Changeset b5c53d for src/analysis_correlation.cpp

Timestamp:

Aug 9, 2010, 6:33:29 PM (15 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:

353e82

Parents:

458447 (diff), e588312 (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 branch 'StructureRefactoring' into stable

Conflicts:

src/Actions/AtomAction/AddAction.cpp
src/Actions/AtomAction/ChangeElementAction.cpp
src/Parser/XyzParser.cpp
src/analysis_correlation.cpp
src/atom.cpp
src/config.cpp
src/molecule.cpp

• AtomInfo::element were privatized in stable and element::symbol, ::name in StructureRefactoring (overlapped in various lines).

File:

• src/analysis_correlation.cpp (modified) (14 diffs)

src/analysis_correlation.cpp

@@ -33 +33 @@
  * \return Map of doubles with values the pair of the two atoms.
  */
-PairCorrelationMap *PairCorrelation(std::vector<molecule *> &molecules, const std::vector<element *> &elements)
+PairCorrelationMap *PairCorrelation(std::vector<molecule *> &molecules, const std::vector<const element *> &elements)
 {
   Info FunctionInfo(__func__);
@@ -48 +48 @@
 
   // create all possible pairs of elements
-  set <pair<element *, element *> > PairsOfElements;
+  set <pair<const element *,const element *> > PairsOfElements;
   if (elements.size() >= 2) {
-    for (vector<element *>::const_iterator type1 = elements.begin(); type1 != elements.end(); ++type1)
-      for (vector<element *>::const_iterator type2 = elements.begin(); type2 != elements.end(); ++type2)
+    for (vector<const element *>::const_iterator type1 = elements.begin(); type1 != elements.end(); ++type1)
+      for (vector<const element *>::const_iterator type2 = elements.begin(); type2 != elements.end(); ++type2)
         if (type1 != type2) {
-          PairsOfElements.insert( pair<element *, element*>(*type1,*type2) );
-          DoLog(1) && (Log() << Verbose(1) << "Creating element pair " << (*type1)->symbol << " and " << (*type2)->symbol << "." << endl);
+          PairsOfElements.insert( make_pair(*type1,*type2) );
+          DoLog(1) && (Log() << Verbose(1) << "Creating element pair " << *(*type1) << " and " << *(*type2) << "." << endl);
         }
   } else if (elements.size() == 1) { // one to all are valid
-    element *elemental = *elements.begin();
-    PairsOfElements.insert( pair<element *, element*>(elemental,(element *)NULL) );
-    PairsOfElements.insert( pair<element *, element*>((element *)NULL,elemental) );
+    const element *elemental = *elements.begin();
+    PairsOfElements.insert( pair<const element *,const element*>(elemental,0) );
+    PairsOfElements.insert( pair<const element *,const element*>(0,elemental) );
   } else { // all elements valid
     PairsOfElements.insert( pair<element *, element*>((element *)NULL, (element *)NULL) );
@@ -74 +74 @@
           DoLog(3) && (Log() << Verbose(3) << "Current otheratom is " << **runner << "." << endl);
           if ((*iter)->getId() < (*runner)->getId()){
-            for (set <pair<element *, element *> >::iterator PairRunner = PairsOfElements.begin(); PairRunner != PairsOfElements.end(); ++PairRunner)
+            for (set <pair<const element *, const element *> >::iterator PairRunner = PairsOfElements.begin(); PairRunner != PairsOfElements.end(); ++PairRunner)
               if ((PairRunner->first == (**iter).getType()) && (PairRunner->second == (**runner).getType())) {
                 distance = domain.periodicDistance((*iter)->getPosition(),(*runner)->getPosition());
@@ -95 +95 @@
  * \return Map of doubles with values the pair of the two atoms.
  */
-PairCorrelationMap *PeriodicPairCorrelation(std::vector<molecule *> &molecules, const std::vector<element *> &elements, const int ranges[NDIM] )
+PairCorrelationMap *PeriodicPairCorrelation(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const int ranges[NDIM] )
 {
   Info FunctionInfo(__func__);
@@ -115 +115 @@
 
   // create all possible pairs of elements
-  set <pair<element *, element *> > PairsOfElements;
+  set <pair<const element *,const element *> > PairsOfElements;
   if (elements.size() >= 2) {
-    for (vector<element *>::const_iterator type1 = elements.begin(); type1 != elements.end(); ++type1)
-      for (vector<element *>::const_iterator type2 = elements.begin(); type2 != elements.end(); ++type2)
+    for (vector<const element *>::const_iterator type1 = elements.begin(); type1 != elements.end(); ++type1)
+      for (vector<const element *>::const_iterator type2 = elements.begin(); type2 != elements.end(); ++type2)
         if (type1 != type2) {
-          PairsOfElements.insert( pair<element *, element*>(*type1,*type2) );
-          DoLog(1) && (Log() << Verbose(1) << "Creating element pair " << (*type1)->symbol << " and " << (*type2)->symbol << "." << endl);
+          PairsOfElements.insert( make_pair(*type1,*type2) );
+          DoLog(1) && (Log() << Verbose(1) << "Creating element pair " << *(*type1) << " and " << *(*type2) << "." << endl);
         }
   } else if (elements.size() == 1) { // one to all are valid
-    element *elemental = *elements.begin();
-    PairsOfElements.insert( pair<element *, element*>(elemental,(element *)NULL) );
-    PairsOfElements.insert( pair<element *, element*>((element *)NULL,elemental) );
+    const element *elemental = *elements.begin();
+    PairsOfElements.insert( pair<const element *,const element*>(elemental,0) );
+    PairsOfElements.insert( pair<const element *,const element*>(0,elemental) );
   } else { // all elements valid
     PairsOfElements.insert( pair<element *, element*>((element *)NULL, (element *)NULL) );
@@ -149 +149 @@
                   DoLog(3) && (Log() << Verbose(3) << "Current otheratom is " << **runner << "." << endl);
                   if ((*iter)->getId() < (*runner)->getId()){
-                    for (set <pair<element *, element *> >::iterator PairRunner = PairsOfElements.begin(); PairRunner != PairsOfElements.end(); ++PairRunner)
+                    for (set <pair<const element *,const element *> >::iterator PairRunner = PairsOfElements.begin(); PairRunner != PairsOfElements.end(); ++PairRunner)
                       if ((PairRunner->first == (**iter).getType()) && (PairRunner->second == (**runner).getType())) {
                         periodicOtherX = FullInverseMatrix * ((*runner)->getPosition()); // x now in [0,1)^3
@@ -178 +178 @@
  * \return Map of dobules with values as pairs of atom and the vector
  */
-CorrelationToPointMap *CorrelationToPoint(std::vector<molecule *> &molecules, const std::vector<element *> &elements, const Vector *point )
+CorrelationToPointMap *CorrelationToPoint(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Vector *point )
 {
   Info FunctionInfo(__func__);
@@ -196 +196 @@
     for (molecule::const_iterator iter = (*MolWalker)->begin(); iter != (*MolWalker)->end(); ++iter) {
       DoLog(3) && (Log() << Verbose(3) << "Current atom is " << **iter << "." << endl);
-      for (vector<element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
+      for (vector<const element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
         if ((*type == NULL) || ((*iter)->getType() == *type)) {
           distance = domain.periodicDistance((*iter)->getPosition(),*point);
@@ -215 +215 @@
  * \return Map of dobules with values as pairs of atom and the vector
  */
-CorrelationToPointMap *PeriodicCorrelationToPoint(std::vector<molecule *> &molecules, const std::vector<element *> &elements, const Vector *point, const int ranges[NDIM] )
+CorrelationToPointMap *PeriodicCorrelationToPoint(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Vector *point, const int ranges[NDIM] )
 {
   Info FunctionInfo(__func__);
@@ -237 +237 @@
     for (molecule::const_iterator iter = (*MolWalker)->begin(); iter != (*MolWalker)->end(); ++iter) {
       DoLog(3) && (Log() << Verbose(3) << "Current atom is " << **iter << "." << endl);
-      for (vector<element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
+      for (vector<const element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
         if ((*type == NULL) || ((*iter)->getType() == *type)) {
           periodicX = FullInverseMatrix * ((*iter)->getPosition()); // x now in [0,1)^3
@@ -263 +263 @@
  * \return Map of doubles with values as pairs of atom and the BoundaryTriangleSet that's closest
  */
-CorrelationToSurfaceMap *CorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<element *> &elements, const Tesselation * const Surface, const LinkedCell *LC )
+CorrelationToSurfaceMap *CorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Tesselation * const Surface, const LinkedCell *LC )
 {
   Info FunctionInfo(__func__);
@@ -284 +284 @@
     for (molecule::const_iterator iter = (*MolWalker)->begin(); iter != (*MolWalker)->end(); ++iter) {
       DoLog(3) && (Log() << Verbose(3) << "\tCurrent atom is " << *(*iter) << "." << endl);
-      for (vector<element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
+      for (vector<const element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
         if ((*type == NULL) || ((*iter)->getType() == *type)) {
           TriangleIntersectionList Intersections((*iter)->getPosition(),Surface,LC);
@@ -309 +309 @@
  * \return Map of doubles with values as pairs of atom and the BoundaryTriangleSet that's closest
  */
-CorrelationToSurfaceMap *PeriodicCorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<element *> &elements, const Tesselation * const Surface, const LinkedCell *LC, const int ranges[NDIM] )
+CorrelationToSurfaceMap *PeriodicCorrelationToSurface(std::vector<molecule *> &molecules, const std::vector<const element *> &elements, const Tesselation * const Surface, const LinkedCell *LC, const int ranges[NDIM] )
 {
   Info FunctionInfo(__func__);
@@ -335 +335 @@
     for (molecule::const_iterator iter = (*MolWalker)->begin(); iter != (*MolWalker)->end(); ++iter) {
       DoLog(3) && (Log() << Verbose(3) << "Current atom is " << **iter << "." << endl);
-      for (vector<element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
+      for (vector<const element *>::const_iterator type = elements.begin(); type != elements.end(); ++type)
         if ((*type == NULL) || ((*iter)->getType() == *type)) {
           periodicX = FullInverseMatrix * ((*iter)->getPosition()); // x now in [0,1)^3