Changeset 17e4fd for src/Jobs

Timestamp:

Oct 13, 2015, 8:14:33 PM (9 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.

Location:

src/Jobs

Files:

• InterfaceVMGJob.cpp (modified) (4 diffs)
• InterfaceVMGJob.hpp (modified) (3 diffs)
• VMGJob.cpp (modified) (4 diffs)
• VMGJob.hpp (modified) (4 diffs)
• WindowGrid_converter.cpp (modified) (5 diffs)
• WindowGrid_converter.hpp (modified) (1 diff)

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) {

src/Jobs/InterfaceVMGJob.hpp

@@ -53 +53 @@
       const ImportParticles_t _ImportParticles=DoImportParticles,
       const bool _DoPrintDebug=false,
+      const bool _DoSmearCharges=false,
       int coarseningSteps=9,
       double alpha=1.6
@@ -63 +64 @@
 
 protected:
+  unsigned int nfc;
+  const double meshwidth;
   VMG::Particle::BSpline spl;
 
@@ -88 +91 @@
   //!> open boundary conditions or not
   const bool OpenBoundaryCondition;
+
+  //!> whether to smear out electronic charge distributions with bsplines or not
+  const bool DoSmearCharges;
 };
 

src/Jobs/VMGJob.cpp

@@ -92 +92 @@
     const bool _DoImportParticles,
     const bool _DoPrintDebug,
-    const bool _OpenBoundaryConditions) :
+    const bool _OpenBoundaryConditions,
+    const bool _DoSmearCharges) :
   FragmentJob(_JobId),
   density_grid(_density_grid),
@@ -102 +103 @@
   DoPrintDebug(_DoPrintDebug),
   OpenBoundaryConditions(_OpenBoundaryConditions),
+  DoSmearCharges(_DoSmearCharges),
   returndata(static_cast<const SamplingGridProperties &>(_density_grid)),
   particles()
@@ -113 +115 @@
   DoPrintDebug(false),
   OpenBoundaryConditions(false),
+  DoSmearCharges(false),
   particles()
 {}
@@ -246 +249 @@
           VMGInterfaces::InterfaceVMGJob::DoImportParticles
           : VMGInterfaces::InterfaceVMGJob::DontImportParticles,
-      DoPrintDebug);
+      DoPrintDebug,
+      DoSmearCharges);
   const int cycle_type = 1; // V-type
   if (OpenBoundaryConditions) {

src/Jobs/VMGJob.hpp

@@ -44 +44 @@
    * @param _DoImportParticles whether we import particles (true) or evaluate only
    * @param _DoPrintDebug whether we do print grid for debug visualization or not
+   * @param _OpenBoundaryConditions whether we have open (true) boundary conditions or periodic (false)
+   * @param _DoSmearCharges whether to smear out electronic charge distributions with bsplines or not
    */
   VMGJob(const JobId_t _JobId,
@@ -53 +55 @@
       const bool _DoImportParticles=true,
       const bool _DoPrintDebug=false,
-      const bool _OpenBoundaryConditions=false
+      const bool _OpenBoundaryConditions=false,
+      const bool _DoSmearCharges=false
       );
   virtual ~VMGJob();
@@ -81 +84 @@
   //!> whether we have open (true) boundary conditions or periodic (false)
   const bool OpenBoundaryConditions;
+  //!> whether to smear out electronic charge distributions with bsplines or not
+  const bool DoSmearCharges;
 
 private:
@@ -134 +139 @@
     ar & const_cast< bool &>(DoPrintDebug);
     ar & const_cast< bool &>(OpenBoundaryConditions);
+    ar & const_cast< bool &>(DoSmearCharges);
     ar & returndata;
   }

src/Jobs/WindowGrid_converter.cpp

@@ -50 +50 @@
 
 #include "Fragmentation/Summation/SetValues/SamplingGrid.hpp"
+#include "Jobs/ChargeSmearer.hpp"
 
 void WindowGrid_converter::addGridOntoWindow(
@@ -178 +179 @@
     const SamplingGrid &grid,
     const double prefactor,
-    const bool OpenBoundaryConditions)
+    const bool OpenBoundaryConditions,
+    const bool DoSmearCharges)
 {
 #ifndef NDEBUG
@@ -265 +267 @@
   griditer = window.Iterators().Local().Begin();
   SamplingGrid::sampledvalues_t::const_iterator copyiter = grid.sampled_grid.begin();
+  const ChargeSmearer &smearer = ChargeSmearer::getInstance();
   // NOTE: GridIterator::operator+=()'s implementation in vmg is broken. DON'T USE!
 //  griditer += pre_offset[0] * total[1] * total[2];
@@ -293 +296 @@
         ASSERT( copyiter != grid.sampled_grid.end(),
             "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
-        window(*griditer++) += prefactor*(*copyiter++);
+        // either smear out charges or not.
+        if (DoSmearCharges) {
+          smearer(window, griditer++, prefactor*(*copyiter++));
+        } else {
+          window(*griditer++) += prefactor*(*copyiter++);
+        }
       }
 //      griditer += post_offset[2];
@@ -324 +332 @@
       "InterfaceVMGJob::addWindowOntoGrid() - copyiter is not at end of window.");
 #endif
-//  LOG(2, "DEBUG: Grid after adding other is " << grid << ".");
+
+  //  LOG(2, "DEBUG: Grid after adding other is " << grid << ".");
 }

src/Jobs/WindowGrid_converter.hpp

@@ -49 +49 @@
       const SamplingGrid &grid,
       const double prefactor,
-      const bool OpenBoundaryConditions = false);
+      const bool OpenBoundaryConditions = false,
+      const bool DoSmearCharges = false);
 
 };