Changeset cd77fc for src/Jobs/VMGJob.cpp

Timestamp:

Nov 15, 2012, 3:12:54 PM (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, 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/VMGJob.cpp (modified) (4 diffs)

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);
 
   /*