Changeset cd77fc for src/Jobs/InterfaceVMGJob.cpp

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().

File:

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

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() );