Changeset de6dfb for src/Jobs/Grid

Timestamp:

Feb 15, 2013, 9:51:49 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:

c6355f

Parents:

e2404f

git-author:

Frederik Heber <heber@…> (02/11/13 09:24:45)

git-committer:

Frederik Heber <heber@…> (02/15/13 09:51:49)

Message:

Extending AddOntoWindow() by prefactor, can deal with differently sized windows.

• also extended unit tests to check on working asymmetry.

Location:

src/Jobs/Grid

Files:

• SamplingGrid.cpp (modified) (4 diffs)
• SamplingGrid.hpp (modified) (1 diff)
• unittests/SamplingGridUnitTest.cpp (modified) (2 diffs)
• unittests/SamplingGridUnitTest.hpp (modified) (2 diffs)

src/Jobs/Grid/SamplingGrid.cpp

@@ -144 +144 @@
       }
     }
+    LOG(2, "DEBUG: max begin is " << max_begin_window[0] << "," << max_begin_window[1] << "," << max_begin_window[2] << ".");
+    LOG(2, "DEBUG: max end is " << max_end_window[0] << "," << max_end_window[1] << "," << max_end_window[2] << ".");
     if (doExtend)
       extendWindow(max_begin_window, max_end_window);
     /// and copy other into larger window, too
-    addOntoWindow(other.begin_window, other.end_window, other.sampled_grid);
-    // then add other's grid onto this one
-    sampledvalues_t::iterator iter = sampled_grid.begin();
-    sampledvalues_t::const_iterator otheriter = other.sampled_grid.begin();
-    for(; iter != sampled_grid.end(); ++iter, ++otheriter )
-      *iter += prefactor * (*otheriter);
+    addOntoWindow(other.begin_window, other.end_window, other.sampled_grid, prefactor);
   } else {
     ASSERT(0, "SamplingGrid::superposeOtherGrids() - superposing incompatible grids is so far not in the cards.");
@@ -290 +287 @@
   }
   sampledvalues_t old_values(sampled_grid);
+  // set new window
+  setWindow(_begin_window,_end_window);
   // now extend it ...
-  addOntoWindow(old_begin_window, old_end_window, old_values);
+  addOntoWindow(old_begin_window, old_end_window, old_values, +1.);
+  LOG(2, "DEBUG: Grid after extension is " << sampled_grid << ".");
 }
 
@@ -297 +297 @@
     const double _begin_window[3],
     const double _end_window[3],
-    const sampledvalues_t &_sampled_grid)
+    const sampledvalues_t &_sampled_grid,
+    const double prefactor)
 {
 #ifndef NDEBUG
@@ -311 +312 @@
   // the only issue are indices
   const size_t gridpoints_axis = pow(2, level);
-  size_t offset[3];
+  size_t pre_offset[3];
+  size_t post_offset[3];
   size_t length[3];
+  size_t total[3];
   for(size_t index=0;index<3;++index) {
-    offset[index] = gridpoints_axis*(_begin_window[index] - begin_window[index]);
-    length[index] =  gridpoints_axis*(_end_window[index] - _begin_window[index]);
+    pre_offset[index] = (_begin_window[index] - begin_window[index])*gridpoints_axis;
+    post_offset[index] = (end_window[index] - _end_window[index])*gridpoints_axis;
+    length[index] = (_end_window[index] - _begin_window[index])*gridpoints_axis;
+    total[index] = (end_window[index] - begin_window[index])*gridpoints_axis;
+    ASSERT( pre_offset[index]+post_offset[index]+length[index] == total[index],
+        "SamplingGrid::addOntoWindow() - pre, past, and length don't sum up to total for "
+        +toString(index)+"th component.");
   }
   ASSERT( length[0]*length[1]*length[2] ==  _sampled_grid.size(),
       "SamplingGrid::addOntoWindow() - not enough sampled values given.");
+  ASSERT( length[0]*length[1]*length[2] <=  sampled_grid.size(),
+      "SamplingGrid::addOntoWindow() - not enough sampled values available.");
   size_t N[3];
-//  sampledvalues_t::iterator griditer = sampled_grid.begin();
+  sampledvalues_t::iterator griditer = sampled_grid.begin();
+  std::advance(griditer, pre_offset[0]*total[1]*total[2]);
   sampledvalues_t::const_iterator copyiter = _sampled_grid.begin();
-  for(N[0]=offset[0]; N[0] < length[0]; ++N[0]) {
-    for(N[1]=offset[1]; N[1] < length[1]; ++N[1]) {
-      for(N[2]=offset[2]; N[2] < length[2]; ++N[2]) {
-        const size_t index =
-            (N[0]*gridpoints_axis+N[1])*gridpoints_axis+N[2];
-        sampled_grid[index] += *copyiter;
+  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]) {
+        *griditer++ += prefactor*(*copyiter++);
       }
+      std::advance(griditer, post_offset[2]);
     }
-  }
+    std::advance(griditer, post_offset[1]*total[2]);
+  }
+  //std::advance(griditer, post_offset[0]*total[1]*total[2]);
+  LOG(2, "DEBUG: Grid after adding other is " << sampled_grid << ".");
 }
 

src/Jobs/Grid/SamplingGrid.hpp

@@ -199 +199 @@
    * \param _end_window end of other window
    * \param _sampled_grid other set of sampled values
+   * @param prefactor +1. is then addition, -1. is subtraction.
    */
   void addOntoWindow(
       const double _begin_window[3],
       const double _end_window[3],
-      const sampledvalues_t &_sampled_grid);
+      const sampledvalues_t &_sampled_grid,
+      const double prefactor);
 
   /** Helper function that contains all the logic of how to superpose two

src/Jobs/Grid/unittests/SamplingGridUnitTest.cpp

@@ -149 +149 @@
   // we have a grid with size of two, extend to twice the size and check
   const double begin[3] = { 0., 0., 0. };
+  const double size = 2.;
+  const double end[3] = { size, size, size };
+  grid->extendWindow(begin, end);
+
+  // check integral
+  CPPUNIT_ASSERT_EQUAL( grid_value/(NUMBEROFSAMPLES(grid->level)/NUMBEROFSAMPLES(grid->level)), grid->integral() );
+
+  // check number of points
+  CPPUNIT_ASSERT_EQUAL( (size_t)NUMBEROFSAMPLES(grid->level), grid->getWindowGridPoints() );
+}
+
+/** UnitTest for extendWindow() with asymmetric values
+ */
+void SamplingGridTest::extendWindow_asymmetric_Test()
+{
+  const double begin[3] = { 0., 0., 0. };
   const double end[3] = { 2., 2., 2. };
+  grid->sampled_grid.clear();
+  SamplingGrid::sampledvalues_t::iterator griditer = grid->sampled_grid.begin();
+  for (size_t i=0; i< NUMBEROFSAMPLES(grid->level); ++i)
+     *griditer++ += grid_value*i;
   grid->extendWindow(begin, end);
 
-  // check integral
-  CPPUNIT_ASSERT_EQUAL( NUMBEROFSAMPLES(2)*grid_value, grid->integral() );
-
-  // check number of points
-  CPPUNIT_ASSERT_EQUAL( (size_t)NUMBEROFSAMPLES(3), grid->getWindowGridPoints() );
+  CPPUNIT_ASSERT_EQUAL( grid_value, grid->integral() );
 }
 
@@ -176 +192 @@
   const double wrongend[3] = { 1.5, 1.5, 1.5 };
   std::cout << "The following assertion is intended and does not indicate a failure of the test." << std::endl;
-  CPPUNIT_ASSERT_THROW( grid->addOntoWindow(begin, wrongend, values), Assert::AssertionFailure );
+  CPPUNIT_ASSERT_THROW( grid->addOntoWindow(begin, wrongend, values, +1.), Assert::AssertionFailure );
 #endif
   // now perform working operation
-  grid->addOntoWindow(begin, end, values);
+  grid->addOntoWindow(begin, end, values, +1.);
 
   // check integral to be one and half times the old value
   CPPUNIT_ASSERT_EQUAL( (1.+pow(.5,3))*grid_value, grid->integral() );
+}
+
+/** UnitTest for addOntoWindow() with asymmetric values
+ */
+void SamplingGridTest::addOntoWindow_asymmetric_Test()
+{
+  // check with asymmetric values
+  grid->sampled_grid.clear();
+  grid->sampled_grid.resize(NUMBEROFSAMPLES(2), 0.);
+
+  for (size_t i=0;i<grid->level*(grid->end[0]-grid->begin[0]);++i)
+    grid->sampled_grid[(i*2+0)*2+0] += .5*grid_value;
+  for (size_t i=0;i<grid->level*(grid->end[1]-grid->begin[1]);++i)
+    grid->sampled_grid[(0*2+i)*2+0] += 1.*grid_value;
+  for (size_t i=0;i<grid->level*(grid->end[2]-grid->begin[2]);++i)
+    grid->sampled_grid[(0*2+0)*2+i] += 1.5*grid_value;
+
+  const double integral = grid->integral();
+  const double begin[3] = { 0., 0., 0. };
+  for(double size=2.; size<=5.; size += 1.) {
+    const double newend[3] = {size, size, size};
+    grid->extendWindow(begin, newend);
+    CPPUNIT_ASSERT_EQUAL( pow(size,3)*integral, grid->integral() );
+  }
 }
 

src/Jobs/Grid/unittests/SamplingGridUnitTest.hpp

@@ -30 +30 @@
     CPPUNIT_TEST ( getWindowSize_Test );
     CPPUNIT_TEST ( extendWindow_Test );
+    CPPUNIT_TEST ( extendWindow_asymmetric_Test );
     CPPUNIT_TEST ( addOntoWindow_Test );
+    CPPUNIT_TEST ( addOntoWindow_asymmetric_Test );
     CPPUNIT_TEST_SUITE_END();
 
@@ -40 +42 @@
       void getWindowSize_Test();
       void extendWindow_Test();
+      void extendWindow_asymmetric_Test();
       void addOntoWindow_Test();
+      void addOntoWindow_asymmetric_Test();
       void operatorPlusEqual_Test();
       void operatorMinusEqual_Test();