Changeset 7111d4 for src/LinkedCell

Timestamp:

Jan 4, 2012, 2:28:41 PM (13 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:

b6f5bc

Parents:

c9cafa

git-author:

Frederik Heber <heber@…> (01/03/12 17:22:09)

git-committer:

Frederik Heber <heber@…> (01/04/12 14:28:41)

Message:

FIX: LinkedCell_Model::setPartition() did not assure Dimensions is integer.

• we now assert that LinkedCell_Model::Dimensions is symmetric, diagonal.
• FIX: its components are integer by slightly enlarging the edge length. This is required to correctly placed nodes inside cells.

File:

• src/LinkedCell/LinkedCell_Model.cpp (modified) (1 diff)

src/LinkedCell/LinkedCell_Model.cpp

@@ -224 +224 @@
 
   RealSpaceMatrix output = Minv * neighborhood;
-
-  //std::cout << Minv << " * " << neighborhood << " = " << output << std::endl;
+  std::cout << Minv << " * " << neighborhood << " = " << output << std::endl;
 
   Dimensions = output.invert();
+  std::cout << "Dimensions are then " << Dimensions << std::endl;
+
+  // now dimensions is floating-point, but we need it to be integer (for allocation)
+  for (size_t col = 0; col < NDIM; ++col) {
+    for (size_t row = 0; row < NDIM; ++row) {
+      ASSERT(fabs(Dimensions.at(row,col) - Dimensions.at(col,row)) < 1.e+3*std::numeric_limits<double>::epsilon(),
+          "LinkedCell_Model::setPartition() - Dimensions is not symmetric by "
+          +toString(fabs(Dimensions.at(row,col) - Dimensions.at(col,row)))+ ".");
+      if (col != row) {
+        ASSERT(fabs(Dimensions.at(row,col)) < 1.e+3*std::numeric_limits<double>::epsilon(),
+            "LinkedCell_Model::setPartition() - Dimensions is not diagonal by "
+            +toString(fabs(Dimensions.at(row,col)))+".");
+      } else {
+        Dimensions.set(row,col, floor(Dimensions.at(row,col)));
+      }
+    }
+  }
+
+
   Partition = Minv*Dimensions; //
 
-  //std::cout << "Dimensions are then " << Dimensions << std::endl;
-  //std::cout << "Partition matrix is then " << Partition << std::endl;
+  std::cout << "Partition matrix is then " << Partition << std::endl;
 }