Changeset cd77fc

Timestamp:

Nov 15, 2012, 3:12:54 PM (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:

fb69e9

Parents:

092be05

git-author:

Frederik Heber <heber@…> (07/26/12 10:17:56)

git-committer:

Frederik Heber <heber@…> (11/15/12 15:12:54)

Message:

Positions and charges of nuclei are also contained in MPQCData and used by VMGJob and InterfaceVMGJob, respectively.

• this is a temporary solution until we finally create the fragments and send prepare the MPQCJobs in one go. I.e. for now mpqc has to fill in the vacant MPQCData entries of positions and charges to be used by the VMGJob created from this information.
• Using CommSerial/MPI in ImportRightHandSide() to getParticleGrid().

Location:

src

Files:

• Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (2 diffs)
• Jobs/InterfaceVMGJob.cpp (modified) (4 diffs)
• Jobs/InterfaceVMGJob.hpp (modified) (3 diffs)
• Jobs/MPQCData.hpp (modified) (2 diffs)
• Jobs/VMGJob.cpp (modified) (4 diffs)
• Jobs/VMGJob.hpp (modified) (3 diffs)

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -517 +517 @@
     LOG(1, "INFO: Creating VMGJob.");
     FragmentJob::ptr testJob(
-        new VMGJob(next_id, iter->sampled_grid) );
+        new VMGJob(next_id, iter->sampled_grid, iter->positions, iter->charges) );
     jobs.push_back(testJob);
   }
@@ -533 +533 @@
         "createLongRangeJobs() - current domain matrix "+toString(M)+" is not cubic.");
     const SamplingGrid full_sampled_grid(begin, size, level, full_sample);
+    const std::vector< std::vector<double> > positions;
+    const std::vector<double> charges;
     const JobId_t next_id = controller.getAvailableId();
     FragmentJob::ptr testJob(
-        new VMGJob(next_id, full_sampled_grid) );
+        new VMGJob(next_id, full_sampled_grid, positions, charges) );
     jobs.push_back(testJob);
   }

src/Jobs/InterfaceVMGJob.cpp

@@ -32 +32 @@
 #endif
 
+#ifdef HAVE_MPI
+#include "mpi.h"
+#endif
+
 #include "CodePatterns/MemDebug.hpp"
 
@@ -40 +44 @@
 
 #include "base/vector.hpp"
+#include "base/math.hpp"
+#ifdef HAVE_MPI
+#include "comm/comm_mpi.hpp"
+#else
+#include "comm/comm_serial.hpp"
+#endif
 #include "grid/grid.hpp"
 #include "grid/multigrid.hpp"
@@ -48 +58 @@
 using VMGInterfaces::InterfaceVMGJob;
 
+InterfaceVMGJob::InterfaceVMGJob(const std::vector< double > &_sampled_input,
+    std::vector< double > &_sampled_output,
+    const std::vector< std::vector<double> > &_particle_positions,
+    const std::vector< double > &_particle_charges,
+    VMG::Boundary boundary,
+    int levelMin,
+    int levelMax,
+    const VMG::Vector &box_begin,
+    vmg_float box_end,
+    const int& near_field_cells,
+    int coarseningSteps,
+    double alpha) :
+  VMG::Interface(boundary, levelMin, levelMax,
+      box_begin, box_end, coarseningSteps, alpha),
+  spl(near_field_cells, Extent(MaxLevel()).MeshWidth().Max()),
+  sampled_input(_sampled_input),
+  sampled_output(_sampled_output),
+  level(levelMax)
+{
+  std::vector< std::vector<double> >::const_iterator positer = _particle_positions.begin();
+  std::vector<double>::const_iterator chargeiter = _particle_charges.begin();
+  double pos[3];
+  for (; positer != _particle_positions.end(); ++positer, ++chargeiter) {
+    ASSERT( (*positer).size() == 3,
+        "InterfaceVMGJob::InterfaceVMGJob() - particle "
+        +toString(distance(_particle_positions.begin(), positer))+" has not exactly 3 coordinates.");
+    for (size_t i=0;i<3;++i)
+      pos[i] = (*positer)[i];
+    particles.push_back(Particle::Particle(pos, *chargeiter));
+  }
+}
+
+InterfaceVMGJob::~InterfaceVMGJob()
+{}
+
 void InterfaceVMGJob::ImportRightHandSide(Multigrid& multigrid)
 {
   Index i;
   Vector pos;
-
-//  VMG::TempGrid *temp_grid = new VMG::TempGrid(129, 0, 0., 1.);
+  //  VMG::TempGrid *temp_grid = new VMG::TempGrid(129, 0, 0., 1.);
 
   Grid& grid = multigrid(multigrid.MaxLevel());
   grid.ClearBoundary();
+
+  /// 1. assign nuclei as smeared-out charges to the grid
+
+  /*
+   * Charge assignment on the grid
+   */
+#ifdef HAVE_MPI
+  CommMPI& comm = *dynamic_cast<CommMPI*>(VMG::MG::GetComm());
+#else
+  CommSerial& comm = *dynamic_cast<CommSerial*>(VMG::MG::GetComm());
+#endif
+  Grid& particle_grid = comm.GetParticleGrid();
+
+  particle_grid.Clear();
+
+  assert(particle_grid.Global().LocalSize().IsComponentwiseGreater(
+      VMG::MG::GetFactory().GetObjectStorageVal<int>("PARTICLE_NEAR_FIELD_CELLS")));
+
+  for (std::list<Particle::Particle>::iterator iter = particles.begin();
+      iter != particles.end(); ++iter)
+    spl.SetSpline(particle_grid, *iter);
+
+  // Communicate charges over halo
+  comm.CommFromGhosts(particle_grid);
+
+  // Assign charge values to the right hand side
+  for (int i=0; i<grid.Local().Size().X(); ++i)
+    for (int j=0; j<grid.Local().Size().Y(); ++j)
+      for (int k=0; k<grid.Local().Size().Z(); ++k)
+  grid(grid.Local().Begin().X() + i,
+       grid.Local().Begin().Y() + j,
+       grid.Local().Begin().Z() + k) = 4.0 * VMG::Math::pi *
+    particle_grid.GetVal(particle_grid.Local().Begin().X() + i,
+             particle_grid.Local().Begin().Y() + j,
+             particle_grid.Local().Begin().Z() + k);
+
+  /// 2. add sampled electron density to the grid
 
   const Index begin_local = grid.Global().LocalBegin() - grid.Local().HaloSize1();
@@ -71 +152 @@
       << "Z in [" << grid.Local().Begin().Z() << "," << grid.Local().End().Z() << "].");
 
+  const double element_volume =
+      grid.Extent().MeshWidth().X() * grid.Extent().MeshWidth().Y() * grid.Extent().MeshWidth().Z();
   std::vector<double>::const_iterator sample_iter = sampled_input.begin();
   for (i.X()=grid.Local().Begin().X(); i.X()<grid.Local().End().X(); ++i.X())
     for (i.Y()=grid.Local().Begin().Y(); i.Y()<grid.Local().End().Y(); ++i.Y())
-      for (i.Z()=grid.Local().Begin().Z(); i.Z()<grid.Local().End().Z(); ++i.Z()) {
-        pos = grid.Extent().MeshWidth() * static_cast<Vector>(begin_local + i);
-//        R.x() = pos.X();
-//        R.y() = pos.Y();
-//        R.z() = pos.Z();
-        grid(i) = *sample_iter; //temp_grid(i);
-        ++sample_iter;
-      }
+      for (i.Z()=grid.Local().Begin().Z(); i.Z()<grid.Local().End().Z(); ++i.Z())
+        grid(i) -= (*sample_iter++) * element_volume; //temp_grid(i);
   assert( sample_iter == sampled_input.end() );
 

src/Jobs/InterfaceVMGJob.hpp

@@ -17 +17 @@
 #include "base/interface.hpp"
 #include "base/vector.hpp"
+#include "units/particle/bspline.hpp"
+#include "units/particle/particle.hpp"
 
 namespace VMG
@@ -32 +34 @@
   InterfaceVMGJob(const std::vector< double > &_sampled_input,
       std::vector< double > &_sampled_output,
+      const std::vector< std::vector< double > > &_particle_positions,
+      const std::vector< double > &_particle_charges,
       VMG::Boundary boundary,
       int levelMin,
@@ -37 +41 @@
       const VMG::Vector &box_begin,
       vmg_float box_end,
+      const int& near_field_cells,
       int coarseningSteps=0,
-      double alpha=1.6) :
-    VMG::Interface(boundary, levelMin, levelMax,
-                   box_begin, box_end, coarseningSteps, alpha),
-                   sampled_input(_sampled_input),
-       sampled_output(_sampled_output),
-                   level(levelMax)
-  {}
+      double alpha=1.6);
 
-  virtual ~InterfaceVMGJob() {}
+  virtual ~InterfaceVMGJob();
 
   void ImportRightHandSide(VMG::Multigrid& multigrid);
   void ExportSolution(VMG::Grid& grid);
 
+protected:
+  VMG::Particle::BSpline spl;
+
 private:
+  //!> sampled density on the grid as input
   const std::vector< double > sampled_input;
+  //!> sampled potential on the grid as output
   std::vector< double > &sampled_output;
+  //!> number of grid points per axis as \f$2^{\text{level}}\f$
   const int level;
+  //!> nuclei charges
+  std::list<VMG::Particle::Particle> particles;
 };
 

src/Jobs/MPQCData.hpp

@@ -82 +82 @@
   SamplingGrid sampled_grid;
 
+  // nuclei positions and charges
+  std::vector< std::vector<double> > positions;
+  std::vector<double> charges;
+
   /// Timing structure
   struct times_t {
@@ -111 +115 @@
     ar & forces;
     ar & sampled_grid;
+    ar & positions;
+    ar & charges;
     ar & times.walltime;
     ar & times.cputime;

src/Jobs/VMGJob.cpp

@@ -76 +76 @@
 VMGJob::VMGJob(
     const JobId_t _JobId,
-    const SamplingGrid _density_grid) :
+    const SamplingGrid &_density_grid,
+    const std::vector< std::vector< double > > &_particle_positions,
+    const std::vector< double > &_particle_charges) :
   FragmentJob(_JobId),
   density_grid(_density_grid),
-  potential_grid(static_cast<const SamplingGridProperties &>(_density_grid))
+  potential_grid(static_cast<const SamplingGridProperties &>(_density_grid)),
+  particle_positions(_particle_positions),
+  particle_charges(_particle_charges)
 {}
 
@@ -125 +129 @@
   // TODO: As a matter of fact should use open boundary conditions
   const Boundary boundary(Periodic, Periodic, Periodic);
-//  int near_field_cells = 10;
+  int near_field_cells = 10;
 
   /*
@@ -139 +143 @@
       density_grid.sampled_grid,
       potential_grid.sampled_grid,
+      particle_positions,
+      particle_charges,
       boundary,
       2,
       density_grid.level,
       Vector(density_grid.begin),
-      density_grid.size);
+      density_grid.size,
+      near_field_cells);
   new LevelOperatorCS(Stencils::RestrictionFullWeight, Stencils::InterpolationTrilinear);
   new Givens<SolverSingular>();
@@ -157 +164 @@
   new ObjectStorage<vmg_float>("PRECISION", 1.0e-10);
   new ObjectStorage<int>("MAX_ITERATION", 15);
-//  new ObjectStorage<int>("PARTICLE_NEAR_FIELD_CELLS", near_field_cells);
-//  new ObjectStorage<int>("PARTICLE_INTERPOLATION_DEGREE", 3);
+  new ObjectStorage<int>("PARTICLE_NEAR_FIELD_CELLS", near_field_cells);
+  new ObjectStorage<int>("PARTICLE_INTERPOLATION_DEGREE", 3);
 
   /*

src/Jobs/VMGJob.hpp

@@ -41 +41 @@
    */
   VMGJob(const JobId_t _JobId,
-      const SamplingGrid density_grid);
+      const SamplingGrid &density_grid,
+      const std::vector< std::vector< double > > &_particle_positions,
+      const std::vector< double > &_particle_charges);
   virtual ~VMGJob();
 
@@ -54 +56 @@
   //!> sampled potential as output of the job
   SamplingGrid potential_grid;
+  //!> positions of all nuclei
+  const std::vector< std::vector< double > > particle_positions;
+  //!> charges of all nuclei
+  const std::vector< double > particle_charges;
 
 private:
@@ -68 +74 @@
     ar & const_cast< SamplingGrid &>(density_grid);
     ar & potential_grid;
+    ar & const_cast< std::vector< std::vector< double > > &>(particle_positions);
+    ar & const_cast< std::vector< double > &>(particle_charges);
   }
 };