Changeset 958457 for src

Timestamp:

Jul 28, 2008, 1:45:43 PM (17 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:

b61043

Parents:

390248

Message:

CheckOrderAtSite: BUGFIX - Added MinimumRingSize to parameter list, as otherwise infinite loop

If FragmentBOSSANOVA checks for remaining below MinimumRingSize per atom, CheckOrderAtSite however does not and fills AtomMask with values for atoms not to be included, we end up with an endless loop. Hence, MinimumRingSize is given as an additional parameter and CheckOrderAtSite checks for it for adaptive and for global increase (for stepwise we don't have the loop problem and FragmentBOSSANOVA will do the right thing).

Location:

src

Files:

• molecules.cpp (modified) (5 diffs)
• molecules.hpp (modified) (1 diff)

src/molecules.cpp

@@ -2367 +2367 @@
 };
 
-/** Checks whether the OrderAtSite is still bewloe \a Order at some site.
+/** Checks whether the OrderAtSite is still below \a Order at some site.
  * \param *out output stream for debugging
  * \param *AtomMask defines true/false per global Atom::nr to mask in/out each nuclear site, used to activate given number of site to increment order adaptively
  * \param *GlobalKeySetList list of keysets with global ids (valid in "this" molecule) needed for adaptive increase
  * \param Order desired Order if positive, desired exponent in threshold criteria if negative (0 is single-step)
+ * \param *MinimumRingSize array of max. possible order to avoid loops
  * \param *path path to ENERGYPERFRAGMENT file (may be NULL if Order is non-negative)
  * \return true - needs further fragmentation, false - does not need fragmentation
  */
-bool molecule::CheckOrderAtSite(ofstream *out, bool *AtomMask, Graph *GlobalKeySetList, int Order, char *path)
+bool molecule::CheckOrderAtSite(ofstream *out, bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path)
 {
   atom *Walker = start;
@@ -2466 +2467 @@
       for(map<double, pair<int,int> >::iterator runner = FinalRootCandidates.upper_bound(pow(10.,Order)); runner != FinalRootCandidates.end(); runner++) {
         No = (*runner).second.first;
-        *out << Verbose(2) << "Root " << No << " is still above threshold (10^{" << Order <<"}: " << runner->first << ", setting entry " << No << " of Atom mask to true." << endl; 
-        AtomMask[No] = true;
-        status = true;
+        Walker = FindAtom(No);
+        if (Walker->AdaptiveOrder < MinimumRingSize[Walker->nr]) {
+          *out << Verbose(2) << "Root " << No << " is still above threshold (10^{" << Order <<"}: " << runner->first << ", setting entry " << No << " of Atom mask to true." << endl; 
+          AtomMask[No] = true;
+          status = true;
+        } else
+          *out << Verbose(2) << "Root " << No << " is still above threshold (10^{" << Order <<"}: " << runner->first << ", however MinimumRingSize of " << MinimumRingSize[Walker->nr] << " does not allow further adaptive increase." << endl; 
       }
       // close and done
@@ -2496 +2501 @@
       {
         AtomMask[Walker->nr] = true;  // include all (non-hydrogen) atoms
-        if ((Order != 0) && (Walker->AdaptiveOrder < Order))
+        if ((Order != 0) && (Walker->AdaptiveOrder < Order) && (Walker->AdaptiveOrder < MinimumRingSize[Walker->nr]))
           status = true;
       }
@@ -2624 +2629 @@
   KeyStack *RootStack = new KeyStack[Subgraphs->next->Count()];
   AtomMask = new bool[AtomCount+1];
-  while (CheckOrderAtSite(out, AtomMask, ParsedFragmentList, Order, configuration->configpath)) {
+  while (CheckOrderAtSite(out, AtomMask, ParsedFragmentList, Order, MinimumRingSize, configuration->configpath)) {
     AtomMask[AtomCount] = true;   // last plus one entry is used as marker that we have been through this loop once already in CheckOrderAtSite()
     // ===== 6b. fill RootStack for each subgraph (second adaptivity check) ===== 
@@ -3974 +3979 @@
   // with the order along the cells as this: 5433222211111111 for BondOrder 5 needing 16=pow(2,5-1) cells (only we use bit-shifting which is faster)
   RootNr = 0;   // counts through the roots in RootStack
-  while (RootNr < UpgradeCount) {
+  while ((RootNr < UpgradeCount) && (!RootStack.empty())) {
     RootKeyNr = RootStack.front();
     RootStack.pop_front();
     Walker = FindAtom(RootKeyNr);
     // check cyclic lengths
-    if ((MinimumRingSize[Walker->GetTrueFather()->nr] != -1) && (Walker->GetTrueFather()->AdaptiveOrder+1 >= MinimumRingSize[Walker->GetTrueFather()->nr])) {
+    if ((MinimumRingSize[Walker->GetTrueFather()->nr] != -1) && (Walker->GetTrueFather()->AdaptiveOrder+1 > MinimumRingSize[Walker->GetTrueFather()->nr])) {
       *out << Verbose(0) << "Bond order " << Walker->GetTrueFather()->AdaptiveOrder << " of Root " << *Walker << " greater than or equal to Minimum Ring size of " << MinimumRingSize << " found is not allowed." << endl;
     } else {

src/molecules.hpp

@@ -242 +242 @@
   /// Fragment molecule by two different approaches:
   void FragmentMolecule(ofstream *out, int Order, config *configuration);
-  bool CheckOrderAtSite(ofstream *out, bool *AtomMask, Graph *GlobalKeySetList, int Order, char *path = NULL);
+  bool CheckOrderAtSite(ofstream *out, bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path = NULL);
   bool StoreAdjacencyToFile(ofstream *out, char *path);
   bool CheckAdjacencyFileAgainstMolecule(ofstream *out, char *path, atom **ListOfAtoms);