Changeset 9df680 for src

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:

ea430a

Parents:

d6f886

git-author:

Frederik Heber <heber@…> (01/15/11 15:04:18)

git-committer:

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

Message:

FIX: FillVoidWithMolecule() now centers filler molecule at its center of gravity.

• this is the only sensible option if we later rotate the molecule.
• atom::clone() reduced a lot, as copy constructors contains it all.
• FillVoidWithMolecule() - filler is now selected to reside entirely within the domain. Otherwise, we seg'fault on save on exit, as one of the father atoms for all copied atoms is missing and hence, we cannot look at its additional...Data for various parsers.
• new function molecule::removeAtomsInMolecule() which destroys all the molecule's atoms.

TESTFIXES:

• Filling/3: filled water box has changed due to different center of water molecules.

Location:

src

Files:

• atom.cpp (modified) (2 diffs)
• boundary.cpp (modified) (6 diffs)
• molecule.cpp (modified) (1 diff)
• molecule.hpp (modified) (1 diff)

src/atom.cpp

@@ -49 +49 @@
     ParticleInfo(pointer),
     father(pointer),
-    sort(&nr)
+    sort(&nr),
+    mol(0)
 {
   setType(pointer->getType());  // copy element of atom
@@ -55 +56 @@
   AtomicVelocity = pointer->AtomicVelocity; // copy velocity
   FixedIon = pointer->FixedIon;
-  mol = 0;
 };
 
 atom *atom::clone(){
   atom *res = new atom(this);
-  res->father = this;
-  res->sort = &res->nr;
-  res->setType(getType());
-  res->setPosition(this->getPosition());
-  res->AtomicVelocity = this->AtomicVelocity;
-  res->FixedIon = FixedIon;
-  res->mol = 0;
   World::getInstance().registerAtom(res);
   return res;

src/boundary.cpp

@@ -852 +852 @@
         if (DoRandomRotation)
           for (int i=0;i<NDIM;i++)
-            phi[i] = rand()/(RAND_MAX/(2.*M_PI));
+            phi[i] = (rand()/RAND_MAX)*(2.*M_PI);
 
         for(molecule::const_iterator iter = filler->begin(); iter !=filler->end();++iter){
@@ -961 +961 @@
  * @param Filling molecule whose atoms to check, removed if eventually left
  *        empty.
- */
-void RemoveAtomsOutsideDomain(molecule *&Filling)
-{
+ * @return true - atoms had to be removed, false - no atoms have been removed
+ */
+bool RemoveAtomsOutsideDomain(molecule *&Filling)
+{
+  bool status = false;
   Box &Domain = World::getInstance().getDomain();
   // check if all is still inside domain
@@ -969 +971 @@
     // check whether each atom is inside box
     if (!Domain.isInside((*miter)->getPosition())) {
+      status = true;
       atom *Walker = *miter;
       ++miter;
@@ -980 +983 @@
     World::getInstance().destroyMolecule(Filling);
   }
+  return status;
 }
 
@@ -1069 +1073 @@
     }
 
-  // Center filler at origin
-  filler->CenterEdge(&Inserter);
+  // Center filler at its center of gravity
+  Vector *gravity = filler->DetermineCenterOfGravity();
+  filler->CenterAtVector(gravity);
+  delete gravity;
   //const int FillerCount = filler->getAtomCount();
   DoLog(2) && (Log() << Verbose(2) << "INFO: Filler molecule has the following bonds:" << endl);
@@ -1124 +1130 @@
           DoLog(1) && (Log() << Verbose(1) << "INFO: Position at " << Inserter << " is void point." << endl);
           // fill!
-          if (firstInsertion) { // use filler as first molecule
+          Filling = filler->CopyMolecule();
+          RandomizeMoleculePositions(Filling, RandomAtomDisplacement, Rotations);
+          // translation
+          Filling->Translate(&Inserter);
+          // remove out-of-bounds atoms
+          const bool status = RemoveAtomsOutsideDomain(Filling);
+          if ((firstInsertion) && (!status)) { // no atom has been removed
+            // remove copied atoms and molecule again
+            Filling->removeAtomsinMolecule();
+            World::getInstance().destroyMolecule(Filling);
+            // and mark is final filler position
             Filling = filler;
             firstInsertion = false;
             firstInserter = Inserter;
-          } else { // copy from filler molecule
-            Filling = filler->CopyMolecule();
-            RandomizeMoleculePositions(Filling, RandomAtomDisplacement, Rotations);
-            // translation
-            Filling->Translate(&Inserter);
-            // remove out-of-bounds atoms
-            RemoveAtomsOutsideDomain(Filling);
+          } else {
             // TODO: Remove when World has no MoleculeListClass anymore
             MolList->insert(Filling);
           }
         } else {
-          DoLog(1) && (Log() << Verbose(1) << "INFO: Position at " << Inserter << " is non-void point, within boundary or outside of MaxDistance." << endl);
+         DoLog(1) && (Log() << Verbose(1) << "INFO: Position at " << Inserter << " is non-void point, within boundary or outside of MaxDistance." << endl);
           continue;
         }

src/molecule.cpp

@@ -678 +678 @@
 
 
+/** Destroys all atoms inside this molecule.
+ */
+void molecule::removeAtomsinMolecule()
+{
+  // remove each atom from world
+  for(molecule::const_iterator AtomRunner = begin(); !empty(); AtomRunner = begin())
+    World::getInstance().destroyAtom(*AtomRunner);
+};
+
+
 /**
  * Copies all atoms of a molecule which are within the defined parallelepiped.

src/molecule.hpp

@@ -171 +171 @@
   bool UnlinkAtom(atom *pointer);
   bool CleanupMolecule();
+  void removeAtomsinMolecule();
 
   /// Add/remove atoms to/from molecule.