Changeset ed0f88 for src/Actions

Timestamp:

May 18, 2016, 10:02:54 PM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, 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_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, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, 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:

c4aeda

Parents:

91f907

git-author:

Frederik Heber <heber@…> (03/07/16 22:20:45)

git-committer:

Frederik Heber <heber@…> (05/18/16 22:02:54)

Message:

Using unique graph set as key to particle name in FitPartialChargesAction.

File:

• src/Actions/PotentialAction/FitPartialChargesAction.cpp (modified) (7 diffs)

src/Actions/PotentialAction/FitPartialChargesAction.cpp

@@ -91 +91 @@
   typedef std::set<size_t> AtomsGraphIndices_t;
   typedef boost::bimaps::bimap<
-      AtomsGraphIndices_t,
-      boost::bimaps::multiset_of<atomId_t> > GraphIndices_t;
-
-  typedef std::map<atomId_t, std::string> AtomParticleNames_t;
+      boost::bimaps::multiset_of<AtomsGraphIndices_t>,
+      atomId_t > GraphIndices_t;
+
+  typedef std::map<std::set<size_t>, std::map<atomicNumber_t, std::string> > AtomParticleNames_t;
 
   typedef std::map<std::set<size_t>, std::string> GraphToNameMap_t;
@@ -277 +277 @@
 }
 
-double fitAverageChargeToAtom(
-    const atom * const _walker,
-    const AtomFragmentsMap &_atomfragments,
-    const detail::KeysetsToGraph_t &_keyset_graphs,
-    const detail::GraphFittedChargeMap_t &_fittedcharges_per_fragment)
+const atom * getNonHydrogenSurrogate(const atom * const _walker)
 {
   const atom * surrogate = _walker;
@@ -289 +285 @@
     const BondList &ListOfBonds = surrogate->getListOfBonds();
     if ( ListOfBonds.size() != 1) {
-      ELOG(1, "Solitary hydrogen in atom " << surrogate->getId() << " detected, skipping.");
-      return 0.;
+      ELOG(1, "Solitary hydrogen in atom " << surrogate->getId() << " detected.");
+      return _walker;
     }
     surrogate = (*ListOfBonds.begin())->GetOtherAtom(surrogate);
   }
+  return surrogate;
+}
+
+double fitAverageChargeToAtom(
+    const atom * const _walker,
+    const AtomFragmentsMap &_atomfragments,
+    const detail::KeysetsToGraph_t &_keyset_graphs,
+    const detail::GraphFittedChargeMap_t &_fittedcharges_per_fragment)
+{
+  const atom * const surrogate = getNonHydrogenSurrogate(_walker);
   const atomId_t walkerid = surrogate->getId();
   const AtomFragmentsMap::AtomFragmentsMap_t &atommap = _atomfragments.getMap();
@@ -357 +363 @@
     detail::AtomParticleNames_t &_atom_particlenames)
 {
-  detail::GraphToNameMap_t GraphToNameMap;
   for (detail::fitted_charges_t::const_iterator chargeiter = _fitted_charges.begin();
       chargeiter != _fitted_charges.end(); ++chargeiter) {
     const atomId_t &atomid = chargeiter->first;
-    const detail::GraphIndices_t::right_const_iterator graphiter = _GraphIndices.right.find(atomid);
-    const detail::GraphToNameMap_t::const_iterator nameiter = GraphToNameMap.find(graphiter->second);
+    const atom * const walker = World::getInstance().getAtom(AtomById(atomid));
+    ASSERT( walker != NULL,
+        "addToParticleRegistry() - atom "+toString(atomid)
+        +" not present in the World?");
+    const detail::GraphIndices_t::right_const_iterator graphiter =
+        _GraphIndices.right.find(atomid);
+    ASSERT(graphiter != _GraphIndices.right.end(),
+        "addToParticleRegistry() - atom #"+toString(atomid)
+        +" not contained in GraphIndices.");
+    const detail::AtomParticleNames_t::iterator nameiter =
+        _atom_particlenames.find(graphiter->second);
+    const atomicNumber_t elementno = walker->getElementNo();
     std::string name;
-    if (nameiter != GraphToNameMap.end()) {
-      name = nameiter->second;
+    if ((nameiter != _atom_particlenames.end()) && (nameiter->second.count(elementno))) {
+        name = (nameiter->second)[elementno];
     } else {
-      const atom * const walker = World::getInstance().getAtom(AtomById(atomid));
-      ASSERT( walker != NULL,
-          "addToParticleRegistry() - atom "+toString(atomid)+" not present in the World?");
+      if (nameiter == _atom_particlenames.end())
+        _atom_particlenames.insert(
+            std::make_pair(graphiter->second, std::map<atomicNumber_t, std::string>()) );
       const double &charge = chargeiter->second;
-      const atomicNumber_t elementno = walker->getElementNo();
       name = Particle::findFreeName(periode, elementno);
-      GraphToNameMap[graphiter->second] = name;
+      _atom_particlenames[graphiter->second][elementno] = name;
       LOG(1, "INFO: Adding particle " << name << " for atom "
           << *walker << " with element " << elementno << ", charge " << charge);
       factory.createInstance(name, elementno, charge);
     }
-    _atom_particlenames.insert( std::make_pair(atomid, name) );
   }
 }
@@ -439 +452 @@
   LOG(2, "DEBUG: There are " << index << " unique graphs in the homology container.");
 
-  // go through every atom, get all graphs, convert to GraphIndex and store
-
+  // go through every non-hydrogen atom, get all graphs, convert to GraphIndex and store
   detail::GraphIndices_t GraphIndices;
   const AtomFragmentsMap::AtomFragmentsMap_t &atommap = atomfragments.getMap();
   for (World::AtomSelectionConstIterator atomiter = world.beginAtomSelection();
       atomiter != world.endAtomSelection(); ++atomiter) {
-    const atomId_t walkerid = atomiter->first;
+    // use the non-hydrogen here
+    const atomId_t walkerid = getNonHydrogenSurrogate(atomiter->second)->getId();
+    if (walkerid != atomiter->first)
+      continue;
     const AtomFragmentsMap::AtomFragmentsMap_t::const_iterator keysetsiter =
-        atommap.find(walkerid);
+        atommap.find(atomiter->first);
     ASSERT(keysetsiter != atommap.end(),
         "PotentialFitPartialChargesAction::performCall() - we checked already that "
@@ -453 +468 @@
     const AtomFragmentsMap::keysets_t & keysets = keysetsiter->second;
 
+    // go over all fragments associated to this atom
     detail::AtomsGraphIndices_t AtomsGraphIndices;
-
-    // go over all fragments associated to this atom
     for (AtomFragmentsMap::keysets_t::const_iterator keysetsiter = keysets.begin();
         keysetsiter != keysets.end(); ++keysetsiter) {
@@ -471 +485 @@
       AtomsGraphIndices.insert( indexiter->second );
     }
-    GraphIndices.left.insert( std::make_pair(AtomsGraphIndices, walkerid) );
-    LOG(2, "DEBUG: Atom " << *atomiter->second << " has graph indices " << AtomsGraphIndices);
+
+    GraphIndices.insert( detail::GraphIndices_t::value_type(AtomsGraphIndices, atomiter->first) );
+
+    LOG(2, "DEBUG: Atom #" << atomiter->first << "," << *atomiter->second
+        << ". has graph indices " << AtomsGraphIndices);
+  }
+  // then graphs from non-hydrogen bond partner for all hydrogens
+  for (World::AtomSelectionConstIterator atomiter = world.beginAtomSelection();
+      atomiter != world.endAtomSelection(); ++atomiter) {
+    // use the non-hydrogen here
+    const atomId_t walkerid = getNonHydrogenSurrogate(atomiter->second)->getId();
+    if (walkerid == atomiter->first)
+      continue;
+    detail::GraphIndices_t::right_const_iterator graphiter = GraphIndices.right.find(walkerid);
+    ASSERT( graphiter != GraphIndices.right.end(),
+        "PotentialFitPartialChargesAction::performCall() - atom #"+toString(walkerid)
+        +" not contained in GraphIndices.");
+    const detail::AtomsGraphIndices_t &AtomsGraphIndices = graphiter->second;
+    GraphIndices.insert( detail::GraphIndices_t::value_type(AtomsGraphIndices, atomiter->first) );
+    LOG(2, "DEBUG: Hydrogen #" << atomiter->first << ", " << *atomiter->second
+        << ", has graph indices " << AtomsGraphIndices);
   }