Changeset 64bafe0 for src/Jobs/Grid

Timestamp:

Feb 15, 2013, 9:52:02 AM (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:

8f3cdd

Parents:

c6355f

git-author:

Frederik Heber <heber@…> (12/19/12 12:46:23)

git-committer:

Frederik Heber <heber@…> (02/15/13 09:52:02)

Message:

SamplingGrid's Window start and end are now always set on a grid point

• also made addWindowOntoWindow() safe with respect to rounding.
• TESTFIX: this fixes SamplingGridUnitTest, removed expected to fail.

Location:

src/Jobs/Grid

Files:

• SamplingGrid.cpp (modified) (4 diffs)
• SamplingGrid.hpp (modified) (1 diff)
• unittests/Makefile.am (modified) (1 diff)

src/Jobs/Grid/SamplingGrid.cpp

@@ -233 +233 @@
 }
 
+double SamplingGrid::getNearestLowerGridPoint(
+    const double value, const size_t axis) const
+{
+  const double length = end[axis] - begin[axis];
+  if ((fabs(length) < std::numeric_limits<double>::epsilon()) || (getGridPointsPerAxis() == 0)) {
+    return 0.;
+  } else {
+    const double offset = value - begin[axis];
+    const double factor = floor((double)getGridPointsPerAxis()*(offset/length));
+    return factor*(length/(double)getGridPointsPerAxis());
+  }
+}
+
+double SamplingGrid::getNearestHigherGridPoint(
+    const double value, const size_t axis) const
+{
+  const double length = end[axis] - begin[axis];
+  if ((fabs(length) < std::numeric_limits<double>::epsilon()) || (getGridPointsPerAxis() == 0)) {
+    return 0.;
+  } else {
+    const double offset = value - begin[axis];
+    const double factor = ceil((double)getGridPointsPerAxis()*(offset/length));
+    return factor*(length/(double)getGridPointsPerAxis());
+  }
+}
+
 void SamplingGrid::setWindowSize(
     const double _begin_window[3],
@@ -238 +264 @@
 {
   for (size_t index=0;index<3;++index) {
-    ASSERT( _begin_window[index] >= begin[index],
+    begin_window[index] = getNearestLowerGridPoint(_begin_window[index], index);
+    ASSERT( begin_window[index] >= begin[index],
         "SamplingGrid::setWindowSize() - window starts earlier than domain on "
         +toString(index)+"th component.");
-    begin_window[index] = _begin_window[index];
-    ASSERT( _end_window[index] <= end[index],
+    end_window[index] = getNearestHigherGridPoint(_end_window[index], index);
+    ASSERT( end_window[index] <= end[index],
         "SamplingGrid::setWindowSize() - window ends later than domain on "
         +toString(index)+"th component.");
-    end_window[index] = _end_window[index];
   }
 }
@@ -339 +365 @@
   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) {
-    pre_offset[index] = (_begin_window[index] - begin_window[index])*gridpoints_axis;
-    length[index] = (_end_window[index] - _begin_window[index])*gridpoints_axis;
-    post_offset[index] = (end_window[index] - _end_window[index])*gridpoints_axis;
-    total[index] = (end_window[index] - begin_window[index])*gridpoints_axis;
+    // 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 = (double)gridpoints_axis/(end[index] - begin[index]);
+    // delta is conversion factor from box length to discrete length, i.e. number of points
+    pre_offset[index] = delta*(_begin_window[index] - begin_window[index])+round_offset;
+    length[index] = delta*(_end_window[index] - _begin_window[index])+round_offset;
+    post_offset[index] = delta*(end_window[index] - _end_window[index])+round_offset;
+    total[index] = delta*(end_window[index] - 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],
         "SamplingGrid::addOntoWindow() - pre, post, and length don't sum up to total for "
         +toString(index)+"th component.");
   }
+  // assert that calculated lengths match with given vector sizes
 #ifndef NDEBUG
   const size_t calculated_size = length[0]*length[1]*length[2];
@@ -362 +398 @@
 #endif
   size_t N[3];
-  size_t counter = 0;
+//  size_t counter = 0;
   sampledvalues_t::iterator griditer = sampled_grid.begin();
   std::advance(griditer, pre_offset[0]*total[1]*total[2]);

src/Jobs/Grid/SamplingGrid.hpp

@@ -246 +246 @@
   void setWindowSize(const double _begin_window[3], const double _end_window[3]);
 
+  /** Helper function to get point at grid point for given \a axis and less than value.
+   *
+   * @param value value to find nearest grid point to
+   * @param axis axis of the value
+   * @return nearest lower grid point
+   */
+  double getNearestLowerGridPoint(
+      const double value, const size_t axis) const;
+
+  /** Helper function to get point at grid point for given \a axis and greater than value.
+   *
+   * @param value value to find nearest grid point to
+   * @param axis axis of the value
+   * @return nearest lower grid point
+   */
+  double getNearestHigherGridPoint(
+      const double value, const size_t axis) const;
+
 public:
   /// We do not store the whole grid if many entries are actually zero

src/Jobs/Grid/unittests/Makefile.am

@@ -14 +14 @@
   SamplingGridUnitTest
 
-XFAIL_TESTS += SamplingGridUnitTest
 TESTS += $(JOBSGRIDTESTS)
 check_PROGRAMS += $(JOBSGRIDTESTS)