Changeset c1a9d6 for src/Actions/AnalysisAction

Timestamp:

Feb 22, 2012, 11:29:05 AM (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:

b49c5d

Parents:

8fc1a6

git-author:

Frederik Heber <heber@…> (01/13/12 12:39:04)

git-committer:

Frederik Heber <heber@…> (02/22/12 11:29:05)

Message:

Rewrote PairCorrelation() to make use of new LinkedCell construct.

• removed PeriodicPairCorrelation() as this case is now contained.
• TESTFIX: Modified regression test Analysis/PairCorrelation-RangeTest because with new LinkedCell the given range can now actually be heeded.

File:

• src/Actions/AnalysisAction/PairCorrelationAction.cpp (modified) (2 diffs)

src/Actions/AnalysisAction/PairCorrelationAction.cpp

@@ -23 +23 @@
 #include "CodePatterns/Verbose.hpp"
 #include "CodePatterns/Log.hpp"
+#include "Descriptors/AtomTypeDescriptor.hpp"
 #include "Element/element.hpp"
 #include "molecule.hpp"
 #include "Element/periodentafel.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "LinearAlgebra/Vector.hpp"
 #include "World.hpp"
@@ -55 +57 @@
   binoutput.open(params.binoutputname.string().c_str());
   PairCorrelationMap *correlationmap = NULL;
-  std::vector<molecule*> molecules = World::getInstance().getSelectedMolecules();
-  if (params.periodic)
-    correlationmap = PeriodicPairCorrelation(molecules, params.elements, ranges);
-  else
-    correlationmap = PairCorrelation(molecules, params.elements);
+  ASSERT(params.elements.size() == 2,
+      "AnalysisPairCorrelationAction::performCall() - Exactly two elements are required for pair correlation.");
+  std::vector<const element *>::const_iterator elemiter = params.elements.begin();
+  const World::AtomComposite atoms_first = World::getInstance().getAllAtoms(AtomByType(*(elemiter++)));
+  const World::AtomComposite atoms_second = World::getInstance().getAllAtoms(AtomByType(*(elemiter++)));
+  ASSERT(elemiter == params.elements.end(),
+      "AnalysisPairCorrelationAction::performCall() - Exactly two elements are required for pair correlation.");
+  double max_distance = params.BinEnd;
+  if (params.BinEnd <= 0.) {
+    // find max distance within box from diagonal
+    const RealSpaceMatrix &Minv = World::getInstance().getDomain().getMinv();
+    max_distance = (Minv * Vector(1.,1.,1.)).NormSquared();
+  }
+  correlationmap = PairCorrelation(atoms_first, atoms_second, max_distance);
   OutputCorrelationMap<PairCorrelationMap>(&output, correlationmap, OutputPairCorrelation_Header, OutputPairCorrelation_Value);
   binmap = BinData( correlationmap, params.BinWidth, params.BinStart, params.BinEnd );