Changeset b47f9c for src/Jobs

Timestamp:

Oct 20, 2013, 11:45:34 AM (11 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:

5e1443

Parents:

e0cf82

git-author:

Frederik Heber <heber@…> (10/15/13 13:41:44)

git-committer:

Frederik Heber <heber@…> (10/20/13 11:45:34)

Message:

FIX: WindowGrid_converter::addWindowOntoGrid() never used OpenBoundaryConditions branch.

• We did not use the parameter, it always fell back to default (false).
• open boundary conditions use one extra grid point right-hand-side layer to account Dirichlet boundary conditions. This has to be skipped when filling the grid.
• density looks sensible in both cases, in open boundary case neither electron nor nuclei longrange show any (significant) box size dependency.

Location:

src/Jobs

Files:

• InterfaceVMGJob.cpp (modified) (5 diffs)
• InterfaceVMGJob.hpp (modified) (1 diff)
• WindowGrid_converter.cpp (modified) (1 diff)

src/Jobs/InterfaceVMGJob.cpp

@@ -83 +83 @@
   level(levelMax),
   ImportParticles(_ImportParticles),
-  DoPrintDebug(_DoPrintDebug)
+  DoPrintDebug(_DoPrintDebug),
+  OpenBoundaryCondition(boundary[0] == VMG::Open)
 {
   for (size_t i=0;i<3;++i) {
@@ -160 +161 @@
       grid,
       sampled_input,
-      1.);
+      1.,
+      OpenBoundaryCondition);
 
   if (DoPrintDebug) {
@@ -207 +209 @@
   Particle::CommMPI& comm = *dynamic_cast<Particle::CommMPI*>(MG::GetComm());
 
-  const Index begin_local = grid.Global().LocalBegin() - grid.Local().HaloSize1();
-  Index i;
 
   if (DoPrintDebug) {
@@ -223 +223 @@
       grid,
       returndata.sampled_potential,
-      +1.
+      +1.,
+      OpenBoundaryCondition
       );
 
@@ -270 +271 @@
   Grid& particle_grid = comm.GetParticleGrid();
 
-  for (i.X()=0; i.X()<grid.Local().Size().X(); ++i.X())
-    for (i.Y()=0; i.Y()<grid.Local().Size().Y(); ++i.Y())
-      for (i.Z()=0; i.Z()<grid.Local().Size().Z(); ++i.Z())
-        particle_grid(i + particle_grid.Local().Begin()) = grid.GetVal(i + grid.Local().Begin());
-
-  comm.CommToGhosts(particle_grid);
+  {
+    Index i;
+    for (i.X()=0; i.X()<grid.Local().Size().X(); ++i.X())
+      for (i.Y()=0; i.Y()<grid.Local().Size().Y(); ++i.Y())
+        for (i.Z()=0; i.Z()<grid.Local().Size().Z(); ++i.Z())
+          particle_grid(i + particle_grid.Local().Begin()) = grid.GetVal(i + grid.Local().Begin());
+    comm.CommToGhosts(particle_grid);
+  }
 
   /*

src/Jobs/InterfaceVMGJob.hpp

@@ -85 +85 @@
   //!> whether we do print grid for debug visualization or not
   const bool DoPrintDebug;
+
+  //!> open boundary conditions or not
+  const bool OpenBoundaryCondition;
 };
 

src/Jobs/WindowGrid_converter.cpp

@@ -230 +230 @@
   if (OpenBoundaryConditions) {
     const VMG::Index size = window.Local().Size();
-    const VMG::Index halosize = window.Local().HaloSize1();
+    const VMG::Index boundary1size = window.Local().BoundarySize1();
+    const VMG::Index boundary2size = window.Local().BoundarySize2();
+    const VMG::Index halo1size = window.Local().HaloSize1();
+    const VMG::Index halo2size = window.Local().HaloSize2();
+    // this mimicks VMG::GridIndexTranslations::EndOffset()
+    const size_t off = OpenBoundaryConditions ? 1 : 0;
     for (size_t i=0;i<3;++i)
-      pre_offset[i] += size[i] / 4;
+      pre_offset[i] += (size[i] - off) / 4;
     for (size_t i=0;i<3;++i)
-      total[i] = size[i];
+      total[i] = (size[i]);
     for (size_t i=0;i<3;++i)
-      post_offset[i] = size[i] - pre_offset[i] - length[i];
+      post_offset[i] = (size[i]) - pre_offset[i] - length[i];
   }