Changeset 3d9a8d for src/Jobs/Grid

Timestamp:

Feb 14, 2013, 1:29:24 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:

98f8fe

Parents:

e089fb

git-author:

Frederik Heber <heber@…> (12/04/12 09:32:04)

git-committer:

Frederik Heber <heber@…> (02/14/13 13:29:24)

Message:

SamplingGrid has no more size parameter but an end array.

• this rather fits into scheme with the later to come window.
• also several changes in interface due to SamplingGrid::size -> ::end[3] replacement.

Location:

src/Jobs/Grid

Files:

• SamplingGrid.cpp (modified) (4 diffs)
• SamplingGrid.hpp (modified) (3 diffs)
• SamplingGridProperties.cpp (modified) (2 diffs)
• SamplingGridProperties.hpp (modified) (4 diffs)
• unittests/Makefile.am (modified) (1 diff)
• unittests/SamplingGridPropertiesUnitTest.cpp (modified) (3 diffs)
• unittests/SamplingGridUnitTest.cpp (modified) (7 diffs)
• unittests/SamplingGridUnitTest.hpp (modified) (2 diffs)

src/Jobs/Grid/SamplingGrid.cpp

@@ -46 +46 @@
 
 SamplingGrid::SamplingGrid(const double _begin[3],
-    const double _size,
+    const double _end[3],
     const int _level,
     const sampledvalues_t &_sampled_grid) :
-  SamplingGridProperties(_begin, _size, _level),
+  SamplingGridProperties(_begin, _end, _level),
   sampled_grid(_sampled_grid)
 {}
@@ -110 +110 @@
 }
 
+double SamplingGrid::getVolume() const
+{
+  double volume = 1.;
+  for (size_t i=0;i<3;++i)
+    volume *= end[i]-begin[i];
+  return volume;
+}
+
 double SamplingGrid::integral() const
 {
   const size_t gridpoints = pow(2, level);
-  const double volume_element = pow(size/(double)gridpoints, 3);
+  const double volume_element = getVolume()/pow((double)gridpoints, 3);
   double int_value = 0.;
   for (sampledvalues_t::const_iterator iter = sampled_grid.begin();
@@ -128 +136 @@
   if (isCompatible(weight)) {
     const size_t gridpoints = pow(2, level);
-    const double volume_element = pow(size/(double)gridpoints, 3);
+    const double volume_element = getVolume()/pow((double)gridpoints, 3);
     double int_value = 0.;
     sampledvalues_t::const_iterator iter = sampled_grid.begin();
@@ -144 +152 @@
 {
   ost << "SamplingGrid starting at " << other.begin[0] << "," << other.begin[1] << "," << other.begin[2];
-  ost << ", size of " << other.size;
+  ost << ", ending at " << other.end[0] << "," << other.end[1] << "," << other.end[2];
   ost << ", level of " << other.level;
   ost << " and integrated value of " << other.integral();

src/Jobs/Grid/SamplingGrid.hpp

@@ -27 +27 @@
 /** This class stores a sample function on a three-dimensional grid.
  *
+ *  \note We do not use boost::multi_array because it is not trivial to serialize.
+ *
  */
 class SamplingGrid : public SamplingGridProperties
@@ -40 +42 @@
   /** Constructor for class SamplingGrid.
    *
-   * \param _begin offset for grid
-   * \param _size edge length of grid
-   * \param _level number of grid points in \f$2^{\text{level}}\f$
+   * \param _begin offset for grid per axis
+   * \param _end edge length of grid per axis
+   * \param _level number of grid points in \f$2^{\mathrm{level}}\f$
    * \param _sampled_grid sample points
    */
   SamplingGrid(const double _begin[3],
-      const double _size,
+      const double _end[3],
       const int _level,
       const sampledvalues_t &_sampled_grid);
@@ -127 +129 @@
 
 private:
+  /** Returns the volume of the domain for this sampled function.
+   *
+   * @return volume
+   */
+  double getVolume() const;
+
   /** Helper function that contains all the logic of how to superpose two
    * grids.

src/Jobs/Grid/SamplingGridProperties.cpp

@@ -44 +44 @@
 SamplingGridProperties::SamplingGridProperties(
     const double _begin[3],
-    const double _size,
+    const double _end[3],
     const int _level) :
-  size(_size),
   level(_level)
 {
-  for(size_t i=0; i<3; ++i)
+  for(size_t i=0; i<3; ++i) {
     begin[i] = _begin[i];
+    end[i] = _end[i];
+  }
 }
 
 SamplingGridProperties::SamplingGridProperties(const SamplingGridProperties &_props) :
-  size(_props.size),
   level(_props.level)
 {
-  for(size_t i=0; i<3; ++i)
+  for(size_t i=0; i<3; ++i) {
     begin[i] = _props.begin[i];
+    end[i] = _props.end[i];
+  }
 }
 
 SamplingGridProperties::SamplingGridProperties() :
-  size(0.),
   level(0)
 {
-  for(size_t i=0; i<3; ++i)
+  for(size_t i=0; i<3; ++i) {
     begin[i] = 0.;
+    end[i] = 0.;
+  }
 }
 
@@ -72 +75 @@
 {}
 
+SamplingGridProperties& SamplingGridProperties::operator=(const SamplingGridProperties& other)
+{
+  // check for self-assignment
+  if (this != &other) {
+    for(size_t index=0; index<3; ++index) {
+      begin[index] = other.begin[index];
+      end[index] = other.end[index];
+    }
+    level = other.level;
+  }
+  return *this;
+}
+
 bool SamplingGridProperties::operator==(const SamplingGridProperties &_props) const
 {
   bool status = true;
-  for (size_t i=0; i<3; ++i)
+  for (size_t i=0; i<3; ++i) {
     status &= begin[i] == _props.begin[i];
-  status &= size == _props.size;
+    status &= end[i] == _props.end[i];
+  }
   status &= level == _props.level;
   return status;

src/Jobs/Grid/SamplingGridProperties.hpp

@@ -25 +25 @@
    *
    * \param _begin offset of grid
-   * \param _size edge length of cubic(!) domain
-   * \param _level number of gridpoints as \f$2^{\text{level}}\f$
+   * \param _end edge length per axis
+   * \param _level number of gridpoints as \f$2^{\mathrm{level}}\f$ per unit(!) length
    */
   SamplingGridProperties(
       const double _begin[3],
-      const double _size,
+      const double _end[3],
       const int _level);
 
@@ -55 +55 @@
   }
 
+  /** Assignment operator.
+   *
+   * \param other other instance to assign ourselves to
+   */
+  SamplingGridProperties& operator=(const SamplingGridProperties& other);
+
   /** Equality operator for class SamplingGridProperties.
    *
@@ -73 +79 @@
   //!> offset of grid
   double begin[3];
-  //!> size of grid, i.e. edge length of cubic(!) domain
-  double size;
-  //!> level, i.e. \f$2^{\text{level}}\f$ grid points per axis
+  //!> size of grid, i.e. edge length per axis of domain
+  double end[3];
+  //!> level, i.e. \f$2^{\mathrm{level}}\f$ grid points per axis per unit(!) length
   int level;
 
@@ -88 +94 @@
     for (i=0; i<3; ++i)
       ar & begin[i];
-    ar & size;
+    for (i=0; i<3; ++i)
+      ar & end[i];
     ar & level;
   }

src/Jobs/Grid/unittests/Makefile.am

@@ -25 +25 @@
 SamplingGridPropertiesUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
         ../Jobs/Grid/unittests/SamplingGridPropertiesUnitTest.cpp \
-        ../Jobs/Grid/unittests/SamplingGridPropertiesUnitTest.hpp
+        ../Jobs/Grid/unittests/SamplingGridPropertiesUnitTest.hpp \
+        ../Jobs/Grid/SamplingGridProperties.cpp \
+        ../Jobs/Grid/SamplingGriPropertiesd.hpp
 SamplingGridPropertiesUnitTest_LDADD = ${JOBSGRIDLIBS}
 
 SamplingGridUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
         ../Jobs/Grid/unittests/SamplingGridUnitTest.cpp \
-        ../Jobs/Grid/unittests/SamplingGridUnitTest.hpp
+        ../Jobs/Grid/unittests/SamplingGridUnitTest.hpp \
+        ../Jobs/Grid/SamplingGridProperties.cpp \
+        ../Jobs/Grid/SamplingGriPropertiesd.hpp \
+        ../Jobs/Grid/SamplingGrid.cpp \
+        ../Jobs/Grid/SamplingGrid.hpp
+SamplingGridUnitTest_LDADD = \
+        ${CodePatterns_LIBS} \
+        $(BOOST_LIB)
 
-SamplingGridUnitTest_LDADD = ${JOBSGRIDLIBS}
 
 #AUTOMAKE_OPTIONS = parallel-tests

src/Jobs/Grid/unittests/SamplingGridPropertiesUnitTest.cpp

@@ -60 +60 @@
   // create the grid
   const double begin[3] = { 0., 0., 0. };
-  props = new SamplingGridProperties(begin, 1., 2);
+  const double end[3] = { 1., 1., 1. };
+  props = new SamplingGridProperties(begin, end, 2);
 }
 
@@ -75 +76 @@
   const double begin[3] = { 0., 0., 0. };
   const double otherbegin[3] = { 1., 0.1, -0.5 };
+  const double end[3] = { 1., 1., 1. };
+  const double otherend[3] = { 2., 2., 2. };
 
   // create other props
-  SamplingGridProperties sameprops(begin, 1., 2);
-  SamplingGridProperties otherprops(otherbegin, 1., 2);
-  SamplingGridProperties anotherprops(begin, 2., 2);
-  SamplingGridProperties moreotherprops(begin, 1., 4);
+  SamplingGridProperties sameprops(begin, end, 2);
+  SamplingGridProperties otherprops(otherbegin, end, 2);
+  SamplingGridProperties anotherprops(begin, otherend, 2);
+  SamplingGridProperties moreotherprops(begin, end, 4);
 
   CPPUNIT_ASSERT( props->isCompatible(*props) );
@@ -99 +102 @@
   const double begin[3] = { 0., 0., 0. };
   const double otherbegin[3] = { 1., 0.1, -0.5 };
+  const double end[3] = { 1., 1., 1. };
+  const double otherend[3] = { 2., 2., 2. };
 
   // create other props
-  SamplingGridProperties sameprops(begin, 1., 2);
-  SamplingGridProperties otherprops(otherbegin, 1., 2);
-  SamplingGridProperties anotherprops(begin, 2., 2);
-  SamplingGridProperties moreotherprops(begin, 1., 4);
+  SamplingGridProperties sameprops(begin, end, 2);
+  SamplingGridProperties otherprops(otherbegin, end, 2);
+  SamplingGridProperties anotherprops(begin, otherend, 2);
+  SamplingGridProperties moreotherprops(begin, end, 4);
 
   CPPUNIT_ASSERT( *props == *props );

src/Jobs/Grid/unittests/SamplingGridUnitTest.cpp

@@ -56 +56 @@
 const double grid_value=1.;
 
+#define NUMBEROFSAMPLES(n) (size_t)(pow(pow(2,n),3))
+
 // Registers the fixture into the 'registry'
 CPPUNIT_TEST_SUITE_REGISTRATION( SamplingGridTest );
@@ -67 +69 @@
   // create the grid
   const double begin[3] = { 0., 0., 0. };
-  for (size_t i=0; i< pow(pow(2,2),3); ++i)
+  const double end[3] = { 1., 1., 1. };
+  for (size_t i=0; i< pow(1,3)*NUMBEROFSAMPLES(2); ++i)
     values += grid_value;
-  grid = new SamplingGrid(begin, 1., 2, values);
+  grid = new SamplingGrid(begin, end, 2, values);
   CPPUNIT_ASSERT_EQUAL( grid_value, *(grid->sampled_grid.begin()) );
 }
@@ -87 +90 @@
   // check illegal grid
   const double begin[3] = { 0., 0., 0. };
-  SamplingGridProperties illegal_props(begin, 2., 1);
+  const double end[3] = { 2., 2., 2. };
+  SamplingGridProperties illegal_props(begin, end, 1);
   CPPUNIT_ASSERT( !grid->isCompatible(illegal_props) );
   SamplingGrid::sampledvalues_t illegal_values;
@@ -94 +98 @@
   SamplingGrid illegal_grid(illegal_props, illegal_values);
 #ifndef NDEBUG
+  std::cout << "The following assertion is intended and does not indicate a failure of the test." << std::endl;
   CPPUNIT_ASSERT_THROW( *grid += illegal_grid, Assert::AssertionFailure );
 #else
@@ -105 +110 @@
 }
 
+/** UnitTest for getVolume_Test
+ */
+void SamplingGridTest::getVolume_Test()
+{
+  CPPUNIT_ASSERT_EQUAL( 1., grid->getVolume() );
+}
+
 /** UnitTest for operator+=()
  */
@@ -111 +123 @@
   // create other grid
   const double begin[3] = { 0., 0., 0. };
+  const double end[3] = { 1., 1., 1. };
   SamplingGrid::sampledvalues_t othervalues;
   const double othergrid_value = 1.5;
   for (size_t i=0; i< NUMBEROFSAMPLES(2); ++i)
     othervalues += othergrid_value;
-  SamplingGrid othergrid(begin, 1., 2, othervalues);
+  SamplingGrid othergrid(begin, end, 2, othervalues);
   CPPUNIT_ASSERT_EQUAL( othergrid_value, *(othergrid.sampled_grid.begin()) );
 
@@ -134 +147 @@
   // create other grid
   const double begin[3] = { 0., 0., 0. };
+  const double end[3] = { 1., 1., 1. };
   SamplingGrid::sampledvalues_t othervalues;
   const double othergrid_value = 1.5;
   for (size_t i=0; i< NUMBEROFSAMPLES(2); ++i)
     othervalues += othergrid_value;
-  SamplingGrid othergrid(begin, 1., 2, othervalues);
+  SamplingGrid othergrid(begin, end, 2, othervalues);
   CPPUNIT_ASSERT_EQUAL( othergrid_value, *(othergrid.sampled_grid.begin()) );
 

src/Jobs/Grid/unittests/SamplingGridUnitTest.hpp

@@ -27 +27 @@
     CPPUNIT_TEST ( operatorPlusEqual_Test );
     CPPUNIT_TEST ( operatorMinusEqual_Test );
+    CPPUNIT_TEST ( getVolume_Test );
     CPPUNIT_TEST_SUITE_END();
 
@@ -33 +34 @@
       void tearDown();
       void superposeOtherGrid_Test();
+      void getVolume_Test();
       void operatorPlusEqual_Test();
       void operatorMinusEqual_Test();