Changeset e355b31 for src

Timestamp:

Aug 9, 2013, 2:20:37 PM (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:

c4a323

Parents:

bf1d1b

git-author:

Frederik Heber <heber@…> (07/25/13 17:35:59)

git-committer:

Frederik Heber <heber@…> (08/09/13 14:20:37)

Message:

Added both_sampled_potential to VMGData, analogous to nuclei_longrange.

• AnalyseFragmentationResultsAction sets both both_sampled_potential and nuclei_longrange from second set of longrange calculations.
• we require the combined potential for fitting partial nuclei charges
• fixed typo in testsuite-fragmentation-analyse-fragment-results.at

Location:

src

Files:

• Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) (2 diffs)
• Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (1 diff)
• Fragmentation/Summation/Containers/VMGData.hpp (modified) (3 diffs)
• Fragmentation/Summation/Containers/VMGDataFused.hpp (modified) (1 diff)
• Fragmentation/Summation/Containers/VMGDataMap.hpp (modified) (2 diffs)
• Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp (modified) (1 diff)
• Fragmentation/Summation/Converter/DataConverter.hpp (modified) (1 diff)

src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp

@@ -44 +44 @@
 #include <boost/mpl/remove.hpp>
 
-#include <vector>
 #include <fstream>
 #include <iostream>
+//#include <numeric>
 #include <string>
 #include <vector>
@@ -283 +283 @@
           "appendToHomologyFile() - cannot find index "+toString(*index)
           +" in FragmentResults.");
-      value.potential_distribution = boost::fusion::at_key<VMGDataFused::sampled_potential>(potentialiter->second.second); // contributions
+      // add e+n potentials
+      value.potential_distribution = boost::fusion::at_key<VMGDataFused::both_sampled_potential>(potentialiter->second.second); // contributions
+//      // and re-average to zero (integral is times volume_element which we don't need here)
+//      const double sum =
+//          std::accumulate(
+//              value.potential_distribution.sampled_grid.begin(),
+//              value.potential_distribution.sampled_grid.end(),
+//              0.);
+//      const double offset = sum/(double)value.potential_distribution.sampled_grid.size();
+//      for (SamplingGrid::sampledvalues_t::iterator iter = value.potential_distribution.sampled_grid.begin();
+//          iter != value.potential_distribution.sampled_grid.end();
+//          ++iter)
+//        *iter -= offset;
     }
     values.insert( std::make_pair( graph, value) );

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -208 +208 @@
           "FragmentationFragmentationAutomationAction::performCall() - longrange results have different sizes.");
       std::map<JobId_t, VMGData>::iterator destiter = longrangedata.begin();
-      std::map<JobId_t, VMGData>::iterator srciter = longrangedata_both.begin();
-      for (;destiter != longrangedata.end(); ++srciter, ++destiter)
+      std::map<JobId_t, VMGData>::const_iterator srciter = longrangedata_both.begin();
+      for (;destiter != longrangedata.end(); ++srciter, ++destiter) {
+        destiter->second.both_sampled_potential = srciter->second.sampled_potential;
         destiter->second.nuclei_long = srciter->second.nuclei_long;
+      }
     }
   }

src/Fragmentation/Summation/Containers/VMGData.hpp

@@ -42 +42 @@
   //!> sampled potential on the grid as output
   SamplingGrid sampled_potential;
+  //!> sampled potential on the grid as output
+  SamplingGrid both_sampled_potential;
   //!> nuclei long-range contribution to energy
   double nuclei_long;
@@ -54 +56 @@
   {
     ar & sampled_potential;
+    if (version > 1)
+      ar & both_sampled_potential;
     if (version > 0)
       ar & nuclei_long;
@@ -60 +64 @@
 };
 
-BOOST_CLASS_VERSION(VMGData, 1)
+BOOST_CLASS_VERSION(VMGData, 2)
 
 std::ostream & operator<<(std::ostream &ost, const VMGData &data);

src/Fragmentation/Summation/Containers/VMGDataFused.hpp

@@ -26 +26 @@
   // keys for sampled_potential
   struct sampled_potential {};
-  struct energy_potential {};
+  struct both_sampled_potential {};
   struct nuclei_long {};
   struct electron_long {};

src/Fragmentation/Summation/Containers/VMGDataMap.hpp

@@ -31 +31 @@
 typedef boost::fusion::map<
     boost::fusion::pair<VMGDataFused::sampled_potential, SamplingGrid >,
-    boost::fusion::pair<VMGDataFused::energy_potential, double >,
+    boost::fusion::pair<VMGDataFused::both_sampled_potential, SamplingGrid >,
     boost::fusion::pair<VMGDataFused::nuclei_long, double >,
     boost::fusion::pair<VMGDataFused::electron_long, double >
@@ -38 +38 @@
 typedef boost::mpl::list<
     VMGDataFused::sampled_potential,
-    VMGDataFused::energy_potential,
+    VMGDataFused::both_sampled_potential,
     VMGDataFused::nuclei_long,
     VMGDataFused::electron_long

src/Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp

@@ -35 +35 @@
 #define tokensequence \
         (sampled_potential) \
-  (energy_potential) \
+  (both_sampled_potential) \
   (nuclei_long) \
   (electron_long) \

src/Fragmentation/Summation/Converter/DataConverter.hpp

@@ -89 +89 @@
     VMGDataMap_t instance;
     boost::fusion::at_key<VMGDataFused::sampled_potential>(instance) = extractedData.sampled_potential;
-    boost::fusion::at_key<VMGDataFused::energy_potential>(instance) = extractedData.sampled_potential.integral();
+    boost::fusion::at_key<VMGDataFused::both_sampled_potential>(instance) = extractedData.both_sampled_potential;
     boost::fusion::at_key<VMGDataFused::nuclei_long>(instance) = extractedData.nuclei_long;
     boost::fusion::at_key<VMGDataFused::electron_long>(instance) = extractedData.electron_long;