Changeset 336da8 for src

Timestamp:

Sep 14, 2016, 6:42:53 PM (9 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, 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_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, GeometryObjects, Gui_displays_atomic_force_velocity, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, RotateToPrincipalAxisSystem_UndoRedo, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, Ubuntu_1604_changes, stable

Children:

ca4b372

Parents:

c1948c

git-author:

Frederik Heber <heber@…> (06/01/16 08:51:01)

git-committer:

Frederik Heber <heber@…> (09/14/16 18:42:53)

Message:

WindowGrid_converter's refactored a bit with getDiscreteWindowOffsets().

• Added SamplingGrid::getDiscreteWindowOffsets().
• WindowGrid_converter now also use NDIM instead of 3 to clarify the use of the spatial degrees of freedom (and not some grid level or else).

Location:

src

Files:

• Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) (1 diff)
• Fragmentation/Summation/SetValues/SamplingGrid.hpp (modified) (1 diff)
• Jobs/WindowGrid_converter.cpp (modified) (7 diffs)

src/Fragmentation/Summation/SetValues/SamplingGrid.cpp

@@ -452 +452 @@
     ASSERT( (_wend[index] - _wbegin[index]) == _wlength[index],
         "SamplingGrid::getDiscreteWindowCopyIndices() - end - begin is not equal to length for "
+        +toString(index)+"th component.");
+  }
+}
+
+void SamplingGrid::getDiscreteWindowOffsets(
+    size_t _pre_offset[NDIM],
+    size_t _post_offset[NDIM],
+    size_t _length[NDIM],
+    size_t _total[NDIM]) const
+{
+  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<NDIM;++index) {
+    if (fabs(end[index] - begin[index]) > std::numeric_limits<double>::epsilon()*1e4) {
+      // we refrain from using floor/ceil as the window's starts and ends,
+      // the grids have to be compatible (equal level), should always be on
+      // discrete grid point locations.
+      const double delta = getDeltaPerAxis(index);
+      // delta is conversion factor from box length to discrete length, i.e. number of points
+      _pre_offset[index] = (begin_window[index] - begin[index])/delta+round_offset;
+      _post_offset[index] = (end[index] - end_window[index])/delta+round_offset;
+      _length[index] = (end_window[index] - begin_window[index])/delta+round_offset;
+      _total[index] = (end[index] - begin[index])/delta+round_offset;
+    } else {
+      _pre_offset[index] = 0;
+      _post_offset[index] = 0;
+      _length[index] = 0;
+      _total[index] = 0;
+    }
+    // total is used as safe-guard against loss due to discrete conversion
+    ASSERT( (_pre_offset[index] + _post_offset[index]) + _length[index] == _total[index],
+        "SamplingGrid::getDiscreteWindowCopyIndices() - pre, length, post are not equal to total for "
         +toString(index)+"th component.");
   }

src/Fragmentation/Summation/SetValues/SamplingGrid.hpp

@@ -253 +253 @@
       size_t _wend[NDIM]) const;
 
+  /** Returns number of grid points before the window, during the window, and
+   * after the window including the total length of the domain for check.
+   *
+   * \param _pre_offset grid points before start of window
+   * \param _post_offset grid points after end of window
+   * \param _length grid points in window
+   * \param _total grid points in domain
+   */
+  void getDiscreteWindowOffsets(
+      size_t _pre_offset[NDIM],
+      size_t _post_offset[NDIM],
+      size_t _length[NDIM],
+      size_t _total[NDIM]) const;
+
   /** Equality operator.
    *

src/Jobs/WindowGrid_converter.cpp

@@ -59 +59 @@
 {
 #ifndef NDEBUG
-  for(size_t index=0;index<3;++index) {
+  for(size_t index=0;index<NDIM;++index) {
     ASSERT( window.begin[index] >= window.begin_window[index],
         "InterfaceVMGJob::addGridOntoWindow() - given grid starts earlier than window in component "
@@ -69 +69 @@
 #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*(window.begin[index] - window.begin_window[index])+round_offset;
-    length[index] = delta*(window.end[index] - window.begin[index])+round_offset;
-    post_offset[index] = delta*(window.end_window[index] - window.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.");
-  }
+  size_t pre_offset[NDIM];
+  size_t post_offset[NDIM];
+  size_t length[NDIM];
+  size_t total[NDIM];
+  window.getDiscreteWindowOffsets(pre_offset, post_offset, length, total);
 #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: "
@@ -103 +84 @@
       +toString(total_size)+" != "+toString(window.sampled_grid.size())+".");
 #endif
-  size_t N[3];
+  size_t N[NDIM];
   SamplingGrid::sampledvalues_t::iterator griditer = window.sampled_grid.begin();
   std::advance(griditer, pre_offset[0]*total[1]*total[2]);
@@ -183 +164 @@
 {
 #ifndef NDEBUG
-  for(size_t index=0;index<3;++index) {
+  for(size_t index=0;index<NDIM;++index) {
     ASSERT( grid.begin_window[index] >= grid.begin[index],
         "InterfaceVMGJob::addWindowOntoGrid() - given window starts earlier than grid in component "
@@ -193 +174 @@
 #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] - grid.begin[index])+round_offset;
-    length[index] = delta*(grid.end_window[index] - grid.begin_window[index])+round_offset;
-    post_offset[index] = delta*(grid.end[index] - grid.end_window[index])+round_offset;
-    total[index] = delta*(grid.end[index] - grid.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.");
-  }
+  size_t pre_offset[NDIM];
+  size_t post_offset[NDIM];
+  size_t length[NDIM];
+  size_t total[NDIM];
+  grid.getDiscreteWindowOffsets(pre_offset, post_offset, length, total);
 #ifndef NDEBUG
   const size_t calculated_size = length[0]*length[1]*length[2];
@@ -218 +184 @@
       "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];
+#endif
+  size_t N[NDIM];
   // 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
@@ -238 +197 @@
     // this mimicks VMG::GridIndexTranslations::EndOffset()
     const size_t off = OpenBoundaryConditions ? 1 : 0;
-    for (size_t i=0;i<3;++i)
+    for (size_t i=0;i<NDIM;++i)
       pre_offset[i] += ((size_t)size[i] - off) / 4;
-    for (size_t i=0;i<3;++i)
+    for (size_t i=0;i<NDIM;++i)
       total[i] = ((size_t)size[i]);
-    for (size_t i=0;i<3;++i)
+    for (size_t i=0;i<NDIM;++i)
       post_offset[i] = ((size_t)size[i]) - pre_offset[i] - length[i];
   }