Changeset d9d028 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:

ee9018

Parents:

27ef5c

git-author:

Frederik Heber <heber@…> (07/26/13 12:24:17)

git-committer:

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

Message:

FIX: addGridOntoWindow() now working, too.

• with this open boundary calculation runs through smoothly, including all asserts do not fail. Also, we did check the sampled density on the grid.
• results are not checked so far, but accuracy is according to Julian only second order. Hence, we must not expect too much.

Location:

src/Jobs

Files:

• WindowGrid_converter.cpp (modified) (2 diffs)
• WindowGrid_converter.hpp (modified) (1 diff)

src/Jobs/WindowGrid_converter.cpp

@@ -54 +54 @@
     VMG::Grid &grid,
     SamplingGrid &window,
-    const double prefactor)
+    const double prefactor,
+    const bool OpenBoundaryConditions)
 {
 #ifndef NDEBUG
@@ -104 +105 @@
   SamplingGrid::sampledvalues_t::iterator griditer = window.sampled_grid.begin();
   std::advance(griditer, pre_offset[0]*total[1]*total[2]);
+
   VMG::Grid::iterator copyiter = grid.Iterators().Local().Begin();
+  const VMG::Index size = grid.Local().Size();
+  if (OpenBoundaryConditions)
+    for(N[0]=0; N[0] < size[0]/4; ++N[0])
+      for(N[1]=0; N[1] < size[1]; ++N[1])
+        for(N[2]=0; N[2] < size[2]; ++N[2]) {
+          ASSERT( copyiter != grid.Iterators().Local().End(),
+              "InterfaceVMGJob::addGridOntoWindow() - copyiter is already at end of window.");
+          ++copyiter;
+        }
   for(N[0]=0; N[0] < length[0]; ++N[0]) {
     std::advance(griditer, pre_offset[1]*total[2]);
+    if (OpenBoundaryConditions)
+      for(N[1]=0; N[1] < size[1]/4; ++N[1])
+        for(N[2]=0; N[2] < size[2]; ++N[2]) {
+          ASSERT( copyiter != grid.Iterators().Local().End(),
+              "InterfaceVMGJob::addGridOntoWindow() - copyiter is already at end of window.");
+          ++copyiter;
+        }
     for(N[1]=0; N[1] < length[1]; ++N[1]) {
       std::advance(griditer, pre_offset[2]);
+      if (OpenBoundaryConditions)
+        for(N[2]=0; N[2] < size[2]/4; ++N[2]) {
+          ASSERT( copyiter != grid.Iterators().Local().End(),
+              "InterfaceVMGJob::addGridOntoWindow() - copyiter is already at end of window.");
+          ++copyiter;
+        }
       for(N[2]=0; N[2] < length[2]; ++N[2]) {
         ASSERT( griditer != window.sampled_grid.end(),
             "InterfaceVMGJob::addGridOntoWindow() - griditer is already at end of window.");
         ASSERT( copyiter != grid.Iterators().Local().End(),
-            "InterfaceVMGJob::addGridOntoWindow() - griditer is already at end of window.");
+            "InterfaceVMGJob::addGridOntoWindow() - copyiter is already at end of window.");
         *griditer++ += prefactor*grid(*copyiter++);
       }
       std::advance(griditer, post_offset[2]);
+      if (OpenBoundaryConditions)
+        for(N[2]=0; N[2] < size[2] - size[2]/4 - length[2]; ++N[2]) {
+          ASSERT( copyiter != grid.Iterators().Local().End(),
+              "InterfaceVMGJob::addGridOntoWindow() - copyiter is already at end of window.");
+          ++copyiter;
+        }
     }
     std::advance(griditer, post_offset[1]*total[2]);
-  }
+    if (OpenBoundaryConditions)
+      for(N[1]=0; N[1] < size[1] - size[1]/4 - length[1]; ++N[1])
+        for(N[2]=0; N[2] < size[2]; ++N[2]) {
+          ASSERT( copyiter != grid.Iterators().Local().End(),
+              "InterfaceVMGJob::addGridOntoWindow() - copyiter is already at end of window.");
+          ++copyiter;
+        }
+  }
+  if (OpenBoundaryConditions)
+    for(N[0]=0; N[0] < size[0] - size[0]/4 - length[0]; ++N[0])
+      for(N[1]=0; N[1] < size[1]; ++N[1])
+        for(N[2]=0; N[2] < size[2]; ++N[2]) {
+          ASSERT( copyiter != grid.Iterators().Local().End(),
+              "InterfaceVMGJob::addGridOntoWindow() - copyiter is already at end of window.");
+          ++copyiter;
+        }
 #ifndef NDEBUG
   std::advance(griditer, post_offset[0]*total[1]*total[2]);

src/Jobs/WindowGrid_converter.hpp

@@ -27 +27 @@
    * @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 addGridOntoWindow(
       VMG::Grid& grid,
       SamplingGrid &window,
-      const double prefactor);
+      const double prefactor,
+      const bool OpenBoundaryConditions = false);
 
   /** Helper function to copy non-zero window in SamplingGrid onto VMG's Grid.