Changeset d8821e for src/Actions/PotentialAction/FitParticleChargesAction.cpp

Timestamp:

Jul 14, 2014, 11:16:23 AM (11 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:

2a03b0

Parents:

c73e35 (diff), a61dbb (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'Fragmentation_Automation_wo_JobMarket' into stable

Conflicts:

src/Actions/ActionQueue.cpp
src/Actions/FragmentationAction/FragmentationAction.cpp
src/Actions/PotentialAction/FitParticleChargesAction.cpp

• in ActionQueue taking over both changes.
• FragmentationAction added Status message where we don't complain for not having HAVE_JOBMARKET anymore. Removed.
• FitParticleChargesAction had charge averaging and error message in case of no present fragments overlapping.

File:

• src/Actions/PotentialAction/FitParticleChargesAction.cpp (modified) (3 diffs)

src/Actions/PotentialAction/FitParticleChargesAction.cpp

@@ -47 +47 @@
 #include <boost/foreach.hpp>
 #include <algorithm>
+#include <functional>
 #include <iostream>
 #include <string>
@@ -128 +129 @@
     return Action::failure;
   }
+
+  // average partial charges over all fragments
   HomologyContainer::const_iterator iter = range.first;
   if (!iter->second.containsGrids) {
@@ -133 +136 @@
     return Action::failure;
   }
-  const Fragment &fragment = iter->second.fragment;
-//  const double &energy = iter->second.energy;
-//  const SamplingGrid &charge = iter->second.charge_distribution;
-  const SamplingGrid &potential = iter->second.potential_distribution;
-
-  // then we extract positions from fragment
-  PartialNucleiChargeFitter::positions_t positions;
-  Fragment::positions_t fragmentpositions = fragment.getPositions();
-  positions.reserve(fragmentpositions.size());
-  BOOST_FOREACH( Fragment::position_t pos, fragmentpositions) {
-    positions.push_back( Vector(pos[0], pos[1], pos[2]) );
-  }
-  PartialNucleiChargeFitter fitter(potential, positions, params.radius.get());
-  fitter();
-  PartialNucleiChargeFitter::charges_t return_charges = fitter.getSolutionAsCharges_t();
+  PartialNucleiChargeFitter::charges_t averaged_charges;
+  averaged_charges.resize(iter->second.fragment.getCharges().size(), 0.);
+  size_t NoFragments = 0;
+  for (;
+      iter != range.second; ++iter, ++NoFragments) {
+    if (!iter->second.containsGrids) {
+      ELOG(2, "This HomologyGraph does not contain sampled grids,\ndid you forget to add '--store-grids 1' to AnalyseFragmentResults.");
+      return Action::failure;
+    }
+    const Fragment &fragment = iter->second.fragment;
+  //  const double &energy = iter->second.energy;
+  //  const SamplingGrid &charge = iter->second.charge_distribution;
+    const SamplingGrid &potential = iter->second.potential_distribution;
+    if ((potential.level == 0)
+        || ((potential.begin[0] == potential.end[0])
+            && (potential.begin[1] == potential.end[1])
+            && (potential.begin[2] == potential.end[2]))) {
+      ELOG(1, "Sampled grid contains grid made of zero points.");
+      return Action::failure;
+    }
+
+    // then we extract positions from fragment
+    PartialNucleiChargeFitter::positions_t positions;
+    Fragment::positions_t fragmentpositions = fragment.getPositions();
+    positions.reserve(fragmentpositions.size());
+    BOOST_FOREACH( Fragment::position_t pos, fragmentpositions) {
+      positions.push_back( Vector(pos[0], pos[1], pos[2]) );
+    }
+    PartialNucleiChargeFitter fitter(potential, positions, params.radius.get());
+    fitter();
+    PartialNucleiChargeFitter::charges_t return_charges = fitter.getSolutionAsCharges_t();
+    std::transform(
+        return_charges.begin(), return_charges.end(),
+        averaged_charges.begin(),
+        averaged_charges.begin(),
+        std::plus<PartialNucleiChargeFitter::charge_t>());
+  }
+  std::transform(averaged_charges.begin(),averaged_charges.end(),
+      averaged_charges.begin(),
+      std::bind1st(std::multiplies<PartialNucleiChargeFitter::charge_t>(),1./NoFragments)
+  );
+
 
   // output fitted charges
-  LOG(0, "STATUS: We have fitted the following charges " << return_charges << ".");
+  LOG(0, "STATUS: We have fitted the following charges " << averaged_charges
+      << ", averaged over " << NoFragments << " fragments.");
 
   return Action::success;