Changeset 17e4fd for src/Jobs/InterfaceVMGJob.cpp

Timestamp:

Oct 13, 2015, 8:14:33 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:

62d092

Parents:

445ce6

git-author:

Frederik Heber <heber@…> (09/07/15 19:03:37)

git-committer:

Frederik Heber <heber@…> (10/13/15 20:14:33)

Message:

Added new option DoSmearElectronicCharges to FragmentationAutomationAction.

• this uses ChargeSmearer: is prepared in InterfaceVMGJob and used in WindowGrid_converter.
• VMGJob and VMGFragmentController need to pass along the DoSmearCharges option from the command-line.

File:

• src/Jobs/InterfaceVMGJob.cpp (modified) (4 diffs)

src/Jobs/InterfaceVMGJob.cpp

@@ -59 +59 @@
 #include "Fragmentation/Summation/SetValues/FragmentForces.hpp"
 #include "Jobs/WindowGrid_converter.hpp"
+#include "Jobs/ChargeSmearer.hpp"
 
 using namespace VMG;
@@ -75 +76 @@
     const ImportParticles_t _ImportParticles,
     const bool _DoPrintDebug,
+    const bool _DoSmearCharges,
     int coarseningSteps,
     double alpha) :
   VMG::Interface(boundary, levelMin, levelMax,
       _box_begin, _box_end, coarseningSteps, alpha),
-  spl(near_field_cells, Extent(MaxLevel()).MeshWidth().Max()),
+  nfc(near_field_cells),
+  meshwidth(Extent(MaxLevel()).MeshWidth().Max()),
+  spl(nfc, meshwidth),
   sampled_input(_sampled_input),
   returndata(_returndata),
@@ -85 +89 @@
   ImportParticles(_ImportParticles),
   DoPrintDebug(_DoPrintDebug),
-  OpenBoundaryCondition(boundary[0] == VMG::Open)
+  OpenBoundaryCondition(boundary[0] == VMG::Open),
+  DoSmearCharges(_DoSmearCharges)
 {
   for (size_t i=0;i<3;++i) {
@@ -159 +164 @@
 
   // add sampled electron charge density onto grid
+  if (DoSmearCharges) {
+    ChargeSmearer &smearer = ChargeSmearer::getInstance();
+    smearer.initializeSplineArray(spl, nfc, meshwidth);
+  }
   WindowGrid_converter::addWindowOntoGrid(
       grid,
       sampled_input,
       1.,
-      OpenBoundaryCondition);
+      OpenBoundaryCondition,
+      DoSmearCharges);
 
   if (DoPrintDebug) {