Changeset 91207d for src/Fragmentation

Timestamp:

Dec 3, 2012, 9:50:01 AM (12 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:

0fad93

Parents:

2ab6b6

git-author:

Frederik Heber <heber@…> (09/20/12 16:09:37)

git-committer:

Frederik Heber <heber@…> (12/03/12 09:50:01)

Message:

AtomMask is now fully used, only marked atoms end up in fragments.

• i.e. now only the selected atoms are fragmented.
• AdaptivityMap::MarkUpdateCandidates() now marks all false who are already below threshold.
• Fragmentation::CheckOrderAtSite() does not clear AtomMask anymore and does not set to true only to false when order has been reached.
• We reversed direction as the AtomMask is not cleared anymore but just subsequently all sites are removed who are below threshold or have reached desired order.

Location:

src/Fragmentation

Files:

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

src/Fragmentation/AdaptivityMap.cpp

@@ -199 +199 @@
 bool AdaptivityMap::MarkUpdateCandidates(AtomMask_t &AtomMask, int Order, molecule *mol) const
 {
-  atom *Walker = NULL;
-  int No = -1;
-  bool status = false;
   ASSERT( FinalRootCandidates != NULL,
       "AdaptivityMap::MarkUpdateCandidates() - FinalRootCandidates is not allocated yet.");
-  for(AdaptiveCriteriaValueMap::const_iterator runner = FinalRootCandidates->upper_bound(pow(10.,Order)); runner != FinalRootCandidates->end(); runner++) {
-    No = (*runner).second.first;
-    Walker = mol->FindAtom(No);
-    //if (Walker->AdaptiveOrder < MinimumRingSize[Walker->getNr()]) {
-      LOG(2, "Root " << No << " is still above threshold (10^{" << Order <<"}: " << runner->first << ", setting entry " << No << " of Atom mask to true.");
-      AtomMask.setTrue(No);
-      status = true;
-    //} else {
-      //AtomMask.setFalse(No);
-      //LOG(2, "Root " << No << " is still above threshold (10^{" << Order <<"}: " << runner->first << ", however MinimumRingSize of " << MinimumRingSize[Walker->getNr()] << " does not allow further adaptive increase.");
-    //}
-  }
-  return status;
+  const AdaptiveCriteriaValueMap::const_iterator enditer = FinalRootCandidates->upper_bound(pow(10.,Order));
+  for(AdaptiveCriteriaValueMap::const_iterator runner = FinalRootCandidates->begin();
+      runner != enditer; ++runner) {
+    const int No = (*runner).second.first;
+    const atom *Walker = mol->FindAtom(No);
+    LOG(2, "Root " << No << " is already below threshold (10^{" << Order <<"}: " << runner->first << ", setting entry " << No << " of Atom mask to false.");
+    AtomMask.setFalse(No);
+  }
+  return enditer != FinalRootCandidates->end();
 };
 

src/Fragmentation/Fragmentation.cpp

@@ -91 +91 @@
  * of vertex indices: Global always means the index in "this" molecule, whereas local refers to the molecule or
  * subgraph in the MoleculeListClass.
- * \param atomids atoms to fragment, used in AtomMask
+ * \param atomids atomic ids (local to Fragmentation::mol) to fragment, used in AtomMask
  * \param Order up to how many neighbouring bonds a fragment contains in BondOrderScheme::BottumUp scheme
  * \param prefix prefix string for every fragment file name (may include path)
@@ -103 +103 @@
   bool CheckOrder = false;
   int TotalNumberOfKeySets = 0;
-  AtomMask_t AtomMask(atomids);
 
   LOG(0, std::endl);
@@ -126 +125 @@
     const std::vector<atomId_t> globalids = getGlobalIdsFromLocalIds(*mol, atomids);
     FragmentationToDo = FragmentationToDo && FileChecker(globalids);
+  }
+
+  // ===== 2. create AtomMask that takes Saturation condition into account
+  AtomMask_t AtomMask(atomids);
+  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
+    // remove in hydrogen and we do saturate
+    if ((saturation == DoSaturate) && ((*iter)->getType()->getAtomicNumber() == 1)) // skip hydrogen
+      AtomMask.setFalse((*iter)->getNr());
   }
 
@@ -335 +342 @@
   bool status = false;
 
-  // initialize mask list
-  AtomMask.clear();
-
   if (Order < 0) { // adaptive increase of BondOrder per site
     if (LoopDoneAlready)  // break after one step
@@ -353 +357 @@
     if (IndexKeySetList->IsAdaptiveCriteriaListEmpty()) {
       ELOG(2, "Unable to parse file, incrementing all.");
-      for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-        if ((saturation == DontSaturate) || ((*iter)->getType()->getAtomicNumber() != 1)) // skip hydrogen
-        {
-          AtomMask.setTrue((*iter)->getNr());  // include all (non-hydrogen) atoms
-          status = true;
-        }
-      }
+      status = true;
     } else {
-      IndexKeySetList->MarkUpdateCandidates(AtomMask, Order, mol);
+      // mark as false all sites that are below threshold already
+      status = IndexKeySetList->MarkUpdateCandidates(AtomMask, Order, mol);
     }
 
@@ -367 +366 @@
   } else { // global increase of Bond Order
     for(molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-      if ((saturation == DontSaturate) || ((*iter)->getType()->getAtomicNumber() != 1)) // skip hydrogen
-      {
-        AtomMask.setTrue((*iter)->getNr());  // include all (non-hydrogen) atoms
-        if ((Order != 0) && ((*iter)->AdaptiveOrder < Order)) // && ((*iter)->AdaptiveOrder < MinimumRingSize[(*iter)->getNr()]))
+      if (AtomMask.isTrue((*iter)->getNr())) { // skip masked out
+        // remove all that have reached desired order
+        if ((Order != 0) && ((*iter)->AdaptiveOrder >= Order)) // && ((*iter)->AdaptiveOrder < MinimumRingSize[(*iter)->getNr()]))
+          AtomMask.setFalse((*iter)->getNr());
+        else
           status = true;
       }