Changeset d7bb9b1 for src/Fragmentation/Automation

Timestamp:

Jul 2, 2012, 7:54:12 AM (13 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:

a2d653

Parents:

3add4f

git-author:

Frederik Heber <heber@…> (05/18/12 07:21:43)

git-committer:

Frederik Heber <heber@…> (07/02/12 07:54:12)

Message:

Controller now links to libMolecuilderFragmentation, has extended printReceivedMPQCResults().

• extended printReceivedMPQCResults to use FragmentMatrix and alikes.

Location:

src/Fragmentation/Automation

Files:

• Makefile.am (modified) (2 diffs)
• controller.cpp (modified) (5 diffs)

src/Fragmentation/Automation/Makefile.am

@@ -2 +2 @@
 # Also indentation by a single tab
 
-INCLUDES = -I$(top_srcdir)/LinearAlgebra/src
+INCLUDES = -I$(top_srcdir)/LinearAlgebra/src -I$(top_srcdir)/src
 
 MOSTLYCLEANFILES =
@@ -139 +139 @@
   libMolecuilderFragmentationOperations.la \
   libMolecuilderFragmentJobs.la \
+  $(top_builddir)/src/libMolecuilderFragmentation.la \
+  $(top_builddir)/src/libMolecuilderHelpers.la \
   $(BOOST_ASIO_LIBS) \
   $(BOOST_SERIALIZATION_LIBS) \

src/Fragmentation/Automation/controller.cpp

@@ -39 +39 @@
 #include "CodePatterns/Info.hpp"
 #include "CodePatterns/Log.hpp"
+#include "Fragmentation/EnergyMatrix.hpp"
+#include "Fragmentation/ForceMatrix.hpp"
+#include "Fragmentation/KeySetsContainer.hpp"
 #include "FragmentController.hpp"
 #include "Jobs/MPQCCommandJob.hpp"
+#include "Jobs/MPQCCommandJob_MPQCData.hpp"
 #include "Jobs/SystemCommandJob.hpp"
 #include "Results/FragmentResult.hpp"
@@ -107 +111 @@
 }
 
-/** Print received results.
+/** Print MPQCData from received results.
  *
  * @param results vector of all received FragmentResult's
  * @param KeySetFilename filename containing keysets
  */
-void printreceivedmpqcresults(std::vector<FragmentResult::ptr> &results, const std::string &KeySetFilename)
-{
-  // parse in KeySetfile
-//  const size_t MAXBUFFER = 256;
-  std::ifstream inputfile;
-  inputfile.open(KeySetFilename.c_str());
-//  while (inputfile.getline(buffer, MAXBUFFER)) {
-//
-//  }
-  inputfile.close();
-
+bool printReceivedMPQCResults(
+    std::vector<FragmentResult::ptr> &results,
+    const std::string &KeySetFilename)
+{
+  EnergyMatrix Energy;
+  EnergyMatrix EnergyFragments;
+  ForceMatrix Force;
+  ForceMatrix ForceFragments;
+  KeySetsContainer KeySet;
+
+  // place results into EnergyMatrix and ForceMatrix
+  //if (!Energy.ParseFragmentMatrix(argv[1], dir, EnergySuffix, 0,0)) return false;
+  //if (!Force.ParseFragmentMatrix(argv[1], dir, ForcesSuffix, 0,0)) return false;
   // combine all found data
   std::vector<MPQCData> fragmentData(results.size());
@@ -137 +143 @@
     LOG(1, "INFO: extracted data is " << extractedData << ".");
   }
-}
+
+  if (!Energy.InitialiseIndices()) return false;
+
+  if (!Force.ParseIndices(KeySetFilename.c_str())) return false;
+
+  if (!KeySet.ParseKeySets(KeySetFilename.c_str(), Force.RowCounter, Force.MatrixCounter)) return false;
+
+  if (!KeySet.ParseManyBodyTerms()) return false;
+
+  if (!EnergyFragments.AllocateMatrix(Energy.Header, Energy.MatrixCounter, Energy.RowCounter, Energy.ColumnCounter)) return false;
+  if (!ForceFragments.AllocateMatrix(Force.Header, Force.MatrixCounter, Force.RowCounter, Force.ColumnCounter)) return false;
+
+  if(!Energy.SetLastMatrix(0., 0)) return false;
+  if(!Force.SetLastMatrix(0., 2)) return false;
+
+  for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
+    // --------- sum up energy --------------------
+    LOG(1, "INFO: Summing energy of order " << BondOrder+1 << " ...");
+    if (!EnergyFragments.SumSubManyBodyTerms(Energy, KeySet, BondOrder)) return false;
+    if (!Energy.SumSubEnergy(EnergyFragments, NULL, KeySet, BondOrder, 1.)) return false;
+
+    // --------- sum up Forces --------------------
+    LOG(1, "INFO: Summing forces of order " << BondOrder+1 << " ...");
+    if (!ForceFragments.SumSubManyBodyTerms(Force, KeySet, BondOrder)) return false;
+    if (!Force.SumSubForces(ForceFragments, KeySet, BondOrder, 1.)) return false;
+  }
+
+  return true;
+}
+
 
 /** Returns a unique index for every command to allow switching over it.
@@ -183 +218 @@
         std::cerr << "\t" << iter->first << std::endl;
       }
-      return 1;
+      return false;
     }
 
@@ -325 +360 @@
           LOG(1, "INFO: Parsing id associations from " << KeySetFilename << ".");
           std::vector<FragmentResult::ptr> results = controller.getReceivedResults();
-          printreceivedmpqcresults(results, KeySetFilename);
+          printReceivedMPQCResults(results, KeySetFilename);
         }
         break;