Changeset b123a5 for src/Jobs

Timestamp:

Feb 15, 2013, 5:07:49 PM (12 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:

620517

Parents:

8f3cdd

git-author:

Frederik Heber <heber@…> (01/19/13 13:38:57)

git-committer:

Frederik Heber <heber@…> (02/15/13 17:07:49)

Message:

Shifted functions to add window onto grid into own namespace.

• InterfaceVMG...Job now receive SamplingGrid and not the samples directly.

Location:

src/Jobs

Files:

• InterfaceVMGDebugGridJob.cpp (modified) (4 diffs)
• InterfaceVMGDebugGridJob.hpp (modified) (4 diffs)
• InterfaceVMGJob.cpp (modified) (4 diffs)
• InterfaceVMGJob.hpp (modified) (3 diffs)
• Makefile.am (modified) (2 diffs)
• VMGDebugGridJob.cpp (modified) (1 diff)
• WindowGrid_converter.cpp (added)
• WindowGrid_converter.hpp (added)

src/Jobs/InterfaceVMGDebugGridJob.cpp ¶

@@ -52 +52 @@
 #include "CodePatterns/Log.hpp"
 
+#include "Jobs/WindowGrid_converter.hpp"
 
 using namespace VMG;
@@ -57 +58 @@
 
 InterfaceVMGDebugGridJob::InterfaceVMGDebugGridJob(
-    const std::vector< double > &_sampled_input,
+    const SamplingGrid &_sampled_input,
     VMG::Boundary boundary,
     int levelMin,
@@ -72 +73 @@
 {
 }
-
-InterfaceVMGDebugGridJob::~InterfaceVMGDebugGridJob()
-{}
 
 void InterfaceVMGDebugGridJob::ImportRightHandSide(Multigrid& multigrid)
@@ -95 +93 @@
 
   // add sampled grid points to grid
-  std::vector<double>::const_iterator sample_iter = sampled_input.begin();
-  for (Grid::iterator iter = grid.Iterators().Local().Begin();
-      iter != grid.Iterators().Local().End();
-      ++iter)
-    grid(*iter) = -1. * (*sample_iter++);
-  assert( sample_iter == sampled_input.end() );
+  WindowGrid_converter::addWindowOntoGrid(
+      grid,
+      sampled_input,
+      -1.);
 
   // print electron grid to vtk

src/Jobs/InterfaceVMGDebugGridJob.hpp ¶

@@ -22 +22 @@
 }
 
+#include "Jobs/Grid/SamplingGrid.hpp"
+
 namespace VMGInterfaces
 {
@@ -34 +36 @@
 public:
   InterfaceVMGDebugGridJob(
-      const std::vector< double > &_sampled_input,
+      const SamplingGrid &_sampled_input,
       VMG::Boundary boundary,
       int levelMin,
@@ -44 +46 @@
       double alpha=1.6);
 
-  virtual ~InterfaceVMGDebugGridJob();
+  ~InterfaceVMGDebugGridJob() {}
 
   void ImportRightHandSide(VMG::Multigrid& multigrid);
@@ -51 +53 @@
 private:
   //!> sampled density on the grid as input
-  const std::vector< double > sampled_input;
-  //!> number of grid points per axis as \f$2^{\text{level}}\f$
+  const SamplingGrid sampled_input;
+  //!> number of grid points per axis as \f$2^{\mathrm{level}}\f$
   const int level;
 };

src/Jobs/InterfaceVMGJob.cpp ¶

@@ -56 +56 @@
 #include "CodePatterns/Log.hpp"
 
-#include "Jobs/Grid/SamplingGrid.hpp"
+#include "Jobs/WindowGrid_converter.hpp"
 
 using namespace VMG;
@@ -97 +97 @@
 }
 
-InterfaceVMGJob::~InterfaceVMGJob()
-{}
-
-void InterfaceVMGJob::addGridOntoWindow(
-    VMG::Grid &grid,
-    SamplingGrid &window,
-    const double prefactor) const
-{
-#ifndef NDEBUG
-  for(size_t index=0;index<3;++index) {
-    ASSERT( box_begin[index] >= window.begin_window[index],
-        "InterfaceVMGJob::addGridOntoWindow() - given grid starts earlier than window in component "
-        +toString(index)+".");
-    ASSERT( box_end[index] <= window.end_window[index],
-        "InterfaceVMGJob::addGridOntoWindow() - given grid ends later than window in component "
-        +toString(index)+".");
-  }
-#endif
-  // the only issue are indices
-  const size_t gridpoints_axis = window.getGridPointsPerAxis();
-  size_t pre_offset[3];
-  size_t post_offset[3];
-  size_t length[3];
-  size_t total[3];
-  const double round_offset =
-      (std::numeric_limits<size_t>::round_style == std::round_toward_zero) ?
-          0.5 : 0.; // need offset to get to round_toward_nearest behavior
-  for(size_t index=0;index<3;++index) {
-    const double delta = (double)gridpoints_axis/(window.end[index] - window.begin[index]);
-    // delta is conversion factor from box length to discrete length, i.e. number of points
-    pre_offset[index] = delta*(box_begin[index] - window.begin_window[index])+round_offset;
-    length[index] = delta*(box_end[index] - box_begin[index])+round_offset;
-    post_offset[index] = delta*(window.end_window[index] - box_end[index])+round_offset;
-    total[index] = delta*(window.end_window[index] - window.begin_window[index])+round_offset;
-    // total is used as safe-guard against loss due to discrete conversion
-    ASSERT( pre_offset[index]+post_offset[index]+length[index] == total[index],
-        "InterfaceVMGJob::addGridOntoWindow() - pre, post, and length don't sum up to total for "
-        +toString(index)+"th component.");
-  }
-#ifndef NDEBUG
-  const size_t calculated_size = length[0]*length[1]*length[2];
-//  const size_t given_size = std::distance(grid_begin, grid_end);
-//  ASSERT( calculated_size == given_size,
-//      "InterfaceVMGJob::addGridOntoWindow() - not enough sampled values given: "
-//      +toString(calculated_size)+" != "+toString(given_size)+".");
-  ASSERT( calculated_size <=  window.sampled_grid.size(),
-      "InterfaceVMGJob::addGridOntoWindow() - not enough sampled values available: "
-      +toString(calculated_size)+" <= "+toString(window.sampled_grid.size())+".");
-  const size_t total_size = total[0]*total[1]*total[2];
-  ASSERT( total_size == window.sampled_grid.size(),
-      "InterfaceVMGJob::addGridOntoWindow() - total size is not equal to number of present points: "
-      +toString(total_size)+" != "+toString(window.sampled_grid.size())+".");
-#endif
-  size_t N[3];
-  SamplingGrid::sampledvalues_t::iterator griditer = window.sampled_grid.begin();
-  std::advance(griditer, pre_offset[0]*total[1]*total[2]);
-  Grid::iterator copyiter = grid.Iterators().Local().Begin();
-  for(N[0]=0; N[0] < length[0]; ++N[0]) {
-    std::advance(griditer, pre_offset[1]*total[2]);
-    for(N[1]=0; N[1] < length[1]; ++N[1]) {
-      std::advance(griditer, pre_offset[2]);
-      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.");
-        *griditer++ += prefactor*grid(*copyiter++);
-      }
-      std::advance(griditer, post_offset[2]);
-    }
-    std::advance(griditer, post_offset[1]*total[2]);
-  }
-#ifndef NDEBUG
-  std::advance(griditer, post_offset[0]*total[1]*total[2]);
-  ASSERT( griditer == window.sampled_grid.end(),
-      "InterfaceVMGJob::addGridOntoWindow() - griditer is not at end of window.");
-  ASSERT( copyiter == grid.Iterators().Local().End(),
-      "InterfaceVMGJob::addGridOntoWindow() - copyiter is not at end of window.");
-#endif
-}
-
-void InterfaceVMGJob::addWindowOntoGrid(
-    VMG::Grid& window,
-    const SamplingGrid &grid,
-    const double prefactor) const
-{
-#ifndef NDEBUG
-  for(size_t index=0;index<3;++index) {
-    ASSERT( grid.begin_window[index] >= box_begin[index],
-        "InterfaceVMGJob::addWindowOntoGrid() - given window starts earlier than grid in component "
-        +toString(index)+".");
-    ASSERT( grid.end_window[index] <= box_end[index],
-        "InterfaceVMGJob::addWindowOntoGrid() - given window ends later than grid in component "
-        +toString(index)+".");
-  }
-#endif
-  // the only issue are indices
-  const size_t gridpoints_axis = grid.getGridPointsPerAxis();
-  size_t pre_offset[3];
-  size_t post_offset[3];
-  size_t length[3];
-  size_t total[3];
-  const double round_offset =
-      (std::numeric_limits<size_t>::round_style == std::round_toward_zero) ?
-          0.5 : 0.; // need offset to get to round_toward_nearest behavior
-  for(size_t index=0;index<3;++index) {
-    const double delta = (double)gridpoints_axis/(grid.end[index] - grid.begin[index]);
-    // delta is conversion factor from box length to discrete length, i.e. number of points
-    pre_offset[index] = delta*(grid.begin_window[index] - box_begin[index])+round_offset;
-    length[index] = delta*(grid.end_window[index] - grid.begin_window[index])+round_offset;
-    post_offset[index] = delta*(box_end[index] - grid.end_window[index])+round_offset;
-    total[index] = delta*(box_end[index] - box_begin[index])+round_offset;
-    // total is used as safe-guard against loss due to discrete conversion
-    ASSERT( pre_offset[index]+post_offset[index]+length[index] == total[index],
-        "InterfaceVMGJob::addWindowOntoGrid() - pre, post, and length don't sum up to total for "
-        +toString(index)+"th component.");
-  }
-#ifndef NDEBUG
-  const size_t calculated_size = length[0]*length[1]*length[2];
-  ASSERT( calculated_size == grid.sampled_grid.size(),
-      "InterfaceVMGJob::addWindowOntoGrid() - not enough sampled values given: "
-      +toString(calculated_size)+" != "+toString(grid.sampled_grid.size())+".");
-//  ASSERT( calculated_size <=  given_size,
-//      "InterfaceVMGJob::addWindowOntoGrid() - not enough sampled values available: "
-//      +toString(calculated_size)+" <= "+toString(given_size)+".");
-//  const size_t total_size = total[0]*total[1]*total[2];
-//  ASSERT( total_size == given_size,
-//      "InterfaceVMGJob::addWindowOntoGrid() - total size is not equal to number of present points: "
-//      +toString(total_size)+" != "+toString(given_size)+".");
-#endif
-  size_t N[3];
-  Grid::iterator griditer = window.Iterators().Local().Begin();
-  griditer += pre_offset[0]*total[1]*total[2];
-  SamplingGrid::sampledvalues_t::const_iterator copyiter = grid.sampled_grid.begin();
-  for(N[0]=0; N[0] < length[0]; ++N[0]) {
-    griditer += pre_offset[1]*total[2];
-    for(N[1]=0; N[1] < length[1]; ++N[1]) {
-      griditer += pre_offset[2];
-      for(N[2]=0; N[2] < length[2]; ++N[2]) {
-        ASSERT( griditer != window.Iterators().Local().End(),
-            "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
-        ASSERT( copyiter != grid.sampled_grid.end(),
-            "InterfaceVMGJob::addWindowOntoGrid() - griditer is already at end of window.");
-        window(*griditer++) += prefactor*(*copyiter++);
-      }
-      griditer += post_offset[2];
-    }
-    griditer += post_offset[1]*total[2];
-  }
-#ifndef NDEBUG
-  griditer += post_offset[0]*total[1]*total[2];
-  ASSERT( griditer == window.Iterators().Local().End(),
-      "InterfaceVMGJob::addWindowOntoGrid() - griditer is not at end of window.");
-  ASSERT( copyiter == grid.sampled_grid.end(),
-      "InterfaceVMGJob::addWindowOntoGrid() - copyiter is not at end of window.");
-#endif
-//  LOG(2, "DEBUG: Grid after adding other is " << grid << ".");
-}
-
 void InterfaceVMGJob::ImportRightHandSide(Multigrid& multigrid)
 {
@@ -307 +148 @@
 
   // add sampled electron charge density onto grid
-  addWindowOntoGrid(
+  WindowGrid_converter::addWindowOntoGrid(
       grid,
       sampled_input,
@@ -364 +205 @@
       box_end
       );
-  addGridOntoWindow(
+  WindowGrid_converter::addGridOntoWindow(
       grid,
       returndata.sampled_potential,

src/Jobs/InterfaceVMGJob.hpp ¶

@@ -21 +21 @@
 
 #include "Jobs/VMGData.hpp"
-
-class SamplingGrid;
+#include "Jobs/Grid/SamplingGrid.hpp"
 
 namespace VMG
@@ -50 +49 @@
       double alpha=1.6);
 
-  virtual ~InterfaceVMGJob();
+  ~InterfaceVMGJob() {}
 
   void ImportRightHandSide(VMG::Multigrid& multigrid);
@@ -58 +57 @@
   VMG::Particle::BSpline spl;
 
-private:
-  /** Helper function to copy VMG's Grid onto the non-zero window of a SamplingGrid
-   *
-   * The code is very similar to SamplingGrid::addOntoWindow().
-   *
-   * @param grid grid with non-zero window
-   * @param prefactor factor for each added value, e.g. -1. makes a subtraction
-   */
-  void addGridOntoWindow(
-      VMG::Grid& grid,
-      SamplingGrid &window,
-      const double prefactor) const;
-
-  /** Helper function to copy non-zero window in SamplingGrid onto VMG's Grid.
-   *
-   * The code is very similar to SamplingGrid::addOntoWindow().
-   *
-   * @param grid grid with non-zero window
-   * @param prefactor factor for each added value, e.g. -1. makes a subtraction
-   */
-  void addWindowOntoGrid(
-      VMG::Grid& window,
-      const SamplingGrid &grid,
-      const double prefactor) const;
 private:
   //!> sampled density on the grid as input

src/Jobs/Makefile.am ¶

@@ -12 +12 @@
         Jobs/VMGData.cpp \
         Jobs/VMGDebugGridJob.cpp \
-        Jobs/VMGJob.cpp
+        Jobs/VMGJob.cpp \
+        Jobs/WindowGrid_converter.cpp
 endif
 
@@ -35 +36 @@
         Jobs/VMGDebugGridJob_binding.hpp \
         Jobs/VMGJob.hpp \
-        Jobs/VMGJob_binding.hpp
+        Jobs/VMGJob_binding.hpp \
+        Jobs/WindowGrid_converter.hpp
 endif
 

src/Jobs/VMGDebugGridJob.cpp ¶

@@ -133 +133 @@
   new DiscretizationPoissonFD(4);
   new VMGInterfaces::InterfaceVMGDebugGridJob(
-      density_grid.sampled_grid,
+      density_grid,
       boundary,
       2,