Changeset a82602 for src/Jobs/VMGJob.cpp

Timestamp:

Dec 10, 2012, 10:10:59 AM (13 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, Candidate_v1.7.0, Candidate_v1.7.1, 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:

82cbe4

Parents:

5a5196

git-author:

Frederik Heber <heber@…> (09/12/12 15:23:13)

git-committer:

Frederik Heber <heber@…> (12/10/12 10:10:59)

Message:

InterfaceVMGJob now also calculates nuclei interaction energy.

• necessiated to Particle::commMPI().
• CommParticles() call in ImportRightHandSide().
• in ExportSolution() we just copied stuff from interface_particles.cpp from VMG project.
• returndata.e_long now contains calculated energy from there.

File:

• src/Jobs/VMGJob.cpp (modified) (5 diffs)

src/Jobs/VMGJob.cpp

@@ -63 +63 @@
 //#include "solver/solver_regular.hpp"
 #include "solver/solver_singular.hpp"
-//#include "units/particle/comm_mpi_particle.hpp"
+#include "units/particle/comm_mpi_particle.hpp"
 
 #include "CodePatterns/MemDebug.hpp"
@@ -71 +71 @@
 #include "LinearAlgebra/defs.hpp"
 #include "Jobs/InterfaceVMGJob.hpp"
+
+#include "CodePatterns/Assert.hpp"
 
 using namespace VMG;
@@ -85 +87 @@
   particle_charges(_particle_charges),
   near_field_cells(_near_field_cells),
-  returndata(static_cast<const SamplingGridProperties &>(_density_grid))
+  returndata(static_cast<const SamplingGridProperties &>(_density_grid)),
+  num_particles(0),
+  f(NULL),
+  x(NULL),
+  p(NULL),
+  q(NULL)
 {}
 
 VMGJob::VMGJob() :
   FragmentJob(JobId::IllegalJob),
-  near_field_cells(5)
+  near_field_cells(5),
+  num_particles(0),
+  f(NULL),
+  x(NULL),
+  p(NULL),
+  q(NULL)
 {}
 
 VMGJob::~VMGJob()
-{}
+{
+  delete[] f;
+  delete[] x;
+  delete[] p;
+  delete[] q;
+}
+
+void VMGJob::InitVMGArrays()
+{
+  num_particles = particle_charges.size();
+  f = new double[num_particles*3];
+  x = new double[num_particles*3];
+  p = new double[num_particles];
+  q = new double[num_particles];
+
+  {
+    size_t index=0;
+    for (std::vector< std::vector< double > >::const_iterator iter = particle_positions.begin();
+        iter != particle_positions.end(); ++iter) {
+      for (std::vector< double >::const_iterator positer = (*iter).begin();
+          positer != (*iter).end(); ++positer) {
+        f[index] = 0.;
+        x[index++] = *positer;
+      }
+    }
+    ASSERT( index == num_particles*3,
+        "VMGJob::VMGJob() - too many particles or components in particle_positions.");
+  }
+  {
+    size_t index = 0;
+    for (std::vector< double >::const_iterator iter = particle_charges.begin();
+        iter != particle_charges.end(); ++iter) {
+      p[index] = 0.;
+      q[index++] = *iter;
+    }
+    ASSERT( index == num_particles,
+        "VMGJob::VMGJob() - too many charges in particle_charges.");
+  }
+}
+
 
 FragmentResult::ptr VMGJob::Work()
@@ -137 +188 @@
    */
 #ifdef HAVE_MPI
-  new CommMPI(boundary, new DomainDecompositionMPI());
+  new Particle::CommMPI(boundary, new DomainDecompositionMPI());
 #else
   new CommSerial(boundary);
@@ -169 +220 @@
   new ObjectStorage<int>("PARTICLE_INTERPOLATION_DEGREE", 3);
 
+  // first initialize f,x,p,q,... from STL vectors
+  InitVMGArrays();
+  // then initialize as objects with VMG's storage
+  new ObjectStorage<vmg_float*>("PARTICLE_POS_ARRAY", x);
+  new ObjectStorage<vmg_float*>("PARTICLE_CHARGE_ARRAY", q);
+  new ObjectStorage<vmg_float*>("PARTICLE_POTENTIAL_ARRAY", p);
+  new ObjectStorage<vmg_float*>("PARTICLE_FIELD_ARRAY", f);
+  new ObjectStorage<vmg_int>("PARTICLE_NUM_LOCAL", num_particles);
+
   /*
    * Post init