo implemented, regression test inserted.
• Redo is somewhat hard to implement, as one would use performCall() if it only it would not retrieve its values from ValueStorage ...

FillVoidWithMolecule():

• filler is now the zeroth not the last molecule, marked by firstInsertion and firstInserter. Filler is removed if no molecules are filled.
• outsourced stuff into smaller functions
  • RandomizeMoleculePositions()
  • RemoveAtomsOutsideDomain()
  • isSpaceAroundPointVoid()
• removed FillIt to through every atom despite only CurrentPosition, indepedent of atom position, is checked.

TESTFIXES:

• Analysis/3: test.xyz changed because boundary is now 1.5 instead of 2.1 as 2.1 is not enough of molecules get filled in (and the filler already is).
• Analysis/3: tensid.data was actually lacking water at (0,0,0) which is after the rewrite present.

File:

• src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) (5 diffs)

src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp

@@ -28 +28 @@
 #include "World.hpp"
 
+#include "Descriptors/MoleculeIdDescriptor.hpp"
 #include "Parser/MpqcParser.hpp"
 #include "Parser/PcpParser.hpp"
@@ -35 +36 @@
 #include "Parser/FormatParserStorage.hpp"
 
+#include <algorithm>
 #include <iostream>
 #include <string>
@@ -47 +49 @@
 /** =========== define the function ====================== */
 Action::state_ptr MoleculeFillVoidWithMoleculeAction::performCall() {
-
   // obtain information
   getParametersfromValueStorage();
 
-  DoLog(1) && (Log() << Verbose(1) << "Filling Box with water molecules, lengths(" << params.lengths[0] << "," << params.lengths[1] << "," << params.lengths[2] << "), distances (" << params.distances[0] << "," << params.distances[1] << "," << params.distances[2] << "), DoRotate " << params.DoRotate << "." << endl);
+  if (!boost::filesystem::exists(params.fillername)) {
+    DoeLog(1) && (eLog() << Verbose(1) << "File with filler molecule " << params.fillername << " does not exist!" << endl);
+    return Action::failure;
+  }
+
+  DoLog(1) && (Log() << Verbose(1) << "Filling Box with water molecules, lengths(" << params.lengths[0] << "," << params.lengths[1] << "," << params.lengths[2] << "), distances (" << params.distances[0] << "," << params.distances[1] << "," << params.distances[2] << "), MinDistance " << params.MinDistance << ", DoRotate " << params.DoRotate << "." << endl);
   // construct water molecule
-  molecule *filler = World::getInstance().createMolecule();
+  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;
@@ -92 +99 @@
       break;
   }
-  World::MoleculeIterator iter = World::getInstance().getMoleculeIter();
-  for (; iter != World::getInstance().moleculeEnd(); ++iter)
+
+  // 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
   filler->SetNameFromFilename(params.fillername.string().c_str());
@@ -102 +113 @@
   for (int i=0;i<NDIM;i++)
     distance[i] = params.distances[i];
-  FillVoidWithMolecule(filler, *(World::getInstance().getConfig()), distance, params.lengths[0], params.lengths[1], params.lengths[2], params.DoRotate);
+  FillVoidWithMolecule(filler, *(World::getInstance().getConfig()), distance, params.lengths[0], params.lengths[1], params.lengths[2], params.MinDistance, params.DoRotate);
 
-  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 MoleculeFillVoidWithMoleculeState(fillermolecules,params));
 }
 
 Action::state_ptr MoleculeFillVoidWithMoleculeAction::performUndo(Action::state_ptr _state) {
-//  MoleculeFillVoidWithMoleculeState *state = assert_cast<MoleculeFillVoidWithMoleculeState*>(_state.get());
+  MoleculeFillVoidWithMoleculeState *state = assert_cast<MoleculeFillVoidWithMoleculeState*>(_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 MoleculeFillVoidWithMoleculeState(fillermolecules,state->params));
 }
 
 Action::state_ptr MoleculeFillVoidWithMoleculeAction::performRedo(Action::state_ptr _state){
-  // Undo and redo have to do the same for this action
-  return performUndo(_state);
+  //MoleculeFillVoidWithMoleculeState *state = assert_cast<MoleculeFillVoidWithMoleculeState*>(_state.get());
+
+  return Action::failure;
+  //return Action::state_ptr(_state);
 }
 
 bool MoleculeFillVoidWithMoleculeAction::canUndo() {
-  return false;
+  return true;
 }
 
 bool MoleculeFillVoidWithMoleculeAction::shouldUndo() {
-  return false;
+  return true;
 }
 /** =========== end of function ====================== */