Changeset d56e21

Timestamp:

Sep 14, 2016, 6:42:53 PM (8 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:

6a5eb2

Parents:

91e7658

git-author:

Frederik Heber <heber@…> (05/26/16 15:36:26)

git-committer:

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

Message:

Added padWithZerosForEvenNumberedSamples(), required by downsample().

• added unit test function.

Location:

src/Fragmentation/Summation/SetValues

Files:

• SamplingGrid.cpp (modified) (1 diff)
• SamplingGrid.hpp (modified) (1 diff)
• unittests/SamplingGridUnitTest.cpp (modified) (1 diff)
• unittests/SamplingGridUnitTest.hpp (modified) (2 diffs)

src/Fragmentation/Summation/SetValues/SamplingGrid.cpp

@@ -780 +780 @@
 }
 
+void SamplingGrid::padWithZerosForEvenNumberedSamples()
+{
+  size_t wbegin_index[NDIM];
+  size_t wend_index[NDIM];
+  size_t wlength_index[NDIM];
+  getDiscreteWindowIndices(wbegin_index, wlength_index, wend_index);
+
+  // calculate new window (always extend it such that both indices are even)
+  bool changed = false;
+  size_t wnewbegin_index[NDIM];
+  size_t wnewend_index[NDIM];
+  for(size_t i=0;i<NDIM;++i) {
+    // We require begin and end of window on even indices (and inside grid).
+    wnewbegin_index[i] = wbegin_index[i];
+    if ((wnewbegin_index[i] % (size_t)2) != 0) {
+      if (wnewbegin_index[i] > 0)
+        --wnewbegin_index[i];
+      else
+        wnewbegin_index[i] = 0;
+      changed = true;
+    }
+    wnewend_index[i] = wend_index[i];
+    if ((wnewend_index[i] % (size_t)2) != 0) {
+      if (wnewend_index[i] < getGridPointsPerAxis())
+        ++wnewend_index[i];
+      else
+        wnewend_index[i] = getGridPointsPerAxis();
+      changed = true;
+    }
+    ASSERT( (wbegin_index[i] >= 0) && (wend_index[i] <= getGridPointsPerAxis()),
+        "SamplingGrid::padWithZerosForEvenNumberedSamples() - indices "
+        +toString(wbegin_index[i])+" and "+toString(wend_index[i])+" larger than grid "
+        +toString(getGridPointsPerAxis())+".");
+  }
+  if (changed) {
+    double begin_newwindow[NDIM];
+    double end_newwindow[NDIM];
+    for(size_t i=0;i<NDIM;++i) {
+      const double delta = getDeltaPerAxis(i);
+      begin_newwindow[i] = begin[i]+delta*wnewbegin_index[i];
+      end_newwindow[i] = begin[i]+delta*wnewend_index[i];
+    }
+    // extend window
+    extendWindow(begin_newwindow, end_newwindow);
+  }
+  ASSERT( getWindowGridPoints() % (size_t)8 == 0,
+      "SamplingGrid::padWithZerosForEvenNumberedSamples() - new size "
+      +toString(getWindowGridPoints())+" is still not divisible by 8.");
+}
+
 void SamplingGrid::downsample(
     SamplingGrid& instance,

src/Fragmentation/Summation/SetValues/SamplingGrid.hpp

@@ -289 +289 @@
 
 private:
+  /** Extend the window such that the number of sample points stored is an
+   * even number per axis. This is used by downsample()
+   */
+  void padWithZerosForEvenNumberedSamples();
+
   /** Sets the size of the domain.
    *

src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp

@@ -581 +581 @@
       returnthreshold *= third_two;
   return returnthreshold;
+}
+
+/** UnitTest for padWithZerosForEvenNumberedSamples()
+ *
+ */
+void SamplingGridTest::padWithZerosForEvenNumberedSamplesTest()
+{
+  const double begin[NDIM] = { 0., 0., 0. };
+  const double end[NDIM] = { 2., 2., 2. };
+
+  // we check for window of odd numbers
+  {
+  //    LOG(2, "Checking with difference " << grid_difference);
+    const int gridpoints = 1*2*2;
+    const int extended_gridpoints = 2*4*4;
+    SamplingGrid::sampledvalues_t values(gridpoints, 1.); // length in one axis is odd
+    SamplingGrid::sampledvalues_t checkvalues(extended_gridpoints, 0.);
+    {
+      int N[NDIM];
+      int index = 0;
+      for (N[0]=2;N[0]<3;++N[0]) {
+        for (N[1]=0;N[1]<1;++N[1]) {
+          for (N[2]=0;N[2]<4;++N[2]) {
+            checkvalues[index++] = 0.;
+          }
+        }
+        for (N[1]=1;N[1]<3;++N[1]) {
+          checkvalues[index++] = 0.;
+          for (N[2]=1;N[2]<3;++N[2]) {
+            checkvalues[index++] = 1.;
+          }
+          checkvalues[index++] = 0.;
+        }
+        for (N[1]=3;N[1]<4;++N[1]) {
+          for (N[2]=0;N[2]<4;++N[2]) {
+            checkvalues[index++] = 0.;
+          }
+        }
+      }
+      for (N[0]=3;N[0]<4;++N[0]) {
+        for (N[1]=0;N[1]<4;++N[1]) {
+          for (N[2]=0;N[2]<4;++N[2]) {
+            checkvalues[index++] = 0.;
+          }
+        }
+      }
+    }
+
+    /** Here, we must initialize the larger grid with zero window first and
+     * then add the values into the smaller window.
+     */
+    SamplingGrid grid(begin, end, 2);
+    const double window_begin[NDIM] = {
+        grid.getNearestHigherGridPoint(1.0, 0), // index 2
+        grid.getNearestHigherGridPoint(0.5, 1), // index 1 -> 0
+        grid.getNearestHigherGridPoint(0.5, 2) }; // index 1 -> 0
+    const double window_end[NDIM] = {
+        grid.getNearestLowerGridPoint(1.5, 0), // index 3 -> 4
+        grid.getNearestLowerGridPoint(1.5, 1), // index 3 -> 4
+        grid.getNearestLowerGridPoint(1.5, 2) }; // index 3 -> 4
+    grid.setWindow(window_begin, window_end);
+    grid.addOntoWindow(window_begin, window_end, values, +1.);
+    grid.padWithZerosForEvenNumberedSamples();
+
+    SamplingGrid checkgrid(begin, end, 2);
+    const double check_window_begin[NDIM] = {
+        checkgrid.getNearestHigherGridPoint(1., 0),
+        checkgrid.getNearestHigherGridPoint(0., 1),
+        checkgrid.getNearestHigherGridPoint(0., 2) };
+    const double check_window_end[NDIM] = {
+        checkgrid.getNearestHigherGridPoint(2., 0),
+        checkgrid.getNearestHigherGridPoint(2., 1),
+        checkgrid.getNearestHigherGridPoint(2., 2) };
+    checkgrid.setWindow(check_window_begin, check_window_end);
+    checkgrid.addOntoWindow(check_window_begin, check_window_end, checkvalues, +1.);
+
+    std::cout << " grid value " << grid.sampled_grid << std::endl;
+    std::cout << " checkgrid value " << checkgrid.sampled_grid << std::endl;
+    CPPUNIT_ASSERT_EQUAL( checkgrid.sampled_grid.size(), grid.sampled_grid.size());
+    CPPUNIT_ASSERT_EQUAL( checkgrid, grid );
+  }
 }
 

src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.hpp

@@ -38 +38 @@
     CPPUNIT_TEST ( equality_Test );
     CPPUNIT_TEST ( serializeTest );
+    CPPUNIT_TEST ( padWithZerosForEvenNumberedSamplesTest );
     CPPUNIT_TEST ( downsample_gridTest );
     CPPUNIT_TEST ( downsample_smallerwindowTest );
@@ -59 +60 @@
       void equality_Test();
       void serializeTest();
+      void padWithZerosForEvenNumberedSamplesTest();
       void downsample_gridTest();
       void downsample_smallerwindowTest();