Changeset 04b6f9 for src/analysis_correlation.cpp

Timestamp:

Jan 27, 2010, 2:36:09 PM (16 years ago)

Author:

Tillmann Crueger <crueger@…>

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, Candidate_v1.7.0, 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:

2ededc2

Parents:

1ca488f (diff), 244a84 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge commit 'heber/Analysis_PairCorrelation' into MenuRefactoring

Conflicts:

molecuilder/src/unittests/Makefile.am

File:

• src/analysis_correlation.cpp (modified) (16 diffs)

src/analysis_correlation.cpp

@@ -10 +10 @@
 #include "analysis_correlation.hpp"
 #include "element.hpp"
+#include "info.hpp"
 #include "log.hpp"
 #include "molecule.hpp"
@@ -28 +29 @@
 PairCorrelationMap *PairCorrelation(MoleculeListClass * const &molecules, const element * const type1, const element * const type2 )
 {
+  Info FunctionInfo(__func__);
   PairCorrelationMap *outmap = NULL;
   double distance = 0.;
@@ -77 +79 @@
 PairCorrelationMap *PeriodicPairCorrelation(MoleculeListClass * const &molecules, const element * const type1, const element * const type2, const int ranges[NDIM] )
 {
+  Info FunctionInfo(__func__);
   PairCorrelationMap *outmap = NULL;
   double distance = 0.;
@@ -154 +157 @@
 CorrelationToPointMap *CorrelationToPoint(MoleculeListClass * const &molecules, const element * const type, const Vector *point )
 {
+  Info FunctionInfo(__func__);
   CorrelationToPointMap *outmap = NULL;
   double distance = 0.;
@@ -190 +194 @@
 CorrelationToPointMap *PeriodicCorrelationToPoint(MoleculeListClass * const &molecules, const element * const type, const Vector *point, const int ranges[NDIM] )
 {
+  Info FunctionInfo(__func__);
   CorrelationToPointMap *outmap = NULL;
   double distance = 0.;
@@ -243 +248 @@
 CorrelationToSurfaceMap *CorrelationToSurface(MoleculeListClass * const &molecules, const element * const type, const Tesselation * const Surface, const LinkedCell *LC )
 {
+  Info FunctionInfo(__func__);
   CorrelationToSurfaceMap *outmap = NULL;
   double distance = 0;
@@ -261 +267 @@
         Log() << Verbose(3) << "Current atom is " << *Walker << "." << endl;
         if ((type == NULL) || (Walker->type == type)) {
-          triangle = Surface->FindClosestTriangleToPoint(Walker->node, LC );
+          triangle = Surface->FindClosestTriangleToVector(Walker->node, LC );
           if (triangle != NULL) {
             distance = DistanceToTrianglePlane(Walker->node, triangle);
@@ -288 +294 @@
 CorrelationToSurfaceMap *PeriodicCorrelationToSurface(MoleculeListClass * const &molecules, const element * const type, const Tesselation * const Surface, const LinkedCell *LC, const int ranges[NDIM] )
 {
+  Info FunctionInfo(__func__);
   CorrelationToSurfaceMap *outmap = NULL;
   double distance = 0;
@@ -301 +308 @@
   }
   outmap = new CorrelationToSurfaceMap;
+  double ShortestDistance = 0.;
+  BoundaryTriangleSet *ShortestTriangle = NULL;
   for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
     if ((*MolWalker)->ActiveFlag) {
@@ -314 +323 @@
           periodicX.MatrixMultiplication(FullInverseMatrix);  // x now in [0,1)^3
           // go through every range in xyz and get distance
+          ShortestDistance = -1.;
           for (n[0]=-ranges[0]; n[0] <= ranges[0]; n[0]++)
             for (n[1]=-ranges[1]; n[1] <= ranges[1]; n[1]++)
@@ -320 +330 @@
                 checkX.AddVector(&periodicX);
                 checkX.MatrixMultiplication(FullMatrix);
-                triangle = Surface->FindClosestTriangleToPoint(&checkX, LC );
-                if (triangle != NULL) {
-                  distance = DistanceToTrianglePlane(&checkX, triangle);
-                  outmap->insert ( pair<double, pair<atom *, BoundaryTriangleSet*> >(distance, pair<atom *, BoundaryTriangleSet*> (Walker, triangle) ) );
+                triangle = Surface->FindClosestTriangleToVector(&checkX, LC);
+                distance = Surface->GetDistanceSquaredToTriangle(checkX, triangle);
+                if ((ShortestDistance == -1.) || (distance < ShortestDistance)) {
+                  ShortestDistance = distance;
+                  ShortestTriangle = triangle;
                 }
-          }
+              }
+          // insert
+          ShortestDistance = sqrt(ShortestDistance);
+          outmap->insert ( pair<double, pair<atom *, BoundaryTriangleSet*> >(ShortestDistance, pair<atom *, BoundaryTriangleSet*> (Walker, ShortestTriangle) ) );
+          //Log() << Verbose(1) << "INFO: Inserting " << Walker << " with distance " << ShortestDistance << " to " << *ShortestTriangle << "." << endl;
         }
       }
@@ -342 +357 @@
 double GetBin ( const double value, const double BinWidth, const double BinStart )
 {
+  Info FunctionInfo(__func__);
   double bin =(double) (floor((value - BinStart)/BinWidth));
   return (bin*BinWidth+BinStart);
@@ -353 +369 @@
 void OutputCorrelation( ofstream * const file, const BinPairMap * const map )
 {
+  Info FunctionInfo(__func__);
   *file << "# BinStart\tCount" << endl;
   for (BinPairMap::const_iterator runner = map->begin(); runner != map->end(); ++runner) {
@@ -365 +382 @@
 void OutputPairCorrelation( ofstream * const file, const PairCorrelationMap * const map )
 {
+  Info FunctionInfo(__func__);
   *file << "# BinStart\tAtom1\tAtom2" << endl;
   for (PairCorrelationMap::const_iterator runner = map->begin(); runner != map->end(); ++runner) {
@@ -377 +395 @@
 void OutputCorrelationToPoint( ofstream * const file, const CorrelationToPointMap * const map )
 {
+  Info FunctionInfo(__func__);
   *file << "# BinStart\tAtom::x[i]-point.x[i]" << endl;
   for (CorrelationToPointMap::const_iterator runner = map->begin(); runner != map->end(); ++runner) {
@@ -392 +411 @@
 void OutputCorrelationToSurface( ofstream * const file, const CorrelationToSurfaceMap * const map )
 {
+  Info FunctionInfo(__func__);
   *file << "# BinStart\tTriangle" << endl;
   for (CorrelationToSurfaceMap::const_iterator runner = map->begin(); runner != map->end(); ++runner) {
-    *file << runner->first << "\t" << *(runner->second.second) << endl;
-  }
-};
-
+    *file << runner->first << "\t" << *(runner->second.first) << "\t" << *(runner->second.second) << endl;
+  }
+};
+