Changeset 17e4fd for src

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

Files:

• Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (2 diffs)
• Actions/FragmentationAction/FragmentationAutomationAction.def (modified) (2 diffs)
• Fragmentation/Automation/VMGFragmentController.cpp (modified) (3 diffs)
• Fragmentation/Automation/VMGFragmentController.hpp (modified) (2 diffs)
• Fragmentation/Interfragmenter.cpp (modified) (1 diff)
• Jobs/InterfaceVMGJob.cpp (modified) (4 diffs)
• Jobs/InterfaceVMGJob.hpp (modified) (3 diffs)
• Jobs/VMGJob.cpp (modified) (4 diffs)
• Jobs/VMGJob.hpp (modified) (4 diffs)
• Jobs/WindowGrid_converter.cpp (modified) (5 diffs)
• Jobs/WindowGrid_converter.hpp (modified) (1 diff)

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp ¶

@@ -260 +260 @@
         params.DoValenceOnly.get() ? MPQCData::DoSampleValenceOnly : MPQCData::DontSampleValenceOnly,
         params.DoPrintDebug.get(),
-        OpenBoundaryConditions)) {
+        OpenBoundaryConditions,
+        params.DoSmearCharges.get())) {
       STATUS("Could not create long-range jobs for electronic charge distribution.");
       return Action::failure;
@@ -290 +291 @@
           params.DoValenceOnly.get() ? MPQCData::DoSampleValenceOnly : MPQCData::DontSampleValenceOnly,
           params.DoPrintDebug.get(),
-          OpenBoundaryConditions)) {
+          OpenBoundaryConditions,
+          params.DoSmearCharges.get())) {
         STATUS("Could not create long-range jobs for nuclei charge distribution.");
         return Action::failure;

src/Actions/FragmentationAction/FragmentationAutomationAction.def ¶

@@ -18 +18 @@
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
 // "undefine" if no parameters are required, use (NOPARAM_DEFAULT) for each (undefined) default value
-#define paramtypes (std::string)(std::string)(boost::filesystem::path)(unsigned int)(unsigned int)(unsigned int)(bool)(boost::filesystem::path)(bool)(bool)
-#define paramtokens ("server-address")("server-port")("fragment-executable")("grid-level")("near-field-cells")("interpolation-degree")("DoLongrange")("fragment-resultfile")("DoValenceOnly")("DoPrintDebug")
-#define paramdescriptions ("hostname of server")("controller port of server")("executable to launch on clients")("resolution of multigrid")("number of cells used in smearing out core charge")("interpolation degree for getting the nuclei potential from the grid")("whether to calculate long-range contributions")("parse fragment results from the given file")("whether the sampling uses only the valence electron and nuclei charge")("whether to print grids for debug visualization") 
-#define paramdefaults (PARAM_DEFAULT("127.0.0.1"))(NOPARAM_DEFAULT)(PARAM_DEFAULT("mpqc"))(PARAM_DEFAULT(5))(PARAM_DEFAULT(3))(PARAM_DEFAULT(3))(PARAM_DEFAULT("0"))(PARAM_DEFAULT(""))(PARAM_DEFAULT("0"))(PARAM_DEFAULT("0"))
-#define paramreferences (host)(port)(executable)(level)(near_field_cells)(interpolation_degree)(DoLongrange)(resultsfile)(DoValenceOnly)(DoPrintDebug)
+#define paramtypes (std::string)(std::string)(boost::filesystem::path)(unsigned int)(unsigned int)(unsigned int)(bool)(boost::filesystem::path)(bool)(bool)(bool)
+#define paramtokens ("server-address")("server-port")("fragment-executable")("grid-level")("near-field-cells")("interpolation-degree")("DoLongrange")("fragment-resultfile")("DoValenceOnly")("DoPrintDebug")("DoSmearElectronicCharges")
+#define paramdescriptions ("hostname of server")("controller port of server")("executable to launch on clients")("resolution of multigrid")("number of cells used in smearing out core charge")("interpolation degree for getting the nuclei potential from the grid")("whether to calculate long-range contributions")("parse fragment results from the given file")("whether the sampling uses only the valence electron and nuclei charge")("whether to print grids for debug visualization")("whether to smear out electronic charge distributions with bsplines or not") 
+#define paramdefaults (PARAM_DEFAULT("127.0.0.1"))(NOPARAM_DEFAULT)(PARAM_DEFAULT("mpqc"))(PARAM_DEFAULT(5))(PARAM_DEFAULT(3))(PARAM_DEFAULT(3))(PARAM_DEFAULT("0"))(PARAM_DEFAULT(""))(PARAM_DEFAULT("0"))(PARAM_DEFAULT("0"))(PARAM_DEFAULT("0"))
+#define paramreferences (host)(port)(executable)(level)(near_field_cells)(interpolation_degree)(DoLongrange)(resultsfile)(DoValenceOnly)(DoPrintDebug)(DoSmearCharges)
 #define paramvalids \
 (DummyValidator< std::string >()) \
@@ -32 +32 @@
 (DummyValidator< bool >()) \
 (DummyValidator< boost::filesystem::path >()) \
+(DummyValidator< bool >()) \
 (DummyValidator< bool >()) \
 (DummyValidator< bool >())

src/Fragmentation/Automation/VMGFragmentController.cpp ¶

@@ -76 +76 @@
     const MPQCData::DoValenceOnly_t _DoValenceOnly,
     const bool _DoPrintDebug,
-    const bool _OpenBoundaryConditions)
+    const bool _OpenBoundaryConditions,
+    const bool _DoSmearCharges)
 {
   std::vector<FragmentJob::ptr> jobs;
@@ -99 +100 @@
             _SampleParticles == DoSampleParticles,
             _DoPrintDebug,
-            _OpenBoundaryConditions) );
+            _OpenBoundaryConditions,
+            _DoSmearCharges) );
     jobs.push_back(testJob);
   }
@@ -147 +149 @@
             _SampleParticles == DoSampleParticles,
             _DoPrintDebug,
-            _OpenBoundaryConditions) );
+            _OpenBoundaryConditions,
+            _DoSmearCharges) );
     jobs.push_back(testJob);
   }

src/Fragmentation/Automation/VMGFragmentController.hpp ¶

@@ -63 +63 @@
    * \param _OpenBoundaryConditions whether we have open (true) or periodic (false)
    *        boundary conditions
+   * \param _DoSmearCharges whether to smear out electronic charge distributions with bsplines or not
    */
   bool createLongRangeJobs(
@@ -73 +74 @@
       const MPQCData::DoValenceOnly_t _DoValenceOnly,
       const bool _DoPrintDebug,
-      const bool _OpenBoundaryConditions = false);
+      const bool _OpenBoundaryConditions = false,
+      const bool _DoSmearCharges = false);
 
   void waitforResults(const size_t NoExpectedResults)

src/Fragmentation/Interfragmenter.cpp ¶

@@ -270 +270 @@
           ClosestPair.first = (*setiter)->getId();
           ClosestPair.second = Walker->getId();
+          LOG(2, "DEBUG: Found new pair " << ClosestPair << " with distance " << sqrt(Rcut));
         }
       }
     }
   }
-  LOG(1, "INFO: Largest inter-fragment distance to cause no additional fragments: " << Rcut);
-
-  return Rcut;
-}
+  const double largest_distance = sqrt(Rcut);
+  LOG(1, "INFO: Largest inter-fragment distance to cause no additional fragments: "
+      << largest_distance);
+
+  return largest_distance;
+}

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);
 
 };