Changeset b4f72c for src/Actions

Timestamp:

Dec 3, 2012, 9:50:01 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:

2ab6b6

Parents:

dcbb5d

git-author:

Frederik Heber <heber@…> (09/20/12 13:44:17)

git-committer:

Frederik Heber <heber@…> (12/03/12 09:50:01)

Message:

ExportGraph_ToFiles now does not require molecule reference anymore.

• SortIndex is now just a dummy (identity) map.
• FragmentationAction combines all graphs from each Fragmentationm call and exports these in one go.

File:

• src/Actions/FragmentationAction/FragmentationAction.cpp (modified) (4 diffs)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -39 +39 @@
 #include "Fragmentation/Exporters/ExportGraph_ToFiles.hpp"
 #include "Fragmentation/Fragmentation.hpp"
+#include "Fragmentation/Graph.hpp"
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
 #include "Graph/CheckAgainstAdjacencyFile.hpp"
@@ -86 +87 @@
   LOG(1, "INFO: There are " << clusters.size()  << " molecules to consider.");
 
+  // get whether to saturate or not
+  const enum HydrogenSaturation saturation =  params.DoSaturation.get() ? DoSaturate : DontSaturate;
+
   // parse in Adjacency file
   std::ifstream File;
@@ -97 +101 @@
   // go through all keys (i.e. all molecules)
   clusters_t::const_iterator advanceiter;
+  Graph TotalGraph;
+  int keysetcounter = 0;
   for (clusters_t::const_iterator iter = clusters.begin();
       iter != clusters.end();
@@ -124 +130 @@
         ExitFlag = tempFlag; // if we are the first, we set the standard
     }
+    TotalGraph.InsertGraph(Fragmenter.getGraph(), keysetcounter);
 
-    // store molecule's fragment to file
-    ExportGraph_ToFiles exporter(Fragmenter.getGraph(), mol, saturation);
-    exporter.setPrefix(params.prefix.get());
-    exporter.setOutputTypes(params.types.get());
-    exporter();
   }
+  LOG(0, "STATUS: There are " << keysetcounter << " fragments.");
+  // store molecule's fragment to file
+  ExportGraph_ToFiles exporter(TotalGraph, saturation);
+  exporter.setPrefix(params.prefix.get());
+  exporter.setOutputTypes(params.types.get());
+  exporter();
   World::getInstance().setExitFlag(ExitFlag);
   end = clock();