Changeset 27594e for src

Timestamp:

Dec 10, 2012, 10:10:58 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:

4f056e

Parents:

86cfac5

git-author:

Frederik Heber <heber@…> (08/31/12 17:19:30)

git-committer:

Frederik Heber <heber@…> (12/10/12 10:10:58)

Message:

Added FragmentationChargeDensity to contain summed up charge density.

Location:

src

Files:

• Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (6 diffs)
• Fragmentation/Automation/FragmentationChargeDensity.cpp (added)
• Fragmentation/Automation/FragmentationChargeDensity.hpp (added)
• Fragmentation/Automation/Makefile.am (modified) (2 diffs)

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -49 +49 @@
 #include "Fragmentation/Automation/createMatrixNrLookup.hpp"
 #include "Fragmentation/Automation/extractJobIds.hpp"
+#include "Fragmentation/Automation/FragmentationChargeDensity.hpp"
 #include "Fragmentation/Automation/FragmentationResults.hpp"
 #include "Fragmentation/Automation/MPQCFragmentController.hpp"
@@ -62 +63 @@
 #include "Fragmentation/KeySet.hpp"
 #include "Fragmentation/KeySetsContainer.hpp"
-#include "Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp"
 #include "Fragmentation/Summation/writeTable.hpp"
 #include "Graph/DepthFirstSearchAnalysis.hpp"
@@ -69 +69 @@
 #include "Jobs/MPQCData.hpp"
 #include "Jobs/MPQCData_printKeyNames.hpp"
-#include "Jobs/Grid/SamplingGrid.hpp"
 #ifdef HAVE_VMG
 #include "Jobs/VMGDebugGridJob.hpp"
@@ -211 +210 @@
   return true;
 }
+
 /** Print MPQCData from received results.
  *
- * @param fragmentData MPQCData resulting from the jobs, each associated to a job
+ * @param fragmentData MPQCData resulting from the jobs, associated to job id
  * @param KeySetFilename filename with keysets to associate forces correctly
  * @param NoAtoms total number of atoms
- * @param full_sample summed up charge density of electrons from fragments on return
- * @param full_fragment summed up positions and charges of nuclei from fragments on return
- */
-bool sumUpChargeDensity(
-    const std::map<JobId_t,MPQCData> &fragmentData,
+ * @param full_sample summed up charge from fragments on return
+ */
+bool printReceivedMPQCResults(
+    const std::map<JobId_t, MPQCData> &fragmentData,
     const std::string &KeySetFilename,
-    std::vector<SamplingGrid> &full_sample,
-    Fragment &full_fragment)
+    size_t NoAtoms)
 {
   // create a vector of all job ids
@@ -234 +232 @@
   // create lookup from job nr to fragment number
   size_t FragmentCounter = 0;
-  const std::map< JobId_t, size_t > MatrixNrLookup =
-      createMatrixNrLookup(jobids, FragmentCounter);
-
-  // initialise keysets
-  KeySetsContainer KeySet;
-  {
-    // else needs keysets without hydrogens
-    std::stringstream filename;
-    filename << FRAGMENTPREFIX << KEYSETFILE;
-    if (!KeySet.ParseKeySets(KeySetFilename, filename.str(), FragmentCounter)) return false;
-  }
-
-  /// prepare for OrthogonalSummation
-
-  // convert KeySetContainer to IndexSetContainer
-  IndexSetContainer::ptr container(new IndexSetContainer(KeySet));
-  // create the map of all keysets
-  SubsetMap::ptr subsetmap(new SubsetMap(*container));
-
-  /// convert all MPQCData to MPQCDataMap_t
-  std::vector<MPQCDataGridMap_t> Result_Grid_fused(
-    OrthogonalSumUpPerLevel<MPQCDataGridMap_t, MPQCData, MPQCDataGridVector_t>(
-        fragmentData, MatrixNrLookup, container, subsetmap));
-  std::vector<MPQCDataFragmentMap_t> Result_Fragment_fused(
-    OrthogonalSumUpPerLevel<MPQCDataFragmentMap_t, MPQCData, MPQCDataFragmentVector_t>(
-        fragmentData, MatrixNrLookup, container, subsetmap));
-  // obtain full grid
-  full_sample.clear();
-  full_sample.reserve(Result_Grid_fused.size());
-  for (std::vector<MPQCDataGridMap_t>::const_iterator iter = ++Result_Grid_fused.begin();
-      iter !=Result_Grid_fused.end();
-      ++iter)
-    full_sample.push_back(boost::fusion::at_key<MPQCDataFused::sampled_grid>((*iter)));
-  full_fragment = boost::fusion::at_key<MPQCDataFused::fragment>(Result_Fragment_fused.back());
-
-  return true;
-}
-
-/** Print MPQCData from received results.
- *
- * @param fragmentData MPQCData resulting from the jobs, associated to job id
- * @param KeySetFilename filename with keysets to associate forces correctly
- * @param NoAtoms total number of atoms
- * @param full_sample summed up charge from fragments on return
- */
-bool printReceivedMPQCResults(
-    const std::map<JobId_t, MPQCData> &fragmentData,
-    const std::string &KeySetFilename,
-    size_t NoAtoms)
-{
-  // create a vector of all job ids
-  std::vector<JobId_t> jobids;
-  std::transform(fragmentData.begin(),fragmentData.end(),
-      std::back_inserter(jobids),
-      boost::bind( &std::map<JobId_t,MPQCData>::value_type::first, boost::lambda::_1 )
-  );
-
-  // create lookup from job nr to fragment number
-  size_t FragmentCounter = 0;
   const std::map< JobId_t, size_t > MatrixNrLookup=
       createMatrixNrLookup(jobids, FragmentCounter);
-
 
   // place results into maps
@@ -467 +405 @@
   // obtain combined charge density
   LOG(1, "INFO: Parsing fragment files from " << params.path.get() << ".");
-  std::vector<SamplingGrid> full_sample; // have charges from level 2 onward summed up
-  Fragment full_fragment;
-  sumUpChargeDensity(
+  FragmentationChargeDensity summedChargeDensity(
       fragmentData,
-      params.path.get(),
-      full_sample,
-      full_fragment);
+      params.path.get());
+  const std::vector<SamplingGrid> full_sample = summedChargeDensity.getFullSampledGrid();
 
   // Phase Four: obtain more ids
-  vmgcontroller.requestIds(fragmentData.size()+full_sample.size());
+  const size_t NoJobs = fragmentData.size()+full_sample.size();
+  vmgcontroller.requestIds(NoJobs);
 
   // Phase Five: create VMGJobs
   const size_t near_field_cells = params.near_field_cells.get();
-  if (!vmgcontroller.createLongRangeJobs(fragmentData, full_sample, full_fragment, near_field_cells))
+  if (!vmgcontroller.createLongRangeJobs(
+      fragmentData,
+      full_sample,
+      summedChargeDensity.getFragment(), near_field_cells))
     return Action::failure;
 
   // Phase Six: calculate result
-  vmgcontroller.waitforResults(fragmentData.size()+full_sample.size());
+  vmgcontroller.waitforResults(NoJobs);
   std::map<JobId_t, VMGData> longrangeData;
   vmgcontroller.getResults(longrangeData);
-  ASSERT( fragmentData.size()+full_sample.size() == longrangeData.size(),
+  ASSERT( NoJobs == longrangeData.size(),
       "FragmentationFragmentationAutomationAction::performCall() - number of MPQCresults+"
-      +toString(full_sample.size())+" "+toString(fragmentData.size()+full_sample.size())
+      +toString(full_sample)+" "
+      +toString(NoJobs)
       +" and VMGresults "+toString(longrangeData.size())+" don't match.");
 

src/Fragmentation/Automation/Makefile.am

@@ -4 +4 @@
 FRAGMENTATIONAUTOMATIONSOURCE = \
         Fragmentation/Automation/createMatrixNrLookup.cpp \
+        Fragmentation/Automation/FragmentationChargeDensity.cpp \
         Fragmentation/Automation/FragmentationResults.cpp \
         Fragmentation/Automation/MPQCFragmentController.cpp \
@@ -17 +18 @@
         Fragmentation/Automation/createMatrixNrLookup.hpp \
         Fragmentation/Automation/extractJobIds.hpp \
+        Fragmentation/Automation/FragmentationChargeDensity.hpp \
         Fragmentation/Automation/FragmentationResults.hpp \
         Fragmentation/Automation/MPQCFragmentController.hpp \