Changeset 98a293b for src/Actions

Timestamp:

Aug 16, 2014, 3:52:30 PM (10 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:

a8f1d2

Parents:

bdd5a8

git-author:

Frederik Heber <heber@…> (07/18/14 17:08:09)

git-committer:

Frederik Heber <heber@…> (08/16/14 15:52:30)

Message:

SaturatedFragment can deal with a global saturation position map.

• so far, we create an empty one in FragmentationAction such that nothing's changed for the moment.
• similarly in StoreSaturatedFragmentAction. However, there this is intended as only local information is required (it's only a single fragment).

Location:

src/Actions/FragmentationAction

Files:

• FragmentationAction.cpp (modified) (4 diffs)
• StoreSaturatedFragmentAction.cpp (modified) (2 diffs)

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -42 +42 @@
 #include "Fragmentation/Exporters/ExportGraph_ToFiles.hpp"
 #include "Fragmentation/Exporters/ExportGraph_ToJobs.hpp"
+#include "Fragmentation/Exporters/SaturatedFragment.hpp"
 #include "Fragmentation/Fragmentation.hpp"
 #include "Fragmentation/Graph.hpp"
@@ -261 +262 @@
   }
 
+  // create global saturation positions map
+  SaturatedFragment::GlobalSaturationPositions_t globalsaturationpositions;
+
   {
     const enum HydrogenSaturation saturation =  params.DoSaturation.get() ? DoSaturate : DontSaturate;
@@ -266 +270 @@
     if (params.types.get().size() != 0) {
       // store molecule's fragment to file
-      ExportGraph_ToFiles exporter(TotalGraph, treatment, saturation);
+      ExportGraph_ToFiles exporter(TotalGraph, treatment, saturation, globalsaturationpositions);
       exporter.setPrefix(params.prefix.get());
       exporter.setOutputTypes(params.types.get());
@@ -272 +276 @@
     } else {
       // store molecule's fragment in FragmentJobQueue
-      ExportGraph_ToJobs exporter(TotalGraph, treatment, saturation);
+      ExportGraph_ToJobs exporter(TotalGraph, treatment, saturation, globalsaturationpositions);
       exporter.setLevel(params.level.get());
       exporter();

src/Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp

@@ -39 +39 @@
 #include "CodePatterns/Log.hpp"
 #include "Fragmentation/Exporters/ExportGraph_ToFiles.hpp"
+#include "Fragmentation/Exporters/SaturatedFragment.hpp"
 #include "Fragmentation/Graph.hpp"
 #include "World.hpp"
@@ -77 +78 @@
   // store molecule's fragment to file
   {
+    // we use an empty map here such that saturation is done locally
+    SaturatedFragment::GlobalSaturationPositions_t globalsaturationpositions;
+
     const enum HydrogenSaturation saturation =  params.DoSaturation.get() ? DoSaturate : DontSaturate;
-    ExportGraph_ToFiles exporter(TotalGraph, IncludeHydrogen, saturation);
+    ExportGraph_ToFiles exporter(TotalGraph, IncludeHydrogen, saturation, globalsaturationpositions);
     exporter.setPrefix(params.prefix.get());
     exporter.setOutputTypes(params.types.get());