Changeset 27ef5c for src

Timestamp:

Aug 15, 2013, 8:41:17 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:

d9d028

Parents:

e8e472b

git-author:

Frederik Heber <heber@…> (07/26/13 12:24:07)

git-committer:

Frederik Heber <heber@…> (08/15/13 08:41:17)

Message:

Density is now correctly written onto grid with both periodic and open boundary condittions.

Location:

src/Jobs

Files:

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

src/Jobs/WindowGrid_converter.cpp

@@ -132 +132 @@
     VMG::Grid& window,
     const SamplingGrid &grid,
-    const double prefactor)
+    const double prefactor,
+    const bool OpenBoundaryConditions)
 {
 #ifndef NDEBUG
@@ -179 +180 @@
 #endif
   size_t N[3];
+  // in open boundary case grid.Local() contains more than just the inner area. The grid
+  // is actually twice as large to allow for the FV discretization to work. Hence, we first
+  // have to seek our starting point ... see VMG::Grid::GetSpatialPos()
+  if (OpenBoundaryConditions) {
+    const VMG::Index size = window.Local().Size();
+    const VMG::Index halosize = window.Local().HaloSize1();
+    for (size_t i=0;i<3;++i)
+      pre_offset[i] += size[i] / 4;
+    for (size_t i=0;i<3;++i)
+      total[i] = size[i];
+    for (size_t i=0;i<3;++i)
+      post_offset[i] = size[i] - pre_offset[i] - length[i];
+  }
+
   VMG::Grid::iterator griditer = window.Iterators().Local().Begin();
 //  griditer.advance(pre_offset[0]*total[1]*total[2]);
@@ -199 +214 @@
     for(N[1]=0; N[1] < length[1]; ++N[1]) {
 //      griditer.advance(pre_offset[2]);
-        for(N[2]=0; N[2] < pre_offset[2]; ++N[2])
-          window(*griditer++) = 0.;
+      for(N[2]=0; N[2] < pre_offset[2]; ++N[2])
+        window(*griditer++) = 0.;
       for(N[2]=0; N[2] < length[2]; ++N[2]) {
         ASSERT( griditer != window.Iterators().Local().End(),
@@ -223 +238 @@
       }
   }
+  //  griditer.advance(post_offset[0]*total[1]*total[2]);
   for(N[0]=0; N[0] < post_offset[0]; ++N[0])
     for(N[1]=0; N[1] < total[1]; ++N[1])
@@ -231 +247 @@
       }
 #ifndef NDEBUG
-//  griditer.advance(post_offset[0]*total[1]*total[2]);
   ASSERT( griditer == window.Iterators().Local().End(),
       "InterfaceVMGJob::addWindowOntoGrid() - griditer is not at end of window.");

src/Jobs/WindowGrid_converter.hpp

@@ -39 +39 @@
    * @param grid grid with non-zero window
    * @param prefactor factor for each added value, e.g. -1. makes a subtraction
+   * @param OpenBoundaryConditions states whether we have open (true) or 
+   *        periodic (false) boundary conditions
    */
   void addWindowOntoGrid(
       VMG::Grid& window,
       const SamplingGrid &grid,
-      const double prefactor);
+      const double prefactor,
+      const bool OpenBoundaryConditions = false);
 
 };