Changeset ac9ca4 for src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp

Timestamp:

Apr 15, 2013, 10:28:22 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:

4f44ae

Parents:

dd0c8f

git-author:

Frederik Heber <heber@…> (03/04/13 13:54:11)

git-committer:

Frederik Heber <heber@…> (04/15/13 10:28:22)

Message:

FragmentAction creates FragmentJobs if no output-types are given.

• ExportGraph_ToJobs now creates jobs for a FragmentJobQueue.
• new singleton FragmentJobQueue to contain FragmentJobs.
• MPQCFragmentController rewritten to use FragmentJobQueue, too.
• FragmentationAutomationAction just fills FragmentJobQueue with given fragment-jobs.
• added KeySetsContainer::clear().
• removed ExportGraph::operator().
• Smaller fixes to Fragmentation(Automation)Action w.r.t. optional parameters.
• We now require JobMarket 1.1.3, as we need FragmentController::changeId().

File:

• src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) (3 diffs)

src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp

@@ -33 +33 @@
 #endif
 
+// boost asio required before MemDebug due to placement new
+#include <boost/asio.hpp>
+
 #include "CodePatterns/MemDebug.hpp"
 
 #include "Fragmentation/Exporters/ExportGraph_ToJobs.hpp"
 
+#include <algorithm>
+
+#include "Box.hpp"
+#include "Fragmentation/KeySet.hpp"
+#include "Fragmentation/Automation/FragmentJobQueue.hpp"
+#include "Fragmentation/Automation/MPQCFragmentController.hpp"
+#include "Helpers/defs.hpp"
+#include "Jobs/MPQCJob.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
+#include "Parser/FormatParserStorage.hpp"
 #include "World.hpp"
 
@@ -43 +56 @@
     const enum HydrogenTreatment _treatment,
     const enum HydrogenSaturation _saturation) :
-    ExportGraph(_graph, _treatment, _saturation)
+    ExportGraph(_graph, _treatment, _saturation),
+    level(5)
 {}
 
@@ -51 +65 @@
 void ExportGraph_ToJobs::operator()()
 {
-  ExportGraph::operator()();
+  std::vector<FragmentJob::ptr> jobs;
+  KeySetsContainer KeySets;
+  KeySetsContainer FullKeySets;
+  jobs.reserve(TotalGraph.size());
+  LOG(1, "INFO: Creating " << TotalGraph.size() << " possible bond fragmentation jobs.");
+
+  // gather info about the domain
+  double begin[NDIM] = { 0., 0., 0. };
+  RealSpaceMatrix M = World::getInstance().getDomain().getM();
+  M *= 1./AtomicLengthToAngstroem;  // scale to atomic length units
+  const double size = M.at(0,0);
+  double end[NDIM] = { size, size, size };
+  const ParserTypes jobtype =
+      FormatParserStorage::getInstance().getTypeFromName("mpqc");
+
+  // go through all fragments, output to stream and create job therefrom
+  ExportGraph::SaturatedFragment_ptr CurrentFragment = getNextFragment();
+  for (; (CurrentFragment != NULL) && (CurrentFragment->getKeySet() != ExportGraph::EmptySet);
+      CurrentFragment = getNextFragment()) {
+    const KeySet &set = CurrentFragment->getKeySet();
+    LOG(2, "INFO: Creating bond fragment job for set " << set << ".");
+    // store config in stream
+    {
+      std::stringstream output;
+      // save to stream
+      CurrentFragment->OutputConfig(output, jobtype);
+      // create job and insert
+      FragmentJob::ptr testJob( new MPQCJob(JobId::IllegalJob, output.str(), begin, end, level) );
+      jobs.push_back(testJob);
+
+      // order is the same as the number of non-hydrogen atoms
+      const KeySet &keyset = CurrentFragment->getKeySet();
+      const size_t order = keyset.size();
+      const KeySet &fullmolecule = CurrentFragment->getFullMolecule();
+      const KeySet &saturationhydrogens = CurrentFragment->getSaturationHydrogens();
+      KeySetsContainer::IntVector indices(keyset.begin(), keyset.end());
+      KeySetsContainer::IntVector forceindices(fullmolecule.begin(), fullmolecule.end());
+      {
+        // replace all saturated hydrogen indices by "-1"
+        for (KeySetsContainer::IntVector::iterator iter = forceindices.begin();
+            iter != forceindices.end();
+            ++iter)
+          if (saturationhydrogens.find(*iter) != saturationhydrogens.end())
+            *iter = -1;
+      }
+      KeySets.insert(indices, order);
+      FullKeySets.insert(forceindices, order);
+    }
+    // store force index reference file
+    // explicitly release fragment
+    CurrentFragment.reset();
+  }
+  if (CurrentFragment == NULL) {
+    ELOG(1, "Some error while obtaining the next fragment occured.");
+    return;
+  }
+
+  // push final jobs
+  FragmentJobQueue::getInstance().addJobs(jobs, KeySets, FullKeySets);
 }