Changeset a5551b for src/analysis_correlation.cpp

Timestamp:

Nov 4, 2009, 2:54:31 PM (16 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:

c9bce3e

Parents:

eecd33

Message:

Closed ticket #48 (AnalysisCorrelation...() take MoleculeListClass instead of molecule).

• ParseCommandLineOptions() - case C: ActiveFlag ist set for all but the boundary molecule (i.e. the biggest).
• changed parameters of PairCorrelation(), CorrelationToPoint(), CorrelationToSurface()
• adapted unit tests: AnalysisPairCorrelationUnitTest, AnalysisPairCorrelationUnitTest, AnalysisCorrelationToPointUnitTest

• MISSING: AnalysisCorrelationToSurfaceUnitTest yet only deals with a single molecule instead of multiple ones ...

File:

• src/analysis_correlation.cpp (modified) (10 diffs)

src/analysis_correlation.cpp

@@ -14 +14 @@
 #include "tesselationhelpers.hpp"
 #include "vector.hpp"
+#include "verbose.hpp"
 
 
@@ -19 +20 @@
  * Note given element order is unimportant (i.e. g(Si, O) === g(O, Si))
  * \param *out output stream for debugging
- * \param *mol molecule with atoms
+ * \param *molecules list of molecules structure
  * \param *type1 first element or NULL (if any element)
  * \param *type2 second element or NULL (if any element)
  * \return Map of doubles with values the pair of the two atoms.
  */
-PairCorrelationMap *PairCorrelation( const ofstream *out, const molecule * const mol, const element * const type1, const element * const type2 )
+PairCorrelationMap *PairCorrelation( ofstream * const out, MoleculeListClass * const &molecules, const element * const type1, const element * const type2 )
 {
   PairCorrelationMap *outmap = NULL;
   double distance = 0.;
 
-  if ((mol == NULL)) {
-    cout << "No molecule given." << endl;
+  if (molecules->ListOfMolecules.empty()) {
+    cerr << Verbose(1) <<"No molecule given." << endl;
     return outmap;
   }
   outmap = new PairCorrelationMap;
-  atom *Walker = mol->start;
-  while (Walker->next != mol->end) {
-    Walker = Walker->next;
-    if ((type1 == NULL) || (Walker->type == type1)) {
-      atom *OtherWalker = mol->start;
-      while (OtherWalker->next != mol->end) { // only go up to Walker
-        OtherWalker = OtherWalker->next;
-        if (Walker->nr < OtherWalker->nr)
-          if ((type2 == NULL) || (OtherWalker->type == type2)) {
-            distance = Walker->node->Distance(OtherWalker->node);
-            //cout << "Inserting " << *Walker << " and " << *OtherWalker << endl;
-            outmap->insert ( pair<double, pair <atom *, atom*> > (distance, pair<atom *, atom*> (Walker, OtherWalker) ) );
+  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
+    if ((*MolWalker)->ActiveFlag) {
+      cerr << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl;
+      atom *Walker = (*MolWalker)->start;
+      while (Walker->next != (*MolWalker)->end) {
+        Walker = Walker->next;
+        *out << Verbose(3) << "Current atom is " << *Walker << "." << endl;
+        if ((type1 == NULL) || (Walker->type == type1)) {
+          for (MoleculeList::const_iterator MolOtherWalker = MolWalker; MolOtherWalker != molecules->ListOfMolecules.end(); MolOtherWalker++)
+            if ((*MolOtherWalker)->ActiveFlag) {
+              *out << Verbose(2) << "Current other molecule is " << *MolOtherWalker << "." << endl;
+              atom *OtherWalker = (*MolOtherWalker)->start;
+              while (OtherWalker->next != (*MolOtherWalker)->end) { // only go up to Walker
+                OtherWalker = OtherWalker->next;
+                *out << Verbose(3) << "Current otheratom is " << *OtherWalker << "." << endl;
+                if (Walker->nr < OtherWalker->nr)
+                  if ((type2 == NULL) || (OtherWalker->type == type2)) {
+                    distance = Walker->node->Distance(OtherWalker->node);
+                    //*out << Verbose(1) <<"Inserting " << *Walker << " and " << *OtherWalker << endl;
+                    outmap->insert ( pair<double, pair <atom *, atom*> > (distance, pair<atom *, atom*> (Walker, OtherWalker) ) );
+                  }
+              }
           }
+        }
       }
     }
-  }
 
   return outmap;
@@ -56 +67 @@
 /** Calculates the distance (pair) correlation between a given element and a point.
  * \param *out output stream for debugging
- * \param *mol molecule with atoms
+ * \param *molecules list of molecules structure
  * \param *type element or NULL (if any element)
  * \param *point vector to the correlation point
  * \return Map of dobules with values as pairs of atom and the vector
  */
-CorrelationToPointMap *CorrelationToPoint( const ofstream *out, const molecule * const mol, const element * const type, const Vector *point )
+CorrelationToPointMap *CorrelationToPoint(  ofstream * const out, MoleculeListClass * const &molecules, const element * const type, const Vector *point )
 {
   CorrelationToPointMap *outmap = NULL;
   double distance = 0.;
 
-  if ((mol == NULL)) {
-    cout << "No molecule given." << endl;
+  if (molecules->ListOfMolecules.empty()) {
+    *out << Verbose(1) <<"No molecule given." << endl;
     return outmap;
   }
   outmap = new CorrelationToPointMap;
-  atom *Walker = mol->start;
-  while (Walker->next != mol->end) {
-    Walker = Walker->next;
-    if ((type == NULL) || (Walker->type == type)) {
-      distance = Walker->node->Distance(point);
-      outmap->insert ( pair<double, pair<atom *, const Vector*> >(distance, pair<atom *, const Vector*> (Walker, point) ) );
+  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
+    if ((*MolWalker)->ActiveFlag) {
+      *out << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl;
+      atom *Walker = (*MolWalker)->start;
+      while (Walker->next != (*MolWalker)->end) {
+        Walker = Walker->next;
+        *out << Verbose(3) << "Current atom is " << *Walker << "." << endl;
+        if ((type == NULL) || (Walker->type == type)) {
+          distance = Walker->node->Distance(point);
+          *out << Verbose(4) << "Current distance is " << distance << "." << endl;
+          outmap->insert ( pair<double, pair<atom *, const Vector*> >(distance, pair<atom *, const Vector*> (Walker, point) ) );
+        }
+      }
     }
-  }
 
   return outmap;
@@ -85 +102 @@
 /** Calculates the distance (pair) correlation between a given element and a surface.
  * \param *out output stream for debugging
- * \param *mol molecule with atoms
+ * \param *molecules list of molecules structure
  * \param *type element or NULL (if any element)
  * \param *Surface pointer to Tesselation class surface
@@ -91 +108 @@
  * \return Map of doubles with values as pairs of atom and the BoundaryTriangleSet that's closest
  */
-CorrelationToSurfaceMap *CorrelationToSurface( ofstream *out, const molecule * const mol, const element * const type, const Tesselation * const Surface, const LinkedCell *LC )
-{
-
+CorrelationToSurfaceMap *CorrelationToSurface( ofstream * const out, MoleculeListClass * const &molecules, const element * const type, const Tesselation * const Surface, const LinkedCell *LC )
+{
   CorrelationToSurfaceMap *outmap = NULL;
   double distance = 0.;
@@ -99 +115 @@
   Vector centroid;
 
-  if ((Surface == NULL) || (LC == NULL) || (mol == NULL)) {
-    cout << "No Tesselation, no LinkedCell or no molecule given." << endl;
+  if ((Surface == NULL) || (LC == NULL) || (molecules->ListOfMolecules.empty())) {
+    *out << Verbose(1) <<"No Tesselation, no LinkedCell or no molecule given." << endl;
     return outmap;
   }
   outmap = new CorrelationToSurfaceMap;
-  atom *Walker = mol->start;
-  while (Walker->next != mol->end) {
-    Walker = Walker->next;
-    if ((type == NULL) || (Walker->type == type)) {
-      triangle = Surface->FindClosestTriangleToPoint(out, Walker->node, LC );
-      if (triangle != NULL) {
-        distance = DistanceToTrianglePlane(out, Walker->node, triangle);
-        outmap->insert ( pair<double, pair<atom *, BoundaryTriangleSet*> >(distance, pair<atom *, BoundaryTriangleSet*> (Walker, triangle) ) );
+  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
+    if ((*MolWalker)->ActiveFlag) {
+      *out << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl;
+      atom *Walker = (*MolWalker)->start;
+      while (Walker->next != (*MolWalker)->end) {
+        Walker = Walker->next;
+        *out << Verbose(3) << "Current atom is " << *Walker << "." << endl;
+        if ((type == NULL) || (Walker->type == type)) {
+          triangle = Surface->FindClosestTriangleToPoint(out, Walker->node, LC );
+          if (triangle != NULL) {
+            distance = DistanceToTrianglePlane(out, Walker->node, triangle);
+            outmap->insert ( pair<double, pair<atom *, BoundaryTriangleSet*> >(distance, pair<atom *, BoundaryTriangleSet*> (Walker, triangle) ) );
+          }
+        }
       }
     }
-  }
 
   return outmap;
@@ -135 +156 @@
  * \param *map map to write
  */
-void OutputCorrelation( ofstream *file, const BinPairMap * const map )
+void OutputCorrelation( ofstream * const file, const BinPairMap * const map )
 {
   *file << "# BinStart\tCount" << endl;
@@ -147 +168 @@
  * \param *map map to write
  */
-void OutputPairCorrelation( ofstream *file, const PairCorrelationMap * const map )
+void OutputPairCorrelation( ofstream * const file, const PairCorrelationMap * const map )
 {
   *file << "# BinStart\tAtom1\tAtom2" << endl;
@@ -159 +180 @@
  * \param *map map to write
  */
-void OutputCorrelationToPoint( ofstream *file, const CorrelationToPointMap * const map )
+void OutputCorrelationToPoint( ofstream * const file, const CorrelationToPointMap * const map )
 {
   *file << "# BinStart\tAtom::x[i]-point.x[i]" << endl;
@@ -174 +195 @@
  * \param *map map to write
  */
-void OutputCorrelationToSurface( ofstream *file, const CorrelationToSurfaceMap * const map )
+void OutputCorrelationToSurface( ofstream * const file, const CorrelationToSurfaceMap * const map )
 {
   *file << "# BinStart\tTriangle" << endl;