Changeset a1c8fa for src/Fragmentation

Timestamp:

Oct 20, 2016, 8:54:23 PM (8 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, 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_ChronosMutex, Fix_ForceAnnealing, Fix_ParseParticles, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, GeometryObjects, Gui_displays_atomic_force_velocity, IndependentFragmentGrids_IntegrationTest, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, RotateToPrincipalAxisSystem_UndoRedo, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, Ubuntu_1604_changes, stable

Children:

72e40d0

Parents:

064b34

git-author:

Frederik Heber <heber@…> (09/27/16 09:58:43)

git-committer:

Frederik Heber <heber@…> (10/20/16 20:54:23)

Message:

FIX: BondedParticleInfo::MaxOrder and ::AdapativeOrder are now stored per trajectory step.

• adapted uses in AdaptivityMap and Fragmentation as members are now protected.

Location:

src/Fragmentation

Files:

• AdaptivityMap.cpp (modified) (1 diff)
• Fragmentation.cpp (modified) (6 diffs)
• fragmentation_helpers.cpp (modified) (3 diffs)

src/Fragmentation/AdaptivityMap.cpp

@@ -154 +154 @@
     Walker = mol->FindAtom((*runner).first);
     if (Walker != NULL) {
-      //if ((*runner).second.second >= Walker->AdaptiveOrder) { // only insert if this is an "active" root site for the current order
-      if (Walker->MaxOrder > Walker->AdaptiveOrder) {
+      //if ((*runner).second.second >= Walker->getAdaptiveOrder()) { // only insert if this is an "active" root site for the current order
+      if (Walker->getMaxOrder() > Walker->getAdaptiveOrder()) {
         LOG(2, "(" << (*runner).first << ",[" << (*runner).second.first << "," << (*runner).second.second << "])");
         FinalRootCandidates->insert( make_pair( (*runner).second.first, pair<int,int>((*runner).first, (*runner).second.second) ) );

src/Fragmentation/Fragmentation.cpp

@@ -286 +286 @@
     atom *Walker = mol->FindAtom(RootKeyNr);
     // check cyclic lengths
-    //if ((MinimumRingSize[Walker->GetTrueFather()->getNr()] != -1) && (Walker->GetTrueFather()->AdaptiveOrder+1 > MinimumRingSize[Walker->GetTrueFather()->getNr()])) {
-    //  LOG(0, "Bond order " << Walker->GetTrueFather()->AdaptiveOrder << " of Root " << *Walker << " greater than or equal to Minimum Ring size of " << MinimumRingSize << " found is not allowed.");
+    //if ((MinimumRingSize[Walker->GetTrueFather()->getNr()] != -1) && (Walker->GetTrueFather()->getAdaptiveOrder()+1 > MinimumRingSize[Walker->GetTrueFather()->getNr()])) {
+    //  LOG(0, "Bond order " << Walker->GetTrueFather()->getAdaptiveOrder() << " of Root " << *Walker << " greater than or equal to Minimum Ring size of " << MinimumRingSize << " found is not allowed.");
     //} else
     {
       // set adaptive order to desired max order
-      Walker->GetTrueFather()->AdaptiveOrder = Walker->GetTrueFather()->MaxOrder;
-      Order = Walker->AdaptiveOrder = Walker->GetTrueFather()->AdaptiveOrder;
+      Walker->GetTrueFather()->setAdaptiveOrder(Walker->GetTrueFather()->getMaxOrder());
+      Order = Walker->GetTrueFather()->getAdaptiveOrder();
+      Walker->setAdaptiveOrder(Order);
 
       // allocate memory for all lower level orders
@@ -302 +303 @@
       // initialise Order-dependent entries of UniqueFragments structure
       UniqueFragments FragmentSearch(1., FragmentLowerOrdersList[RootNr], Walker);
-      PowerSetGenerator PSG(&FragmentSearch, Walker->AdaptiveOrder);
+      PowerSetGenerator PSG(&FragmentSearch, Walker->getAdaptiveOrder());
 
       // create top order where nothing is reduced
@@ -316 +317 @@
 //        NumMolecules = 0;
 //      }
-      // now, we have completely filled each cell of FragmentLowerOrdersList[] for the current Walker->AdaptiveOrder
-      //NumMoleculesOfOrder[Walker->AdaptiveOrder-1] = NumMolecules;
+      // now, we have completely filled each cell of FragmentLowerOrdersList[] for the current Walker->getAdaptiveOrder()
+      //NumMoleculesOfOrder[Walker->getAdaptiveOrder()-1] = NumMolecules;
       TotalNumMolecules += NumMoleculesOfOrder[RootNr];
-//      LOG(1, "Number of resulting molecules for Order " << (int)Walker->GetTrueFather()->AdaptiveOrder << " is: " << NumMoleculesOfOrder[RootNr] << ".");
+//      LOG(1, "Number of resulting molecules for Order " << (int)Walker->GetTrueFather()->getAdaptiveOrder() << " is: " << NumMoleculesOfOrder[RootNr] << ".");
       RootStack.push_back(RootKeyNr); // put back on stack
       RootNr++;
@@ -407 +408 @@
       atom * const Walker = *iter;
       if (AtomMask.isTrue(Walker->getNr())) { // skip masked out
-        Walker->MaxOrder = (Order != 0 ? Order : Walker->MaxOrder+1);
+        Walker->setMaxOrder((Order != 0 ? Order : Walker->getMaxOrder()+1));
         // remove all that have reached desired order
-        if (Walker->AdaptiveOrder >= Walker->MaxOrder) // && (Walker->AdaptiveOrder < MinimumRingSize[Walker->getNr()]))
+        if (Walker->getAdaptiveOrder() >= Walker->getMaxOrder()) // && (Walker->getAdaptiveOrder() < MinimumRingSize[Walker->getNr()]))
           AtomMask.setFalse(Walker->getNr());
         else
@@ -451 +452 @@
         ++iter) {
       file << (*iter)->getId()
-          << "\t" << (int)(*iter)->AdaptiveOrder
-          << "\t" << (int)(*iter)->MaxOrder << std::endl;
+          << "\t" << (int)(*iter)->getAdaptiveOrder()
+          << "\t" << (int)(*iter)->getMaxOrder() << std::endl;
     }
     file.close();
@@ -513 +514 @@
     // set atom values
     for(molecule::iterator iter=mol->begin();iter!=mol->end();++iter){
-      (*iter)->AdaptiveOrder = OrderArray[(*iter)->getNr()];
-      (*iter)->MaxOrder = OrderArray[(*iter)->getNr()]; //MaxArray.isTrue((*iter)->getNr());
+      (*iter)->setAdaptiveOrder(OrderArray[(*iter)->getNr()]);
+      (*iter)->setMaxOrder(OrderArray[(*iter)->getNr()]); //MaxArray.isTrue((*iter)->getNr());
     }
     //SetAtomValueToIndexedArray( OrderArray, &atom::getNr(), &atom::AdaptiveOrder );

src/Fragmentation/fragmentation_helpers.cpp

@@ -45 +45 @@
 
 #include "Atom/atom.hpp"
-#include "Fragmentation/AdaptivityMap.hpp"
 #include "Fragmentation/AtomMask.hpp"
 #include "Fragmentation/Graph.hpp"
@@ -103 +102 @@
     RootStack.pop_front();
     Walker = mol->FindAtom(RootKeyNr);
-    NumLevels = Walker->AdaptiveOrder;
+    NumLevels = Walker->getAdaptiveOrder();
     ASSERT( NumLevels == FragmentLowerOrdersList[RootNr].size(),
         "CombineAllOrderListIntoOne() - differing size and NumLevels.");
@@ -134 +133 @@
     RootStack.pop_front();
     Walker = mol->FindAtom(RootKeyNr);
-    NumLevels = Walker->AdaptiveOrder;
+    NumLevels = Walker->getAdaptiveOrder();
     for(int i=0;i<NumLevels;i++) {
       if (FragmentLowerOrdersList[RootNr][i] != NULL) {