Changeset 3c58f8

Timestamp:

Feb 4, 2011, 6:56:38 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:

4c2643

Parents:

72d108

git-author:

Frederik Heber <heber@…> (02/02/11 09:43:01)

git-committer:

Frederik Heber <heber@…> (02/04/11 18:56:38)

Message:

Changed molecule::ScanForPeriodicCorrection().

• it still used templated link stuff for the bonds which is deprecated and hence not usable.
• now simply bool is returned, whether periodic fixing _would_ be necessary.
• the number of of periodic fixings is counted and printed in MoleculeListClass::OutputConfigForListOfFragments().

Location:

src

Files:

• molecule.hpp (modified) (1 diff)
• molecule_fragmentation.cpp (modified) (7 diffs)
• moleculelist.cpp (modified) (3 diffs)

src/molecule.hpp

@@ -206 +206 @@
   void SetNameFromFilename(const char *filename);
   void SetBoxDimension(Vector *dim);
-  void ScanForPeriodicCorrection();
+  bool ScanForPeriodicCorrection();
   bool VerletForceIntegration(char *file, config &configuration, const size_t offset);
   double VolumeOfConvexEnvelope(bool IsAngstroem);

src/molecule_fragmentation.cpp

@@ -1768 +1768 @@
  * \param *out ofstream for debugging messages
  */
-void molecule::ScanForPeriodicCorrection()
+bool molecule::ScanForPeriodicCorrection()
 {
   bond *Binder = NULL;
@@ -1777 +1777 @@
   enum Shading *ColorList = NULL;
   double tmp;
+  bool LastBond = true; // only needed to due list construct
   Vector Translationvector;
   //std::deque<atom *> *CompStack = NULL;
@@ -1787 +1788 @@
   for (int i=0;i<getAtomCount();i++)
     ColorList[i] = (enum Shading)0;
-  while (flag) {
+  if (flag) {
     // remove bonds that are beyond bonddistance
     Translationvector.Zero();
@@ -1799 +1800 @@
           //Log() << Verbose(3) << "Checking " << i << "th distance of " << *Binder->leftatom << " to " << *Binder->rightatom << ": " << tmp << "." << endl;
           if (tmp > BondDistance) {
-            OtherBinder = Binder->next; // note down binding partner for later re-insertion
-            unlink(Binder);   // unlink bond
+//            OtherBinder = Binder->next; // note down binding partner for later re-insertion
+//            if (OtherBinder != NULL) {
+//              LastBond = false;
+//            } else {
+//              OtherBinder = Binder->previous;
+//              LastBond = true;
+//            }
+//            unlink(Binder);   // unlink bond
             DoLog(2) && (Log() << Verbose(2) << "Correcting at bond " << *Binder << "." << endl);
             flag = true;
@@ -1807 +1814 @@
         }
       }
-    if (flag) {
+    //if (flag) {
+    if (0) {
       // create translation vector from their periodically modified distance
       for (int i=NDIM;i--;) {
@@ -1837 +1845 @@
       }
       // re-add bond
-      link(Binder, OtherBinder);
+      if (OtherBinder == NULL) { // is the only bond?
+        //Do nothing
+      } else {
+        if (!LastBond) {
+          link(Binder, OtherBinder);
+        } else {
+          link(OtherBinder, Binder);
+        }
+      }
     } else {
       DoLog(3) && (Log() << Verbose(3) << "No corrections for this fragment." << endl);
@@ -1847 +1863 @@
   delete[](ColorList);
   DoLog(2) && (Log() << Verbose(2) << "End of ScanForPeriodicCorrection." << endl);
-};
+
+  return flag;
+};

src/moleculelist.cpp

@@ -506 +506 @@
   RealSpaceMatrix cell_size = World::getInstance().getDomain().getM();
   RealSpaceMatrix cell_size_backup = cell_size;
+  int count=0;
 
   // store the fragments as config and as xyz
@@ -519 +520 @@
 
     // correct periodic
-    (*ListRunner)->ScanForPeriodicCorrection();
+    if ((*ListRunner)->ScanForPeriodicCorrection()) {
+      count++;
+    }
 
     // output xyz file
@@ -591 +594 @@
   // printing final number
   DoLog(2) && (Log() << Verbose(2) << "Final number of fragments: " << FragmentCounter << "." << endl);
+
+  // printing final number
+  DoLog(0) && (Log() << Verbose(0) << "For " << count << " fragments periodic correction would have been necessary." << endl);
 
   // restore cell_size