Changeset a5551b


Ignore:
Timestamp:
Nov 4, 2009, 2:54:31 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:
c9bce3e
Parents:
eecd33
Message:

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

Location:
src
Files:
9 edited

Legend:

Unmodified
Added
Removed

  • src/analysis_correlation.cpp

    reecd33 ra5551b  
    1414#include "tesselationhelpers.hpp"
    1515#include "vector.hpp"
     16#include "verbose.hpp"
    1617
    1718
    … …  
    1920 * Note given element order is unimportant (i.e. g(Si, O) === g(O, Si))
    2021 * \param *out output stream for debugging
    21  * \param *mol molecule with atoms
     22 * \param *molecules list of molecules structure
    2223 * \param *type1 first element or NULL (if any element)
    2324 * \param *type2 second element or NULL (if any element)
    2425 * \return Map of doubles with values the pair of the two atoms.
    2526 */
    26 PairCorrelationMap *PairCorrelation( const ofstream *out, const molecule * const mol, const element * const type1, const element * const type2 )
     27PairCorrelationMap *PairCorrelation( ofstream * const out, MoleculeListClass * const &molecules, const element * const type1, const element * const type2 )
    2728{
    2829  PairCorrelationMap *outmap = NULL;
    2930  double distance = 0.;
    3031
    31   if ((mol == NULL)) {
    32     cout << "No molecule given." << endl;
     32  if (molecules->ListOfMolecules.empty()) {
     33    cerr << Verbose(1) <<"No molecule given." << endl;
    3334    return outmap;
    3435  }
    3536  outmap = new PairCorrelationMap;
    36   atom *Walker = mol->start;
    37   while (Walker->next != mol->end) {
    38     Walker = Walker->next;
    39     if ((type1 == NULL) || (Walker->type == type1)) {
    40       atom *OtherWalker = mol->start;
    41       while (OtherWalker->next != mol->end) { // only go up to Walker
    42         OtherWalker = OtherWalker->next;
    43         if (Walker->nr < OtherWalker->nr)
    44           if ((type2 == NULL) || (OtherWalker->type == type2)) {
    45             distance = Walker->node->Distance(OtherWalker->node);
    46             //cout << "Inserting " << *Walker << " and " << *OtherWalker << endl;
    47             outmap->insert ( pair<double, pair <atom *, atom*> > (distance, pair<atom *, atom*> (Walker, OtherWalker) ) );
     37  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
     38    if ((*MolWalker)->ActiveFlag) {
     39      cerr << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl;
     40      atom *Walker = (*MolWalker)->start;
     41      while (Walker->next != (*MolWalker)->end) {
     42        Walker = Walker->next;
     43        *out << Verbose(3) << "Current atom is " << *Walker << "." << endl;
     44        if ((type1 == NULL) || (Walker->type == type1)) {
     45          for (MoleculeList::const_iterator MolOtherWalker = MolWalker; MolOtherWalker != molecules->ListOfMolecules.end(); MolOtherWalker++)
     46            if ((*MolOtherWalker)->ActiveFlag) {
     47              *out << Verbose(2) << "Current other molecule is " << *MolOtherWalker << "." << endl;
     48              atom *OtherWalker = (*MolOtherWalker)->start;
     49              while (OtherWalker->next != (*MolOtherWalker)->end) { // only go up to Walker
     50                OtherWalker = OtherWalker->next;
     51                *out << Verbose(3) << "Current otheratom is " << *OtherWalker << "." << endl;
     52                if (Walker->nr < OtherWalker->nr)
     53                  if ((type2 == NULL) || (OtherWalker->type == type2)) {
     54                    distance = Walker->node->Distance(OtherWalker->node);
     55                    //*out << Verbose(1) <<"Inserting " << *Walker << " and " << *OtherWalker << endl;
     56                    outmap->insert ( pair<double, pair <atom *, atom*> > (distance, pair<atom *, atom*> (Walker, OtherWalker) ) );
     57                  }
     58              }
    4859          }
     60        }
    4961      }
    5062    }
    51   }
    5263
    5364  return outmap;
    … …  
    5667/** Calculates the distance (pair) correlation between a given element and a point.
    5768 * \param *out output stream for debugging
    58  * \param *mol molecule with atoms
     69 * \param *molecules list of molecules structure
    5970 * \param *type element or NULL (if any element)
    6071 * \param *point vector to the correlation point
    6172 * \return Map of dobules with values as pairs of atom and the vector
    6273 */
    63 CorrelationToPointMap *CorrelationToPoint( const ofstream *out, const molecule * const mol, const element * const type, const Vector *point )
     74CorrelationToPointMap *CorrelationToPoint(  ofstream * const out, MoleculeListClass * const &molecules, const element * const type, const Vector *point )
    6475{
    6576  CorrelationToPointMap *outmap = NULL;
    6677  double distance = 0.;
    6778
    68   if ((mol == NULL)) {
    69     cout << "No molecule given." << endl;
     79  if (molecules->ListOfMolecules.empty()) {
     80    *out << Verbose(1) <<"No molecule given." << endl;
    7081    return outmap;
    7182  }
    7283  outmap = new CorrelationToPointMap;
    73   atom *Walker = mol->start;
    74   while (Walker->next != mol->end) {
    75     Walker = Walker->next;
    76     if ((type == NULL) || (Walker->type == type)) {
    77       distance = Walker->node->Distance(point);
    78       outmap->insert ( pair<double, pair<atom *, const Vector*> >(distance, pair<atom *, const Vector*> (Walker, point) ) );
     84  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
     85    if ((*MolWalker)->ActiveFlag) {
     86      *out << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl;
     87      atom *Walker = (*MolWalker)->start;
     88      while (Walker->next != (*MolWalker)->end) {
     89        Walker = Walker->next;
     90        *out << Verbose(3) << "Current atom is " << *Walker << "." << endl;
     91        if ((type == NULL) || (Walker->type == type)) {
     92          distance = Walker->node->Distance(point);
     93          *out << Verbose(4) << "Current distance is " << distance << "." << endl;
     94          outmap->insert ( pair<double, pair<atom *, const Vector*> >(distance, pair<atom *, const Vector*> (Walker, point) ) );
     95        }
     96      }
    7997    }
    80   }
    8198
    8299  return outmap;
    … …  
    85102/** Calculates the distance (pair) correlation between a given element and a surface.
    86103 * \param *out output stream for debugging
    87  * \param *mol molecule with atoms
     104 * \param *molecules list of molecules structure
    88105 * \param *type element or NULL (if any element)
    89106 * \param *Surface pointer to Tesselation class surface
    … …  
    91108 * \return Map of doubles with values as pairs of atom and the BoundaryTriangleSet that's closest
    92109 */
    93 CorrelationToSurfaceMap *CorrelationToSurface( ofstream *out, const molecule * const mol, const element * const type, const Tesselation * const Surface, const LinkedCell *LC )
    94 {
    95 
     110CorrelationToSurfaceMap *CorrelationToSurface( ofstream * const out, MoleculeListClass * const &molecules, const element * const type, const Tesselation * const Surface, const LinkedCell *LC )
     111{
    96112  CorrelationToSurfaceMap *outmap = NULL;
    97113  double distance = 0.;
    … …  
    99115  Vector centroid;
    100116
    101   if ((Surface == NULL) || (LC == NULL) || (mol == NULL)) {
    102     cout << "No Tesselation, no LinkedCell or no molecule given." << endl;
     117  if ((Surface == NULL) || (LC == NULL) || (molecules->ListOfMolecules.empty())) {
     118    *out << Verbose(1) <<"No Tesselation, no LinkedCell or no molecule given." << endl;
    103119    return outmap;
    104120  }
    105121  outmap = new CorrelationToSurfaceMap;
    106   atom *Walker = mol->start;
    107   while (Walker->next != mol->end) {
    108     Walker = Walker->next;
    109     if ((type == NULL) || (Walker->type == type)) {
    110       triangle = Surface->FindClosestTriangleToPoint(out, Walker->node, LC );
    111       if (triangle != NULL) {
    112         distance = DistanceToTrianglePlane(out, Walker->node, triangle);
    113         outmap->insert ( pair<double, pair<atom *, BoundaryTriangleSet*> >(distance, pair<atom *, BoundaryTriangleSet*> (Walker, triangle) ) );
     122  for (MoleculeList::const_iterator MolWalker = molecules->ListOfMolecules.begin(); MolWalker != molecules->ListOfMolecules.end(); MolWalker++)
     123    if ((*MolWalker)->ActiveFlag) {
     124      *out << Verbose(2) << "Current molecule is " << *MolWalker << "." << endl;
     125      atom *Walker = (*MolWalker)->start;
     126      while (Walker->next != (*MolWalker)->end) {
     127        Walker = Walker->next;
     128        *out << Verbose(3) << "Current atom is " << *Walker << "." << endl;
     129        if ((type == NULL) || (Walker->type == type)) {
     130          triangle = Surface->FindClosestTriangleToPoint(out, Walker->node, LC );
     131          if (triangle != NULL) {
     132            distance = DistanceToTrianglePlane(out, Walker->node, triangle);
     133            outmap->insert ( pair<double, pair<atom *, BoundaryTriangleSet*> >(distance, pair<atom *, BoundaryTriangleSet*> (Walker, triangle) ) );
     134          }
     135        }
    114136      }
    115137    }
    116   }
    117138
    118139  return outmap;
    … …  
    135156 * \param *map map to write
    136157 */
    137 void OutputCorrelation( ofstream *file, const BinPairMap * const map )
     158void OutputCorrelation( ofstream * const file, const BinPairMap * const map )
    138159{
    139160  *file << "# BinStart\tCount" << endl;
    … …  
    147168 * \param *map map to write
    148169 */
    149 void OutputPairCorrelation( ofstream *file, const PairCorrelationMap * const map )
     170void OutputPairCorrelation( ofstream * const file, const PairCorrelationMap * const map )
    150171{
    151172  *file << "# BinStart\tAtom1\tAtom2" << endl;
    … …  
    159180 * \param *map map to write
    160181 */
    161 void OutputCorrelationToPoint( ofstream *file, const CorrelationToPointMap * const map )
     182void OutputCorrelationToPoint( ofstream * const file, const CorrelationToPointMap * const map )
    162183{
    163184  *file << "# BinStart\tAtom::x[i]-point.x[i]" << endl;
    … …  
    174195 * \param *map map to write
    175196 */
    176 void OutputCorrelationToSurface( ofstream *file, const CorrelationToSurfaceMap * const map )
     197void OutputCorrelationToSurface( ofstream * const file, const CorrelationToSurfaceMap * const map )
    177198{
    178199  *file << "# BinStart\tTriangle" << endl;

  • src/analysis_correlation.hpp

    reecd33 ra5551b  
    3232class element;
    3333class LinkedCell;
    34 class molecule;
     34class MoleculeListClass;
    3535class Tesselation;
    3636class Vector;
    … …  
    4545/********************************************** declarations *******************************/
    4646
    47 PairCorrelationMap *PairCorrelation( const ofstream *out, const molecule * const mol, const element * const type1, const element * const  type2 );
    48 CorrelationToPointMap *CorrelationToPoint( const ofstream *out, const molecule * const mol, const element * const type, const Vector *point );
    49 CorrelationToSurfaceMap *CorrelationToSurface( ofstream *out, const molecule * const mol, const element * const type, const Tesselation * const Surface, const LinkedCell *LC );
     47PairCorrelationMap *PairCorrelation( ofstream * const out, MoleculeListClass * const &molecules, const element * const type1, const element * const  type2 );
     48CorrelationToPointMap *CorrelationToPoint( ofstream * const out, MoleculeListClass * const &molecules, const element * const type, const Vector *point );
     49CorrelationToSurfaceMap *CorrelationToSurface( ofstream * const out, MoleculeListClass * const &molecules, const element * const type, const Tesselation * const Surface, const LinkedCell *LC );
    5050double GetBin ( const double value, const double BinWidth, const double BinStart );
    51 void OutputCorrelation( ofstream *file, const BinPairMap * const map );
    52 void OutputPairCorrelation( ofstream *file, const BinPairMap * const map );
    53 void OutputCorrelationToPoint( ofstream *file, const BinPairMap * const map );
    54 void OutputCorrelationToSurface( ofstream *file, const BinPairMap * const map );
     51void OutputCorrelation( ofstream * const file, const BinPairMap * const map );
     52void OutputPairCorrelation( ofstream * const file, const BinPairMap * const map );
     53void OutputCorrelationToPoint( ofstream * const file, const BinPairMap * const map );
     54void OutputCorrelationToSurface( ofstream * const file, const BinPairMap * const map );
    5555
    5656

  • src/builder.cpp

    reecd33 ra5551b  
    16161616                const LinkedCell *LCList = NULL;
    16171617                // find biggest molecule
     1618                int counter  = 0;
    16181619                for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++) {
    16191620                  if ((Boundary == NULL) || (Boundary->AtomCount < (*BigFinder)->AtomCount)) {
    16201621                    Boundary = *BigFinder;
    16211622                  }
     1623                  counter++;
     1624                }
     1625                bool *Actives = Malloc<bool>(counter, "ParseCommandLineOptions() - case C -- *Actives");
     1626                counter = 0;
     1627                for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++) {
     1628                  Actives[counter] = (*BigFinder)->ActiveFlag;
     1629                  (*BigFinder)->ActiveFlag = (*BigFinder == Boundary) ? false : true;
    16221630                }
    16231631                LCList = new LinkedCell(Boundary, 2.*radius);
    16241632                element *elemental = periode->FindElement((const int) atoi(argv[argptr]));
    16251633                FindNonConvexBorder((ofstream *)&cout, Boundary, TesselStruct, LCList, radius, NULL);
    1626                 CorrelationToSurfaceMap *surfacemap = CorrelationToSurface( (ofstream *)&cout, mol, elemental, TesselStruct, LCList );
     1634                CorrelationToSurfaceMap *surfacemap = CorrelationToSurface( (ofstream *)&cout, molecules, elemental, TesselStruct, LCList );
    16271635                BinPairMap *binmap = BinData( (ofstream *)&cout, surfacemap, 0.5, 0., 0. );
    16281636                OutputCorrelation ( &binoutput, binmap );
    16291637                output.close();
    16301638                binoutput.close();
     1639                for (MoleculeList::iterator BigFinder = molecules->ListOfMolecules.begin(); BigFinder != molecules->ListOfMolecules.end(); BigFinder++)
     1640                  (*BigFinder)->ActiveFlag = Actives[counter];
     1641                Free(&Actives);
    16311642                delete(LCList);
    16321643                delete(TesselStruct);

  • src/unittests/AnalysisCorrelationToPointUnitTest.cpp

    reecd33 ra5551b  
    3333
    3434  // init private all pointers to zero
     35  TestList = NULL;
    3536  TestMolecule = NULL;
    3637  hydrogen = NULL;
    … …  
    7374  CPPUNIT_ASSERT_EQUAL( TestMolecule->AtomCount, 4 );
    7475
     76  TestList = new MoleculeListClass;
     77  TestMolecule->ActiveFlag = true;
     78  TestList->insert(TestMolecule);
     79
    7580  // init point
    7681  point = new Vector(1.,1.,1.);
    7782
    7883  // init maps
    79   pointmap = CorrelationToPoint( (ofstream *)&cout, (const molecule * const)TestMolecule, (const element * const)hydrogen, (const Vector *)point );
     84  pointmap = CorrelationToPoint( (ofstream *)&cout, (MoleculeListClass * const)TestList, (const element * const)hydrogen, (const Vector *)point );
    8085  binmap = NULL;
    8186
    … …  
    9196
    9297  // remove
    93   delete(TestMolecule);
     98  delete(TestList);
    9499  // note that all the atoms are cleaned by TestMolecule
    95100  delete(point);

  • src/unittests/AnalysisCorrelationToPointUnitTest.hpp

    reecd33 ra5551b  
    1212
    1313class element;
     14class LinkedCell;
    1415class molecule;
    15 class LinkedCell;
     16class MoleculeListClass;
    1617class periodentafel;
    1718class Tesselation;
    … …  
    3738private:
    3839
     40      MoleculeListClass *TestList;
    3941      molecule *TestMolecule;
    4042      element *hydrogen;

  • src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp

    reecd33 ra5551b  
    3333
    3434  // init private all pointers to zero
     35  TestList = NULL;
    3536  TestMolecule = NULL;
    3637  hydrogen = NULL;
    … …  
    4041  Surface = NULL;
    4142  LC = NULL;
    42 
    4343
    4444  // construct element
    … …  
    7979  CPPUNIT_ASSERT_EQUAL( TestMolecule->AtomCount, 4 );
    8080
     81  TestList = new MoleculeListClass;
     82  TestMolecule->ActiveFlag = true;
     83  TestList->insert(TestMolecule);
     84
    8185  // init tesselation and linked cell
    8286  Surface = new Tesselation;
    … …  
    121125
    122126  // remove
    123   delete(TestMolecule);
     127  delete(TestList);
    124128  delete(Surface);
    125129  // note that all the atoms are cleaned by TestMolecule
    … …  
    133137{
    134138  // do the pair correlation
    135   surfacemap = CorrelationToSurface( (ofstream *)&cout, TestMolecule, hydrogen, Surface, LC );
     139  surfacemap = CorrelationToSurface( (ofstream *)&cout, TestList, hydrogen, Surface, LC );
    136140  CPPUNIT_ASSERT( surfacemap != NULL );
    137141  CPPUNIT_ASSERT_EQUAL( (size_t)4, surfacemap->size() );
    … …  
    141145{
    142146  BinPairMap::iterator tester;
    143   surfacemap = CorrelationToSurface( (ofstream *)&cout, TestMolecule, hydrogen, Surface, LC );
     147  surfacemap = CorrelationToSurface( (ofstream *)&cout, TestList, hydrogen, Surface, LC );
    144148  // put pair correlation into bins and check with no range
    145149  binmap = BinData( (ofstream *)&cout, surfacemap, 0.5, 0., 0. );
    … …  
    155159{
    156160  BinPairMap::iterator tester;
    157   surfacemap = CorrelationToSurface( (ofstream *)&cout, TestMolecule, hydrogen, Surface, LC );
     161  surfacemap = CorrelationToSurface( (ofstream *)&cout, TestList, hydrogen, Surface, LC );
    158162  // ... and check with [0., 2.] range
    159163  binmap = BinData( (ofstream *)&cout, surfacemap, 0.5, 0., 2. );
    … …  
    172176{
    173177  BinPairMap::iterator tester;
    174   surfacemap = CorrelationToSurface( (ofstream *)&cout, TestMolecule, carbon, Surface, LC );
     178  surfacemap = CorrelationToSurface( (ofstream *)&cout, TestList, carbon, Surface, LC );
    175179  // put pair correlation into bins and check with no range
    176180  binmap = BinData( (ofstream *)&cout, surfacemap, 0.5, 0., 0. );
    … …  
    190194{
    191195  BinPairMap::iterator tester;
    192   surfacemap = CorrelationToSurface( (ofstream *)&cout, TestMolecule, carbon, Surface, LC );
     196  surfacemap = CorrelationToSurface( (ofstream *)&cout, TestList, carbon, Surface, LC );
    193197  // ... and check with [0., 2.] range
    194198  binmap = BinData( (ofstream *)&cout, surfacemap, 0.5, -2., 4. );

  • src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp

    reecd33 ra5551b  
    1212
    1313class element;
     14class LinkedCell;
    1415class molecule;
    15 class LinkedCell;
     16class MoleculeListClass;
    1617class periodentafel;
    1718class Tesselation;
    … …  
    4041private:
    4142
     43      MoleculeListClass *TestList;
    4244      molecule *TestMolecule;
    4345      element *hydrogen;

  • src/unittests/AnalysisPairCorrelationUnitTest.cpp

    reecd33 ra5551b  
    3434
    3535  // init private all pointers to zero
     36  TestList = NULL;
    3637  TestMolecule = NULL;
    3738  hydrogen = NULL;
    … …  
    7273  CPPUNIT_ASSERT_EQUAL( TestMolecule->AtomCount, 4 );
    7374
     75  TestList = new MoleculeListClass;
     76  TestMolecule->ActiveFlag = true;
     77  TestList->insert(TestMolecule);
     78
    7479  // init maps
    75   correlationmap = PairCorrelation( (ofstream *)&cout, TestMolecule, hydrogen, hydrogen );
     80  correlationmap = PairCorrelation( (ofstream *)&cout, TestList, hydrogen, hydrogen );
    7681  binmap = NULL;
    7782
    … …  
    8792
    8893  // remove
    89   delete(TestMolecule);
     94  delete(TestList);
    9095  // note that all the atoms are cleaned by TestMolecule
    9196  delete(tafel);

  • src/unittests/AnalysisPairCorrelationUnitTest.hpp

    reecd33 ra5551b  
    1212
    1313class element;
     14class LinkedCell;
    1415class molecule;
    15 class LinkedCell;
     16class MoleculeListClass;
    1617class periodentafel;
    1718class Tesselation;
    … …  
    3738private:
    3839
     40      MoleculeListClass *TestList;
    3941      molecule *TestMolecule;
    4042      element *hydrogen;
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