Changeset 2764e0 for src

Timestamp:

Nov 14, 2012, 10:02:50 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:

d12d621

Parents:

815f60

git-author:

Frederik Heber <heber@…> (07/25/12 18:24:27)

git-committer:

Frederik Heber <heber@…> (11/14/12 10:02:50)

Message:

Added ConvertFragmentResultToMPQCData to FragmentationAutomationAction.

• also printReceivedMPQCResults now gets a vector of MPQCData that is converted beforehand.

File:

• src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (8 diffs)

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -145 +145 @@
 }
 
+/** Extracts MPQCData from received vector of FragmentResults.
+ *
+ * @param results results to extract MPQCData from
+ * @param fragmentData on return array filled with extracted MPQCData
+ */
+void ConvertFragmentResultToMPQCData(
+    const std::vector<FragmentResult::ptr> &results,
+    std::vector<MPQCData> &fragmentData)
+{
+  // extract results
+  fragmentData.clear();
+  fragmentData.reserve(results.size());
+
+  LOG(2, "DEBUG: Parsing now through " << results.size() << " results.");
+  for (std::vector<FragmentResult::ptr>::const_iterator iter = results.begin();
+      iter != results.end(); ++iter) {
+    //LOG(1, "RESULT: job #"+toString((*iter)->getId())+": "+toString((*iter)->result));
+    MPQCData extractedData;
+    std::stringstream inputstream((*iter)->result);
+    LOG(2, "DEBUG: First 50 characters FragmentResult's string: "+(*iter)->result.substr(0, 50));
+    boost::archive::text_iarchive ia(inputstream);
+    ia >> extractedData;
+    LOG(1, "INFO: extracted data is " << extractedData << ".");
+    fragmentData.push_back(extractedData);
+  }
+
+  ASSERT( results.size() == fragmentData.size(),
+      "ConvertFragmentResultToMPQCData() - the number of extracted data differs from the number of results.");
+}
 
 /** Print MPQCData from received results.
  *
- * @param results received results to extract MPQCData from
+ * @param results results with ids to associate with fragment number
+ * @param fragmentData MPQCData resulting from the jobs
  * @param KeySetFilename filename with keysets to associate forces correctly
  * @param NoAtoms total number of atoms
@@ -154 +184 @@
 bool printReceivedMPQCResults(
     const std::vector<FragmentResult::ptr> &results,
+    const std::vector<MPQCData> &fragmentData,
     const std::string &KeySetFilename,
     size_t NoAtoms)
@@ -186 +217 @@
   LOG(1, "INFO: There are " << FragmentCounter << " fragments.");
 
-  // extract results
-  std::vector<MPQCData> fragmentData(results.size());
-  MPQCData combinedData;
-
-  LOG(2, "DEBUG: Parsing now through " << results.size() << " results.");
-  for (std::vector<FragmentResult::ptr>::const_iterator iter = results.begin();
-      iter != results.end(); ++iter) {
-    LOG(1, "RESULT: job #"+toString((*iter)->getId())+": "+toString((*iter)->result));
-    MPQCData extractedData;
-    std::stringstream inputstream((*iter)->result);
-    LOG(2, "DEBUG: First 50 characters FragmentResult's string: "+(*iter)->result.substr(0, 50));
-    boost::archive::text_iarchive ia(inputstream);
-    ia >> extractedData;
-    LOG(1, "INFO: extracted data is " << extractedData << ".");
-
+  std::vector<MPQCData>::const_iterator dataiter = fragmentData.begin();
+  std::vector<FragmentResult::ptr>::const_iterator resultiter = results.begin();
+  for (; dataiter != fragmentData.end(); ++dataiter, ++resultiter) {
+    const MPQCData &extractedData = *dataiter;
     // place results into EnergyMatrix ...
     {
@@ -207 +227 @@
       matrix[0].resize(1, extractedData.energies.total);
       if (!Energy.AddMatrix(
-          std::string("MPQCJob ")+toString((*iter)->getId()),
+          std::string("MPQCJob ")+toString((*resultiter)->getId()),
           matrix,
-          MatrixNrLookup[(*iter)->getId()])) {
+          MatrixNrLookup[(*resultiter)->getId()])) {
         ELOG(1, "Adding energy matrix failed.");
         return false;
@@ -228 +248 @@
       }
       if (!Force.AddMatrix(
-          std::string("MPQCJob ")+toString((*iter)->getId()),
+          std::string("MPQCJob ")+toString((*resultiter)->getId()),
           matrix,
-          MatrixNrLookup[(*iter)->getId()])) {
+          MatrixNrLookup[(*resultiter)->getId()])) {
         ELOG(1, "Adding force matrix failed.");
         return false;
@@ -516 +536 @@
   controller.receiveResults(params.host.get(), params.port.get());
   RunService(io_service, "Requesting short-range results");
+  std::vector<FragmentResult::ptr> MPQCresults = controller.getReceivedResults();
+  std::vector<MPQCData> fragmentData;
+  ConvertFragmentResultToMPQCData(MPQCresults, fragmentData);
 
   // print intermediate short-range results
   {
     LOG(1, "INFO: Parsing fragment files from " << params.path.get() << ".");
-    std::vector<FragmentResult::ptr> MPQCresults = controller.getReceivedResults();
     printReceivedMPQCResults(
         MPQCresults,
+        fragmentData,
         params.path.get(),
         getNoAtomsFromAdjacencyFile(params.path.get()));
@@ -530 +553 @@
   if (params.DoLongrange.get()) {
   // Phase Four: obtain more ids
-  requestIds(controller, params, jobfiles.size()+1); // one more for the big job
+  requestIds(controller, params, fragmentData.size()+1);
   RunService(io_service, "Requesting ids");
 
@@ -539 +562 @@
 
   // Phase Six: calculate result
-  WaitforResults(io_service, controller, params, jobfiles.size()+1);
+  WaitforResults(io_service, controller, params, fragmentData.size()+1);
   controller.receiveResults(params.host.get(), params.port.get());
   RunService(io_service, "Requesting long-range results");
   std::vector<FragmentResult::ptr> VMGresults = controller.getReceivedResults();
+  ASSERT( MPQCresults.size()+1 == VMGresults.size(),
+      "FragmentationFragmentationAutomationAction::performCall() - number of MPQCresultd and VMGresults don't match.");
+
+  // Final phase: print result
+  {
+    LOG(1, "INFO: Parsing fragment files from " << params.path.get() << ".");
+    printReceivedMPQCResults(
+        MPQCresults,
+        fragmentData,
+        params.path.get(),
+        getNoAtomsFromAdjacencyFile(params.path.get()));
+  }
   }
 #endif