Changeset ea7176 for src/molecule_dynamics.cpp

Timestamp:

Mar 19, 2010, 1:29:01 PM (15 years ago)

Author:

Tillmann Crueger <crueger@…>

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:

e0b6fd

Parents:

80c63d

Message:

FIX: Made AtomCount a Cacheable so that the number of atoms in a molecule will always be correct

All unittests working.
All Complete testcases fail.

File:

• src/molecule_dynamics.cpp (modified) (12 diffs)

src/molecule_dynamics.cpp

@@ -213 +213 @@
 void FillDistanceList(molecule *mol, struct EvaluatePotential &Params)
 {
-  for (int i=mol->AtomCount; i--;) {
+  for (int i=mol->getAtomCount(); i--;) {
     Params.DistanceList[i] = new DistanceMap;    // is the distance sorted target list per atom
     Params.DistanceList[i]->clear();
@@ -287 +287 @@
   }
   while ((Potential) > Params.PenaltyConstants[2]) {
-    PrintPermutationMap(mol->AtomCount, Params);
+    PrintPermutationMap(mol->getAtomCount(), Params);
     iter++;
     if (iter == mol->end()) // round-robin at the end
@@ -296 +296 @@
     Potential = TryNextNearestNeighbourForInjectivePermutation(mol, (*iter), Potential, Params);
   }
-  for (int i=mol->AtomCount; i--;) // now each single entry in the DoubleList should be <=1
+  for (int i=mol->getAtomCount(); i--;) // now each single entry in the DoubleList should be <=1
     if (Params.DoubleList[i] > 1) {
       eLog() << Verbose(0) << "Failed to create an injective PermutationMap!" << endl;
@@ -335 +335 @@
   double Potential, OldPotential, OlderPotential;
   struct EvaluatePotential Params;
-  Params.PermutationMap = Calloc<atom*>(AtomCount, "molecule::MinimiseConstrainedPotential: Params.**PermutationMap");
-  Params.DistanceList = Malloc<DistanceMap*>(AtomCount, "molecule::MinimiseConstrainedPotential: Params.**DistanceList");
-  Params.DistanceIterators = Malloc<DistanceMap::iterator>(AtomCount, "molecule::MinimiseConstrainedPotential: Params.*DistanceIterators");
-  Params.DoubleList = Calloc<int>(AtomCount, "molecule::MinimiseConstrainedPotential: Params.*DoubleList");
-  Params.StepList = Malloc<DistanceMap::iterator>(AtomCount, "molecule::MinimiseConstrainedPotential: Params.*StepList");
+  Params.PermutationMap = Calloc<atom*>(getAtomCount(), "molecule::MinimiseConstrainedPotential: Params.**PermutationMap");
+  Params.DistanceList = Malloc<DistanceMap*>(getAtomCount(), "molecule::MinimiseConstrainedPotential: Params.**DistanceList");
+  Params.DistanceIterators = Malloc<DistanceMap::iterator>(getAtomCount(), "molecule::MinimiseConstrainedPotential: Params.*DistanceIterators");
+  Params.DoubleList = Calloc<int>(getAtomCount(), "molecule::MinimiseConstrainedPotential: Params.*DoubleList");
+  Params.StepList = Malloc<DistanceMap::iterator>(getAtomCount(), "molecule::MinimiseConstrainedPotential: Params.*StepList");
   int round;
   atom *Sprinter = NULL;
@@ -372 +372 @@
       iter = begin();
       for (; iter != end(); ++iter) {
-        PrintPermutationMap(AtomCount, Params);
+        PrintPermutationMap(getAtomCount(), Params);
         Sprinter = Params.DistanceIterators[(*iter)->nr]->second;   // store initial partner
         Strider = Params.DistanceIterators[(*iter)->nr];  //remember old iterator
@@ -400 +400 @@
             Params.PermutationMap[(*iter)->nr] = Params.DistanceIterators[(*iter)->nr]->second; // put next farther distance into PermutationMap
             Params.PermutationMap[(*runner)->nr] = Sprinter;  // and hand the old target to its respective owner
-            PrintPermutationMap(AtomCount, Params);
+            PrintPermutationMap(getAtomCount(), Params);
             // calculate the new potential
             //Log() << Verbose(2) << "Checking new potential ..." << endl;
@@ -438 +438 @@
 
   /// free memory and return with evaluated potential
-  for (int i=AtomCount; i--;)
+  for (int i=getAtomCount(); i--;)
     Params.DistanceList[i]->clear();
   Free(&Params.DistanceList);
@@ -483 +483 @@
     MinimiseConstrainedPotential(PermutationMap, startstep, endstep, configuration.GetIsAngstroem());
   else {
-    PermutationMap = Malloc<atom *>(AtomCount, "molecule::LinearInterpolationBetweenConfiguration: **PermutationMap");
+    PermutationMap = Malloc<atom *>(getAtomCount(), "molecule::LinearInterpolationBetweenConfiguration: **PermutationMap");
     SetIndexedArrayForEachAtomTo( PermutationMap, &atom::nr );
   }
@@ -516 +516 @@
 
   // store the list to single step files
-  int *SortIndex = Malloc<int>(AtomCount, "molecule::LinearInterpolationBetweenConfiguration: *SortIndex");
-  for (int i=AtomCount; i--; )
+  int *SortIndex = Malloc<int>(getAtomCount(), "molecule::LinearInterpolationBetweenConfiguration: *SortIndex");
+  for (int i=getAtomCount(); i--; )
     SortIndex[i] = i;
   status = MoleculePerStep->OutputConfigForListOfFragments(&configuration, SortIndex);
@@ -561 +561 @@
       return false;
     }
-    if (Force.RowCounter[0] != AtomCount) {
-      eLog() << Verbose(0) << "Mismatch between number of atoms in file " << Force.RowCounter[0] << " and in molecule " << AtomCount << "." << endl;
+    if (Force.RowCounter[0] != getAtomCount()) {
+      eLog() << Verbose(0) << "Mismatch between number of atoms in file " << Force.RowCounter[0] << " and in molecule " << getAtomCount() << "." << endl;
       performCriticalExit();
       return false;
@@ -568 +568 @@
     // correct Forces
     Velocity.Zero();
-    for(int i=0;i<AtomCount;i++)
+    for(int i=0;i<getAtomCount();i++)
       for(int d=0;d<NDIM;d++) {
         Velocity.x[d] += Force.Matrix[0][i][d+5];
       }
-    for(int i=0;i<AtomCount;i++)
+    for(int i=0;i<getAtomCount();i++)
       for(int d=0;d<NDIM;d++) {
-        Force.Matrix[0][i][d+5] -= Velocity.x[d]/(double)AtomCount;
+        Force.Matrix[0][i][d+5] -= Velocity.x[d]/static_cast<double>(getAtomCount());
       }
     // solve a constrained potential if we are meant to
@@ -677 +677 @@
       delta_alpha = 0.;
       ActOnAllAtoms( &atom::Thermostat_NoseHoover_init, MDSteps, &delta_alpha );
-      delta_alpha = (delta_alpha - (3.*AtomCount+1.) * configuration.TargetTemp)/(configuration.HooverMass*Units2Electronmass);
+      delta_alpha = (delta_alpha - (3.*getAtomCount()+1.) * configuration.TargetTemp)/(configuration.HooverMass*Units2Electronmass);
       configuration.alpha += delta_alpha*configuration.Deltat;
       Log() << Verbose(3) << "alpha = " << delta_alpha << " * " << configuration.Deltat << " = " << configuration.alpha << "." << endl;