Changeset 80ca29 for src/Actions/FillAction/FillRegularGridAction.cpp

Timestamp:

Apr 6, 2012, 11:44:51 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:

531f27

Parents:

72e4c95

git-author:

Frederik Heber <heber@…> (04/05/12 15:42:12)

git-committer:

Frederik Heber <heber@…> (04/06/12 11:44:51)

Message:

Added regression test Filling/RegularGrid with and without a tesselated surface.

• also repaired FillRegularGridAction such that do/undo/redo works.

File:

• src/Actions/FillAction/FillRegularGridAction.cpp (modified) (10 diffs)

src/Actions/FillAction/FillRegularGridAction.cpp

@@ -24 +24 @@
 #include "Atom/AtomicInfo.hpp"
 #include "Atom/CopyAtoms/CopyAtoms_withBonds.hpp"
+#include "Bond/BondInfo.hpp"
 #include "CodePatterns/Log.hpp"
 #include "Descriptors/MoleculeOrderDescriptor.hpp"
@@ -67 +68 @@
   getParametersfromValueStorage();
 
-  // get the filler molecule and move to origin
+  // get the filler molecule
+  std::vector<AtomicInfo> movedatoms;
   const std::vector< molecule *> molecules = World::getInstance().getSelectedMolecules();
   if (molecules.size() != 1) {
@@ -74 +76 @@
   }
   molecule *filler = *(molecules.begin());
+  for(molecule::const_iterator iter = filler->begin(); iter != filler->end(); ++iter)
+    movedatoms.push_back( AtomicInfo(*(*iter)) );
   LOG(1, "INFO: Chosen molecule has " << filler->size() << " atoms.");
 
@@ -82 +86 @@
   Tesselation * TesselStruct = NULL;
   if (params.SphereRadius != 0.) {
-    if ( molecules.size() == 0) {
+    if ( atoms.size() == 0) {
       ELOG(1, "You have given a sphere radius " << params.SphereRadius
           << " != 0, but have not select any molecules.");
+      return Action::failure;
     }
     // create adaptor for the selected atoms
@@ -99 +104 @@
 
   // create predicate, mesh, and filler
-  std::vector<AtomicInfo> clonedatoms;
+  FillRegularGridState *UndoState = NULL;
   bool successflag = false;
   {
@@ -129 +134 @@
       delete fillerFunction;
 
-      // append each cluster's atoms to clonedatoms
+      // append each cluster's atoms to clonedatoms (however not selected ones)
+      std::vector<const atom *> clonedatoms;
+      std::vector<AtomicInfo> clonedatominfos;
       for (Filler::ClusterVector_t::const_iterator iter = ClonedClusters.begin();
           iter != ClonedClusters.end(); ++iter) {
@@ -135 +142 @@
         clonedatoms.reserve(clonedatoms.size()+atoms.size());
         for (AtomIdSet::const_iterator atomiter = atoms.begin(); atomiter != atoms.end(); ++atomiter)
-          clonedatoms.push_back( AtomicInfo(*(*atomiter)) );
+          if (!filler->containsAtom(*atomiter)) {
+            clonedatoms.push_back( *atomiter );
+            clonedatominfos.push_back( AtomicInfo(*(*atomiter)) );
+          }
       }
+      std::vector< BondInfo > clonedbonds;
+      StoreBondInformationFromAtoms(clonedatoms, clonedbonds);
+      LOG(2, "DEBUG: There are " << clonedatominfos.size() << " newly created atoms.");
+
       if (!successflag) {
-        ELOG(1, "Insertion failed, removing inserted clusters again.");
-        RemoveAtomsFromAtomicInfo(clonedatoms);
+        ELOG(1, "Insertion failed, removing inserted clusters, translating original one back");
+        RemoveAtomsFromAtomicInfo(clonedatominfos);
         clonedatoms.clear();
+        SetAtomsFromAtomicInfo(movedatoms);
+      } else {
+        std::vector<Vector> MovedToVector(filler->size(), zeroVec);
+        std::transform(filler->begin(), filler->end(), MovedToVector.begin(),
+            boost::bind(&AtomInfo::getPosition, _1) );
+        UndoState = new FillRegularGridState(clonedatominfos,clonedbonds,movedatoms,MovedToVector,params);
       }
     }
@@ -154 +174 @@
 
   if (successflag)
-    return Action::state_ptr(new FillRegularGridState(clonedatoms,params));
+    return Action::state_ptr(UndoState);
   else
     return Action::failure;
@@ -164 +184 @@
   // remove all created atoms
   RemoveAtomsFromAtomicInfo(state->clonedatoms);
+  // add the original cluster
+  SetAtomsFromAtomicInfo(state->movedatoms);
 
   return Action::state_ptr(_state);
@@ -171 +193 @@
   FillRegularGridState *state = assert_cast<FillRegularGridState*>(_state.get());
 
-  if (AddAtomsFromAtomicInfo(state->clonedatoms))
+  // place filler cluster again at new spot
+  ResetAtomPosition(state->movedatoms, state->MovedToVector);
+
+  // re-create all clusters
+  bool statusflag = AddAtomsFromAtomicInfo(state->clonedatoms);
+
+  // re-create the bonds
+  if (statusflag)
+    AddBondsFromBondInfo(state->clonedbonds);
+  if (statusflag)
     return Action::state_ptr(_state);
   else