Changes in / [60f50a:9757d9]


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Files:
46 added
38 deleted
52 edited

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  • Makefile.am

    r60f50a r9757d9  
    11ACLOCAL_AMFLAGS = -I m4
    2 SUBDIRS = src src/unittests doc tests
     2SUBDIRS = src src/Actions src/unittests doc tests
    33
    44EXTRA_DIST = autogen.sh

  • configure.ac

    r60f50a r9757d9  
    9494# test suite
    9595AC_CONFIG_TESTDIR(tests)
    96 AC_CONFIG_FILES([tests/atlocal tests/Makefile])
    97 AC_CONFIG_FILES([tests/Tesselations/Makefile tests/Tesselations/defs])
     96AC_CONFIG_FILES([
     97        tests/atlocal
     98        tests/Makefile])
     99AC_CONFIG_FILES([
     100        tests/Tesselations/Makefile
     101        tests/Tesselations/defs])
    98102AC_CONFIG_FILES([tests/molecuilder], [chmod +x tests/molecuilder])
    99 AC_CONFIG_FILES([doc/molecuilder.xml])
    100 AC_CONFIG_FILES([Makefile src/Makefile doc/Makefile src/unittests/Makefile])
     103AC_CONFIG_FILES([
     104        doc/molecuilder.xml])
     105AC_CONFIG_FILES([
     106        Makefile
     107        doc/Makefile
     108        src/Makefile
     109        src/Actions/Makefile
     110        src/UIElements/Makefile
     111        src/unittests/Makefile])
    101112AC_OUTPUT

  • src/Actions/MapOfActions.cpp

    r60f50a r9757d9  
    123123  ShortFormMap["suspend-in-water"] = "U";
    124124  ShortFormMap["translate-mol"] = "t";
    125   ShortFormMap["verbose"] = "V";
     125  ShortFormMap["verbose"] = "v";
    126126  ShortFormMap["verlet-integrate"] = "P";
    127   ShortFormMap["version"] = "v";
     127  ShortFormMap["version"] = "V";
    128128
    129129  // value types for the actions

  • src/Helpers/MemDebug.cpp

    r60f50a r9757d9  
    153153  // build the entry in front of the space
    154154  Memory::entry_t *entry = (Memory::entry_t*) res;
     155  memset(res,0,entrySpace);
    155156  entry->info.nbytes = nbytes;
    156157  entry->info.isUsed = true;

  • src/Makefile.am

    r60f50a r9757d9  
    11# PLEASE adhere to the alphabetical ordering in this Makefile!
    22# Also indentation by a single tab
     3
     4SUBDIRS = Actions UIElements
    35
    46# this includes source files that need to be present at multiple points
    … …  
    4951  analysis_correlation.hpp
    5052
    51 ACTIONSSOURCE = Actions/Action.cpp \
    52   ${ANALYSISACTIONSOURCE} \
    53   ${ATOMACTIONSOURCE} \
    54   ${CMDACTIONSOURCE} \
    55   ${FRAGMENTATIONACTIONSOURCE} \
    56   ${MOLECULEACTIONSOURCE} \
    57   ${PARSERACTIONSOURCE} \
    58   ${TESSELATIONACTIONSOURCE} \
    59   ${WORLDACTIONSOURCE} \
     53ACTIONSSOURCE = \
     54  Actions/Action.cpp \
    6055  Actions/ActionHistory.cpp \
    6156  Actions/ActionRegistry.cpp \
    … …  
    6459  Actions/MakroAction.cpp \
    6560  Actions/ManipulateAtomsProcess.cpp \
    66   Actions/MapOfActions.cpp \
    6761  Actions/MethodAction.cpp \
    6862  Actions/Process.cpp
    6963
    70 ACTIONSHEADER = Actions/Action.hpp \
     64ACTIONSHEADER = \
    7165  ${ANALYSISACTIONHEADER} \
    7266  ${ATOMACTIONHEADER} \
    … …  
    7771  ${TESSELATIONACTIONHEADER} \
    7872  ${WORLDACTIONHEADER} \
     73  Actions/Action.hpp \
    7974  Actions/ActionHistory.hpp \
    8075  Actions/ActionRegistry.hpp \
    … …  
    8984  Actions/Process.hpp
    9085 
    91 ANALYSISACTIONSOURCE = \
    92   Actions/AnalysisAction/MolecularVolumeAction.cpp \
    93   Actions/AnalysisAction/PairCorrelationAction.cpp \
    94   Actions/AnalysisAction/PairCorrelationToPointAction.cpp \
    95   Actions/AnalysisAction/PairCorrelationToSurfaceAction.cpp \
    96   Actions/AnalysisAction/PrincipalAxisSystemAction.cpp
    97 ANALYSISACTIONHEADER = \
    98   Actions/AnalysisAction/MolecularVolumeAction.hpp \
    99   Actions/AnalysisAction/PairCorrelationAction.hpp \
    100   Actions/AnalysisAction/PairCorrelationToPointAction.hpp \
    101   Actions/AnalysisAction/PairCorrelationToSurfaceAction.hpp \
    102   Actions/AnalysisAction/PrincipalAxisSystemAction.hpp
    103 
    104 ATOMACTIONSOURCE = \
    105   Actions/AtomAction/AddAction.cpp \
    106   Actions/AtomAction/ChangeElementAction.cpp \
    107   Actions/AtomAction/RemoveAction.cpp
    108 ATOMACTIONHEADER = \
    109   Actions/AtomAction/AddAction.hpp \
    110   Actions/AtomAction/ChangeElementAction.hpp \
    111   Actions/AtomAction/RemoveAction.cpp
    112 
    113 CMDACTIONSOURCE = \
    114   Actions/CmdAction/BondLengthTableAction.cpp \
    115   Actions/CmdAction/ElementDbAction.cpp \
    116   Actions/CmdAction/FastParsingAction.cpp \
    117   Actions/CmdAction/HelpAction.cpp \
    118   Actions/CmdAction/VerboseAction.cpp \
    119   Actions/CmdAction/VersionAction.cpp
    120 CMDACTIONHEADER = \
    121   Actions/CmdAction/BondLengthTableAction.hpp \
    122   Actions/CmdAction/ElementDbAction.hpp \
    123   Actions/CmdAction/FastParsingAction.hpp \
    124   Actions/CmdAction/HelpAction.hpp \
    125   Actions/CmdAction/VerboseAction.hpp \
    126   Actions/CmdAction/VersionAction.hpp
    127 
    128 FRAGMENTATIONACTIONSOURCE = \
    129   Actions/FragmentationAction/DepthFirstSearchAction.cpp \
    130   Actions/FragmentationAction/FragmentationAction.cpp \
    131   Actions/FragmentationAction/SubgraphDissectionAction.cpp               
    132 FRAGMENTATIONACTIONHEADER = \
    133   Actions/FragmentationAction/DepthFirstSearchAction.hpp \
    134   Actions/FragmentationAction/FragmentationAction.hpp \
    135   Actions/FragmentationAction/SubgraphDissectionAction.hpp
    136 
    137 MOLECULEACTIONSOURCE = \
    138   Actions/MoleculeAction/BondFileAction.cpp \
    139   Actions/MoleculeAction/ChangeNameAction.cpp \
    140   Actions/MoleculeAction/FillWithMoleculeAction.cpp \
    141   Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.cpp \
    142   Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.cpp \
    143   Actions/MoleculeAction/SaveAdjacencyAction.cpp \
    144   Actions/MoleculeAction/SaveBondsAction.cpp \
    145   Actions/MoleculeAction/SaveTemperatureAction.cpp \
    146   Actions/MoleculeAction/SuspendInWaterAction.cpp \
    147   Actions/MoleculeAction/TranslateAction.cpp \
    148   Actions/MoleculeAction/VerletIntegrationAction.cpp
    149 MOLECULEACTIONHEADER = \
    150   Actions/MoleculeAction/BondFileAction.hpp \
    151   Actions/MoleculeAction/ChangeNameAction.hpp \
    152   Actions/MoleculeAction/FillWithMoleculeAction.hpp \
    153   Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.hpp \
    154   Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.hpp \
    155   Actions/MoleculeAction/SaveAdjacencyAction.hpp \
    156   Actions/MoleculeAction/SaveBondsAction.hpp \
    157   Actions/MoleculeAction/SaveTemperatureAction.hpp \
    158   Actions/MoleculeAction/SuspendInWaterAction.hpp \
    159   Actions/MoleculeAction/TranslateAction.hpp \
    160   Actions/MoleculeAction/VerletIntegrationAction.hpp
    161                  
    162 PARSERACTIONSOURCE = \
    163   Actions/ParserAction/LoadXyzAction.cpp \
    164   Actions/ParserAction/SaveXyzAction.cpp       
    165 PARSERACTIONHEADER = \
    166   Actions/ParserAction/LoadXyzAction.hpp \
    167   Actions/ParserAction/SaveXyzAction.hpp
    168 
    169 TESSELATIONACTIONSOURCE = \
    170   Actions/TesselationAction/ConvexEnvelopeAction.cpp \
    171   Actions/TesselationAction/NonConvexEnvelopeAction.cpp               
    172 TESSELATIONACTIONHEADER = \
    173   Actions/TesselationAction/ConvexEnvelopeAction.hpp \
    174   Actions/TesselationAction/NonConvexEnvelopeAction.hpp
    175 
    176 WORLDACTIONSOURCE = \
    177   Actions/WorldAction/AddEmptyBoundaryAction.cpp \
    178   Actions/WorldAction/BoundInBoxAction.cpp \
    179   Actions/WorldAction/CenterInBoxAction.cpp \
    180   Actions/WorldAction/CenterOnEdgeAction.cpp \
    181   Actions/WorldAction/ChangeBoxAction.cpp \
    182   Actions/WorldAction/RemoveSphereOfAtomsAction.cpp \
    183   Actions/WorldAction/RepeatBoxAction.cpp \
    184   Actions/WorldAction/ScaleBoxAction.cpp \
    185   Actions/WorldAction/SetDefaultNameAction.cpp \
    186   Actions/WorldAction/SetGaussianBasisAction.cpp               
    187 WORLDACTIONHEADER = \
    188   Actions/WorldAction/AddEmptyBoundaryAction.hpp \
    189   Actions/WorldAction/BoundInBoxAction.hpp \
    190   Actions/WorldAction/CenterInBoxAction.hpp \
    191   Actions/WorldAction/CenterOnEdgeAction.hpp \
    192   Actions/WorldAction/ChangeBoxAction.hpp \
    193   Actions/WorldAction/RemoveSphereOfAtomsAction.hpp \
    194   Actions/WorldAction/RepeatBoxAction.hpp \
    195   Actions/WorldAction/ScaleBoxAction.hpp \
    196   Actions/WorldAction/SetDefaultNameAction.hpp \
    197   Actions/WorldAction/SetGaussianBasisAction.hpp
    198 
    199 
    20086
    20187PARSERSOURCE = \
    … …  
    216102  Patterns/Observer.hpp \
    217103  Patterns/Singleton.hpp
    218 
    219 # Below is all for the User Interface
    220 
    221 VIEWSOURCE = \
    222   Views/View.cpp \
    223   Views/StringView.cpp \
    224   Views/MethodStringView.cpp \
    225   Views/StreamStringView.cpp
    226 VIEWHEADER = \
    227   Views/View.hpp \
    228   Views/StringView.hpp \
    229   Views/MethodStringView.hpp \
    230   Views/StreamStringView.hpp
    231 
    232 MENUSOURCE = \
    233   Menu/Menu.cpp \
    234   Menu/TextMenu.cpp \
    235   Menu/MenuItem.cpp \
    236   Menu/SubMenuItem.cpp \
    237   Menu/ActionMenuItem.cpp \
    238   Menu/SeperatorItem.cpp \
    239   Menu/DisplayMenuItem.cpp
    240  
    241 MENUHEADER = \
    242   Menu/Menu.hpp \
    243   Menu/TextMenu.hpp \
    244   Menu/MenuItem.hpp \
    245   Menu/SubMenuItem.hpp \
    246   Menu/ActionMenuItem.hpp \
    247   Menu/SeperatorItem.hpp \
    248   Menu/DisplayMenuItem.hpp
    249 
    250 UISOURCE = \
    251   ${ACTIONSSOURCE} \
    252   ${COMMANDLINEUISOURCE} \
    253   ${MENUSOURCE} \
    254   ${TEXTUISOURCE} \
    255   ${VIEWSOURCE} \
    256   UIElements/Dialog.cpp \
    257   UIElements/MainWindow.cpp \
    258   UIElements/UIFactory.cpp
    259  
    260 UIHEADER = \
    261   ${ACTIONSHEADER} \
    262   ${COMMANDLINEUIHEADER} \
    263   ${MENUHEADER} \
    264   ${TEXTUIHEADER} \
    265   ${VIEWHEADER} \
    266   UIElements/Dialog.hpp \
    267   UIElements/MainWindow.hpp \
    268   UIElements/UIFactory.hpp
    269 
    270 TEXTUISOURCE = \
    271   UIElements/TextDialog.cpp \
    272   UIElements/TextStatusIndicator.cpp \
    273   UIElements/TextUIFactory.cpp \
    274   UIElements/TextWindow.cpp
    275 TEXTUIHEADER = \
    276   UIElements/TextDialog.hpp \
    277   UIElements/TextStatusIndicator.hpp \
    278   UIElements/TextUIFactory.hpp \
    279   UIElements/TextWindow.hpp
    280 
    281 COMMANDLINEUISOURCE = \
    282   UIElements/CommandLineDialog.cpp \
    283   UIElements/CommandLineStatusIndicator.cpp \
    284   UIElements/CommandLineUIFactory.cpp \
    285   UIElements/CommandLineWindow.cpp
    286 COMMANDLINEUIHEADER = \
    287   UIElements/CommandLineDialog.hpp \
    288   UIElements/CommandLineStatusIndicator.hpp \
    289   UIElements/CommandLineUIFactory.hpp \
    290   UIElements/CommandLineWindow.hpp
    291104
    292105# all these files are only used for legacy reasons while the transition is in progress
    … …  
    321134SOURCE = \
    322135  ${ANALYSISSOURCE} \
     136  ${ACTIONSSOURCE} \
    323137  ${ATOMSOURCE} \
    324138  ${PATTERNSOURCE} \
    325139  ${PARSERSOURCE} \
    326   ${UISOURCE} \
    327140  ${DESCRIPTORSOURCE} \
    328141  ${HELPERSOURCE} \
    … …  
    335148  config.cpp \
    336149  element.cpp \
     150  elements_db.cpp \
    337151  ellipsoid.cpp \
    338152  errorlogger.cpp \
    … …  
    366180HEADER = \
    367181  ${ANALYSISHEADER} \
     182  ${ACTIONSHEADER} \
    368183  ${ATOMHEADER} \
    369184  ${PARSERHEADER} \
    370185  ${PATTERNHEADER} \
    371   ${UIHEADER} \
    372186  ${DESCRIPTORHEADER} \
    373187  ${EXCEPTIONHEADER} \
    … …  
    380194  defs.hpp \
    381195  element.hpp \
     196  elements_db.hpp \
    382197  ellipsoid.hpp \
    383198  errorlogger.hpp \
    … …  
    407222
    408223BOOST_LIB = $(BOOST_LDFLAGS) $(BOOST_MPL_LIB)
    409 INCLUDES = -I$(top_srcdir)/src/unittests
     224INCLUDES = -I$(top_srcdir)/src/unittests -I$(top_srcdir)/src/Actions -I$(top_srcdir)/src/UIElements
    410225
    411226noinst_LIBRARIES = libmolecuilder.a libgslwrapper.a
    … …  
    414229libmolecuilder_a_SOURCES = ${SOURCE} ${HEADER}
    415230libgslwrapper_a_SOURCES = ${LINALGSOURCE} ${LINALGHEADER}
    416 molecuilder_DATA = elements.db valence.db orbitals.db Hbonddistance.db Hbondangle.db
    417231molecuilder_LDFLAGS = $(BOOST_LDFLAGS)
    418232molecuilder_SOURCES = builder.cpp
    419 molecuilder_LDADD = libmolecuilder.a libgslwrapper.a $(BOOST_LIB) ${BOOST_THREAD_LIB} ${BOOST_PROGRAM_OPTIONS_LIB}
     233molecuilder_LDADD =  UIElements/libMolecuilderUI.a Actions/libMolecuilderActions.a libmolecuilder.a libgslwrapper.a $(BOOST_LIB) ${BOOST_THREAD_LIB} ${BOOST_PROGRAM_OPTIONS_LIB}
    420234joiner_SOURCES = joiner.cpp datacreator.cpp parser.cpp datacreator.hpp helpers.hpp parser.hpp periodentafel.hpp
    421235joiner_LDADD = libmolecuilder.a $(BOOST_LIB) ${BOOST_THREAD_LIB}

  • src/UIElements/Dialog.cpp

    r60f50a r9757d9  
    88#include <cassert>
    99
    10 #include "UIElements/Dialog.hpp"
     10#include "Dialog.hpp"
    1111
    1212#include "atom.hpp"

  • src/UIElements/MainWindow.cpp

    r60f50a r9757d9  
    66 */
    77
    8 #include "UIElements/MainWindow.hpp"
     8#include "MainWindow.hpp"
    99
    1010MainWindow::MainWindow()

  • src/UIElements/UIFactory.cpp

    r60f50a r9757d9  
    99#include <cassert>
    1010#include "Patterns/Singleton_impl.hpp"
    11 #include "UIElements/UIFactory.hpp"
     11#include "UIFactory.hpp"
    1212
    1313// all factories that can be used:
    14 #include "UIElements/TextUIFactory.hpp"
    15 #include "UIElements/CommandLineUIFactory.hpp"
     14#include "TextUI/TextUIFactory.hpp"
     15#include "CommandLineUI/CommandLineUIFactory.hpp"
    1616
    1717UIFactory::UIFactory()

  • src/analysis_bonds.cpp

    r60f50a r9757d9  
    5151 * \param &Max maximum distance on return, 0 if no bond between the two elements
    5252 */
    53 void MinMeanMaxBondDistanceBetweenElements(const molecule *mol, element *type1, element *type2, double &Min, double &Mean, double &Max)
     53void MinMeanMaxBondDistanceBetweenElements(const molecule *mol, const element *type1, const element *type2, double &Min, double &Mean, double &Max)
    5454{
    5555  Min = 2e+6;
    … …  
    124124 * \param *InterfaceElement or NULL
    125125 */
    126 int CountHydrogenBridgeBonds(MoleculeListClass *molecules, element * InterfaceElement = NULL)
     126int CountHydrogenBridgeBonds(MoleculeListClass *molecules, const element * InterfaceElement = NULL)
    127127{
    128128  atom *Walker = NULL;
    … …  
    181181                    // check angle
    182182                    if (CheckHydrogenBridgeBondAngle(Walker, OtherAtom, Runner)) {
    183                       DoLog(1) && (Log() << Verbose(1) << Walker->Name << ", " << OtherAtom->Name << " and " << Runner->Name << " has a hydrogen bridge bond with distance " << sqrt(distance) << " and angle " << CalculateAngle(&OtherAtom->x, &Walker->x, &Runner->x)*(180./M_PI) << "." << endl);
     183                      DoLog(1) && (Log() << Verbose(1) << Walker->getName() << ", " << OtherAtom->getName() << " and " << Runner->getName() << " has a hydrogen bridge bond with distance " << sqrt(distance) << " and angle " << CalculateAngle(&OtherAtom->x, &Walker->x, &Runner->x)*(180./M_PI) << "." << endl);
    184184                      count++;
    185185                      break;

  • src/analysis_bonds.hpp

    r60f50a r9757d9  
    3131
    3232void GetMaxMinMeanBondCount(const molecule * const mol, double &Min, double &Mean, double &Max);
    33 void MinMeanMaxBondDistanceBetweenElements(const molecule *mol, element *type1, element *type2, double &Min, double &Mean, double &Max);
     33void MinMeanMaxBondDistanceBetweenElements(const molecule *mol, const element *type1, const element *type2, double &Min, double &Mean, double &Max);
    3434
    35 int CountHydrogenBridgeBonds(MoleculeListClass * const molecules, element * InterfaceElement);
     35int CountHydrogenBridgeBonds(MoleculeListClass * const molecules, const element * InterfaceElement);
    3636int CountBondsOfTwo(MoleculeListClass * const molecules, const element * const first, const element * const second);
    3737int CountBondsOfThree(MoleculeListClass * const molecules, const element * const first, const element * const second, const element * const third);

  • src/atom.cpp

    r60f50a r9757d9  
    4040
    4141atom *atom::clone(){
    42   atom *res = new atom();
     42  atom *res = new atom(this);
    4343  res->previous=0;
    4444  res->next=0;

  • src/atom_bondedparticle.cpp

    r60f50a r9757d9  
    4444void BondedParticle::OutputBondOfAtom() const
    4545{
    46   DoLog(4) && (Log() << Verbose(4) << "Atom " << Name << "/" << nr << " with " << ListOfBonds.size() << " bonds: " << endl);
     46  DoLog(4) && (Log() << Verbose(4) << "Atom " << getName() << "/" << nr << " with " << ListOfBonds.size() << " bonds: " << endl);
    4747  int TotalDegree = 0;
    4848  for (BondList::const_iterator Runner = ListOfBonds.begin(); Runner != ListOfBonds.end(); ++Runner) {

  • src/atom_graphnode.cpp

    r60f50a r9757d9  
    2727void GraphNode::OutputGraphInfo() const
    2828{
    29   DoLog(2) && (Log() << Verbose(2) << "Atom " << Name << " is " << ((SeparationVertex) ? "a" : "not a") << " separation vertex, components are ");
     29  DoLog(2) && (Log() << Verbose(2) << "Atom " << getName() << " is " << ((SeparationVertex) ? "a" : "not a") << " separation vertex, components are ");
    3030  OutputComponentNumber();
    3131  DoLog(3) && (Log() << Verbose(3) << " with Lowpoint " << LowpointNr << " and Graph Nr. " << GraphNr << "." << endl);

  • src/atom_particleinfo.cpp

    r60f50a r9757d9  
    1111/** Constructor of ParticleInfo.
    1212 */
    13 ParticleInfo::ParticleInfo() : nr(-1), Name(NULL) {};
     13ParticleInfo::ParticleInfo() : nr(-1), name("Unknown") {
     14};
    1415
    1516ParticleInfo::ParticleInfo(ParticleInfo *pointer) :
    1617    nr(pointer->nr),
    17     Name(pointer->Name)
    18     {
    19       if (Name == NULL)
    20         Name = " ";
    21     }
     18    name(pointer->name)
     19    {}
    2220
    2321
    … …  
    2523 */
    2624ParticleInfo::~ParticleInfo()
    27 {
    28   Free(&Name);
    29 };
     25{};
     26
     27const string& ParticleInfo::getName() const{
     28  return name;
     29}
     30
     31void ParticleInfo::setName(const string& _name){
     32  name = _name;
     33}
    3034
    3135ostream & operator << (ostream &ost, const ParticleInfo &a)
    3236{
    33   if (a.Name == NULL)
    34     ost << "[NULL]";
    35   else
    36     ost << "[" << a.Name << "|" << &a << "]";
     37  ost << "[" << a.getName() << "|" << &a << "]";
    3738  return ost;
    3839};
    … …  
    4041ostream & ParticleInfo::operator << (ostream &ost) const
    4142{
    42   if (Name == NULL)
    43     ost << "[NULL]";
    44   else
    45     ost << "[" << Name << "|" << this << "]";
     43  ost << "[" << name << "|" << this << "]";
    4644  return ost;
    4745};

  • src/atom_particleinfo.hpp

    r60f50a r9757d9  
    2828public:
    2929  int nr;       // index to easierly identify
    30   char *Name;   // some name to reference to on output
    3130
    3231  ParticleInfo();
    … …  
    3433  ~ParticleInfo();
    3534
     35  const std::string& getName() const;
     36  void setName(const std::string&);
     37
    3638  ostream & operator << (ostream &ost) const;
    3739
    3840private:
     41  std::string name;   // some name to reference to on output
    3942};
    4043

  • src/bond.cpp

    r60f50a r9757d9  
    5353ostream & operator << (ostream &ost, const bond &b)
    5454{
    55   ost << "[" << b.leftatom->Name << " <" << b.BondDegree << "(H" << b.HydrogenBond << ")>" << b.rightatom->Name << "]";
     55  ost << "[" << b.leftatom->getName() << " <" << b.BondDegree << "(H" << b.HydrogenBond << ")>" << b.rightatom->getName() << "]";
    5656  return ost;
    5757};

  • src/builder.cpp

    r60f50a r9757d9  
    5353
    5454#include <cstring>
     55#include <cstdlib>
    5556
    5657#include "analysis_bonds.hpp"
    … …  
    15291530            break;
    15301531          case 'v':
     1532            setVerbosity(atoi(argv[argptr]));
    15311533            ArgcList.insert(argptr-1);
    1532             return(1);
     1534            ArgcList.insert(argptr);
     1535            argptr++;
    15331536            break;
    15341537          case 'V':
    15351538            ArgcList.insert(argptr-1);
    1536             ArgcList.insert(argptr);
    1537             argptr++;
     1539            return(1);
    15381540            break;
    15391541          case 'B':
    … …  
    24882490  ActionRegistry::purgeInstance();
    24892491  ActionHistory::purgeInstance();
     2492  Memory::getState();
    24902493}
    24912494
    … …  
    25012504    bool ArgumentsCopied = false;
    25022505
     2506    // print version check whether arguments are present at all
    25032507    cout << ESPACKVersion << endl;
     2508    if (argc < 2) {
     2509      cout << "Obtain help with " << argv[0] << " -h." << endl;
     2510      cleanUp();
     2511      Memory::getState();
     2512      return(1);
     2513    }
     2514
    25042515
    25052516    setVerbosity(0);
    25062517    // need to init the history before any action is created
    25072518    ActionHistory::init();
     2519
     2520    // from this moment on, we need to be sure to deeinitialize in the correct order
     2521    // this is handled by the cleanup function
     2522    atexit(cleanUp);
    25082523
    25092524    // Parse command line options and if present create respective UI
    … …  
    25572572  }
    25582573
    2559   cleanUp();
    2560   Memory::getState();
    25612574  return (0);
    25622575}

  • src/config.cpp

    r60f50a r9757d9  
    16801680    Walker = Walker->next;
    16811681    *output << Walker->nr << "\t";
    1682     *output << Walker->Name << "\t";
     1682    *output << Walker->getName() << "\t";
    16831683    *output << mol->name << "\t";
    16841684    *output << 0 << "\t";
    … …  
    17561756        Walker = Walker->next;
    17571757        *output << AtomNo+1 << "\t";
    1758         *output << Walker->Name << "\t";
     1758        *output << Walker->getName() << "\t";
    17591759        *output << (*MolWalker)->name << "\t";
    17601760        *output << MolCounter+1 << "\t";

  • src/elements.db

    • Property mode changed from 100755 to 100644
    r60f50a r9757d9  
    22#Element        Name    Symbol  Period  Group   Block   Atomic  Number  AtomicWeight    Covalent        Radius  vdW     Radius
    33Hydrogen        H       1       1       s       1       1.008   0.23    1.09
    4 Helium  He      1       18      p       2       4.003   1.50    1.40
     4Helium  He      1       18      p       2       4.003   1.5     1.4
    55Lithium Li      2       1       s       3       6.941   0.68    1.82
    6 Beryllium       Be      2       2       s       4       9.012   0.35    2.00
    7 Boron   B       2       13      p       5       10.811  0.83    2.00
    8 Carbon  C       2       14      p       6       12.011  0.68    1.70
     6Beryllium       Be      2       2       s       4       9.012   0.35    2
     7Boron   B       2       13      p       5       10.811  0.83    2
     8Carbon  C       2       14      p       6       12.011  0.68    1.7
    99Nitrogen        N       2       15      p       7       14.007  0.68    1.55
    1010Oxygen  O       2       16      p       8       15.999  0.68    1.52
    1111Fluorine        F       2       17      p       9       18.998  0.64    1.47
    12 Neon    Ne      2       18      p       10      20.180  1.50    1.54
     12Neon    Ne      2       18      p       10      20.18   1.5     1.54
    1313Sodium  Na      3       1       s       11      22.991  0.97    2.27
    14 Magnesium       Mg      3       2       s       12      24.305  1.10    1.73
    15 Aluminium       Al      3       13      p       13      26.982  1.35    2.00
    16 Silicon Si      3       14      p       14      28.086  1.20    2.10
    17 Phosphorus      P       3       15      p       15      30.974  1.05    1.80
    18 Sulphur S       3       16      p       16      32.066  1.02    1.80
     14Magnesium       Mg      3       2       s       12      24.305  1.1     1.73
     15Aluminium       Al      3       13      p       13      26.982  1.35    2
     16Silicon Si      3       14      p       14      28.086  1.2     2.1
     17Phosphorus      P       3       15      p       15      30.974  1.05    1.8
     18Sulphur S       3       16      p       16      32.066  1.02    1.8
    1919Chlorine        Cl      3       17      p       17      35.453  0.99    1.75
    2020Argon   Ar      3       18      p       18      39.948  1.51    1.88
    2121Potassium       K       4       1       s       19      39.098  1.33    2.75
    22 Calcium Ca      4       2       s       20      40.078  0.99    2.00
    23 Scandium        Sc      4       3       d       21      44.956  1.44    2.00
    24 Titanium        Ti      4       4       d       22      47.867  1.47    2.00
    25 Vanadium        V       4       5       d       23      50.942  1.33    2.00
    26 Chromium        Cr      4       6       d       24      51.996  1.35    2.00
    27 Manganese       Mn      4       7       d       25      54.938  1.35    2.00
    28 Iron    Fe      4       8       d       26      55.845  1.34    2.00
    29 Cobalt  Co      4       9       d       27      58.933  1.33    2.00
    30 Nickel  Ni      4       10      d       28      58.693  1.50    1.63
    31 Copper  Cu      4       11      d       29      63.546  1.52    1.40
    32 Zinc    Zn      4       12      d       30      65.390  1.45    1.39
     22Calcium Ca      4       2       s       20      40.078  0.99    2
     23Scandium        Sc      4       3       d       21      44.956  1.44    2
     24Titanium        Ti      4       4       d       22      47.867  1.47    2
     25Vanadium        V       4       5       d       23      50.942  1.33    2
     26Chromium        Cr      4       6       d       24      51.996  1.35    2
     27Manganese       Mn      4       7       d       25      54.938  1.35    2
     28Iron    Fe      4       8       d       26      55.845  1.34    2
     29Cobalt  Co      4       9       d       27      58.933  1.33    2
     30Nickel  Ni      4       10      d       28      58.693  1.5     1.63
     31Copper  Cu      4       11      d       29      63.546  1.52    1.4
     32Zinc    Zn      4       12      d       30      65.39   1.45    1.39
    3333Gallium Ga      4       13      p       31      69.723  1.22    1.87
    34 Germanium       Ge      4       14      p       32      72.610  1.17    2.00
     34Germanium       Ge      4       14      p       32      72.61   1.17    2
    3535Arsenic As      4       15      p       33      74.922  1.21    1.85
    36 Selenium        Se      4       16      p       34      78.960  1.22    1.90
     36Selenium        Se      4       16      p       34      78.96   1.22    1.9
    3737Bromine Br      4       17      p       35      79.904  1.21    1.85
    38 Krypton Kr      4       18      p       36      83.800  1.50    2.02
    39 Rubidium        Rb      5       1       s       37      85.468  1.47    2.00
    40 Strontium       Sr      5       2       s       38      87.620  1.12    2.00
    41 Yttrium Y       5       3       d       39      88.906  1.78    2.00
    42 Zirconium       Zr      5       4       d       40      91.224  1.56    2.00
    43 Niobium Nb      5       5       d       41      92.906  1.48    2.00
    44 Molybdenum      Mo      5       6       d       42      95.940  1.47    2.00
    45 Technetium      Tc      5       7       d       43      98      1.35    2.00
    46 Ruthenium       Ru      5       8       d       44      101.070 1.40    2.00
    47 Rhodium Rh      5       9       d       45      102.906 1.45    2.00
    48 Palladium       Pd      5       10      d       46      106.420 1.50    1.63
     38Krypton Kr      4       18      p       36      83.8    1.5     2.02
     39Rubidium        Rb      5       1       s       37      85.468  1.47    2
     40Strontium       Sr      5       2       s       38      87.62   1.12    2
     41Yttrium Y       5       3       d       39      88.906  1.78    2
     42Zirconium       Zr      5       4       d       40      91.224  1.56    2
     43Niobium Nb      5       5       d       41      92.906  1.48    2
     44Molybdenum      Mo      5       6       d       42      95.94   1.47    2
     45Technetium      Tc      5       7       d       43      98      1.35    2
     46Ruthenium       Ru      5       8       d       44      101.07  1.4     2
     47Rhodium Rh      5       9       d       45      102.906 1.45    2
     48Palladium       Pd      5       10      d       46      106.42  1.5     1.63
    4949Silver  Ag      5       11      d       47      107.868 1.59    1.72
    5050Cadmium Cd      5       12      d       48      112.411 1.69    1.58
    5151Indium  In      5       13      p       49      114.818 1.63    1.93
    5252Tin     Sn      5       14      p       50      118.71  1.46    2.17
    53 Antimony        Sb      5       15      p       51      121.760 1.46    2.00
    54 Tellurium       Te      5       16      p       52      127.600 1.47    2.06
    55 Iodine  I       5       17      p       53      126.904 1.40    1.98
    56 Xenon   Xe      5       18      p       54      131.290 1.50    2.16
    57 Caesium Cs      6       1       s       55      132.905 1.67    2.00
    58 Barium  Ba      6       2       s       56      137.327 1.34    2.00
    59 Lutetium        Lu      6       3       d       71      174.967 1.72    2.00
    60 Hafnium Hf      6       4       d       72      178.490 1.57    2.00
    61 Tantalum        Ta      6       5       d       73      180.948 1.43    2.00
    62 Tungsten        W       6       6       d       74      183.840 1.37    2.00
    63 Rhenium Re      6       7       d       75      186.207 1.35    2.00
    64 Osmium  Os      6       8       d       76      190.230 1.37    2.00
    65 Iridium Ir      6       9       d       77      192.217 1.32    2.00
    66 Platinum        Pt      6       10      d       78      195.078 1.50    1.72
    67 Gold    Au      6       11      d       79      196.967 1.50    1.66
    68 Mercury Hg      6       12      d       80      200.590 1.70    1.55
     53Antimony        Sb      5       15      p       51      121.76  1.46    2
     54Tellurium       Te      5       16      p       52      127.6   1.47    2.06
     55Iodine  I       5       17      p       53      126.904 1.4     1.98
     56Xenon   Xe      5       18      p       54      131.29  1.5     2.16
     57Caesium Cs      6       1       s       55      132.905 1.67    2
     58Barium  Ba      6       2       s       56      137.327 1.34    2
     59Lanthanum       La      6Lan    19      f       57      138.906 1.87    2
     60Cerium  Ce      6Lan    19      f       58      140.116 1.83    2
     61Praseodymium    Pr      6Lan    19      f       59      140.908 1.82    2
     62Neodymium       Nd      6Lan    19      f       60      144.24  1.81    2
     63Promethium      Pm      6Lan    19      f       61      145     1.8     2
     64Samarium        Sm      6Lan    19      f       62      150.36  1.8     2
     65Europium        Eu      6Lan    19      f       63      151.964 1.99    2
     66Gadolinium      Gd      6Lan    19      f       64      157.25  1.79    2
     67Terbium Tb      6Lan    19      f       65      158.925 1.76    2
     68Dysprosium      Dy      6Lan    19      f       66      162.5   1.75    2
     69Holmium Ho      6Lan    19      f       67      164.93  1.74    2
     70Erbium  Er      6Lan    19      f       68      167.26  1.73    2
     71Thulium Tm      6Lan    19      f       69      168.934 1.72    2
     72Ytterbium       Yb      6Lan    19      f       70      173.04  1.94    2
     73Lutetium        Lu      6       3       d       71      174.967 1.72    2
     74Hafnium Hf      6       4       d       72      178.49  1.57    2
     75Tantalum        Ta      6       5       d       73      180.948 1.43    2
     76Tungsten        W       6       6       d       74      183.84  1.37    2
     77Rhenium Re      6       7       d       75      186.207 1.35    2
     78Osmium  Os      6       8       d       76      190.23  1.37    2
     79Iridium Ir      6       9       d       77      192.217 1.32    2
     80Platinum        Pt      6       10      d       78      195.078 1.5     1.72
     81Gold    Au      6       11      d       79      196.967 1.5     1.66
     82Mercury Hg      6       12      d       80      200.59  1.7     1.55
    6983Thallium        Tl      6       13      p       81      204.383 1.55    1.96
    70 Lead    Pb      6       14      p       82      207.200 1.54    2.02
    71 Bismuth Bi      6       15      p       83      208.980 1.54    2.00
    72 Polonium        Po      6       16      p       84      210     1.68    2.00
    73 Astatine        At      6       17      p       85      210     1.21    2.00
    74 Radon   Rn      6       18      p       86      222     1.50    2.00
    75 Cerium  Ce      6Lan    19      f       58      140.116 1.83    2.00
    76 Dysprosium      Dy      6Lan    19      f       66      162.500 1.75    2.00
    77 Erbium  Er      6Lan    19      f       68      167.260 1.73    2.00
    78 Europium        Eu      6Lan    19      f       63      151.964 1.99    2.00
    79 Gadolinium      Gd      6Lan    19      f       64      157.250 1.79    2.00
    80 Holmium Ho      6Lan    19      f       67      164.930 1.74    2.00
    81 Lanthanum       La      6Lan    19      f       57      138.906 1.87    2.00
    82 Neodymium       Nd      6Lan    19      f       60      144.240 1.81    2.00
    83 Promethium      Pm      6Lan    19      f       61      145     1.80    2.00
    84 Praseodymium    Pr      6Lan    19      f       59      140.908 1.82    2.00
    85 Samarium        Sm      6Lan    19      f       62      150.360 1.80    2.00
    86 Terbium Tb      6Lan    19      f       65      158.925 1.76    2.00
    87 Thulium Tm      6Lan    19      f       69      168.934 1.72    2.00
    88 Ytterbium       Yb      6Lan    19      f       70      173.040 1.94    2.00
    89 Francium        Fr      7       1       s       87      223     1.50    2.00
    90 Radium  Ra      7       2       s       88      226     1.90    2.00
    91 Lawrencium      Lr      7       3       d       103     262     1.50    2.00
    92 Rutherfordium   Rf      7       4       d       104     261     1.50    2.00
    93 Dubnium Db      7       5       d       105     262     1.50    2.00
    94 Seaborgium      Sg      7       6       d       106     266     1.50    2.00
    95 Bohrium Bh      7       7       d       107     264     1.50    2.00
    96 Hassium Hs      7       8       d       108     269     1.50    2.00
    97 Meitnerium      Mt      7       9       d       109     268     1.50    2.00
    98 Darmstadtium    Ds      7       10      d       110     271     1.50    2.00
    99 Actinium        Ac      7Act    20      f       89      227     1.88    2.00
    100 Americium       Am      7Act    20      f       95      243     1.51    2.00
    101 Berkelium       Bk      7Act    20      f       97      247     1.54    2.00
    102 Californium     Cf      7Act    20      f       98      251     1.83    2.00
    103 Curium  Cm      7Act    20      f       96      247     0.99    2.00
    104 Einsteinium     Es      7Act    20      f       99      252     1.50    2.00
    105 Fermium Fm      7Act    20      f       100     257     1.50    2.00
    106 Mendelevium     Md      7Act    20      f       101     258     1.50    2.00
    107 Nobelium        No      7Act    20      f       102     259     1.50    2.00
    108 Neptunium       Np      7Act    20      f       93      237     1.55    2.00
    109 Protactinium    Pa      7Act    20      f       91      231.036 1.61    2.00
    110 Plutonium       Pu      7Act    20      f       94      244     1.53    2.00
    111 Thorium Th      7Act    20      f       90      232.038 1.79    2.00
     84Lead    Pb      6       14      p       82      207.2   1.54    2.02
     85Bismuth Bi      6       15      p       83      208.98  1.54    2
     86Polonium        Po      6       16      p       84      210     1.68    2
     87Astatine        At      6       17      p       85      210     1.21    2
     88Radon   Rn      6       18      p       86      222     1.5     2
     89Francium        Fr      7       1       s       87      223     1.5     2
     90Radium  Ra      7       2       s       88      226     1.9     2
     91Actinium        Ac      7Act    20      f       89      227     1.88    2
     92Thorium Th      7Act    20      f       90      232.038 1.79    2
     93Protactinium    Pa      7Act    20      f       91      231.036 1.61    2
    11294Uranium U       7Act    20      f       92      238.029 1.58    1.86
     95Neptunium       Np      7Act    20      f       93      237     1.55    2
     96Plutonium       Pu      7Act    20      f       94      244     1.53    2
     97Americium       Am      7Act    20      f       95      243     1.51    2
     98Curium  Cm      7Act    20      f       96      247     0.99    2
     99Berkelium       Bk      7Act    20      f       97      247     1.54    2
     100Californium     Cf      7Act    20      f       98      251     1.83    2
     101Einsteinium     Es      7Act    20      f       99      252     1.5     2
     102Fermium Fm      7Act    20      f       100     257     1.5     2
     103Mendelevium     Md      7Act    20      f       101     258     1.5     2
     104Nobelium        No      7Act    20      f       102     259     1.5     2
     105Lawrencium      Lr      7       3       d       103     262     1.5     2
     106Rutherfordium   Rf      7       4       d       104     261     1.5     2
     107Dubnium Db      7       5       d       105     262     1.5     2
     108Seaborgium      Sg      7       6       d       106     266     1.5     2
     109Bohrium Bh      7       7       d       107     264     1.5     2
     110Hassium Hs      7       8       d       108     269     1.5     2
     111Meitnerium      Mt      7       9       d       109     268     1.5     2
     112Darmstadtium    Ds      7       10      d       110     271     1.5     2

  • src/helpers.cpp

    r60f50a r9757d9  
    209209 */
    210210void performCriticalExit() {
    211   map<void*, size_t> pointers = MemoryUsageObserver::getInstance()->getPointersToAllocatedMemory();
    212   for (map<void*, size_t>::iterator runner = pointers.begin(); runner != pointers.end(); runner++) {
    213     Free(((void**) &runner->first));
    214   }
     211//  map<void*, size_t> pointers = MemoryUsageObserver::getInstance()->getPointersToAllocatedMemory();
     212//  for (map<void*, size_t>::iterator runner = pointers.begin(); runner != pointers.end(); runner++) {
     213//    Free(((void**) &runner->first));
     214//  }
    215215
    216216  exit(255);

  • src/molecule.cpp

    r60f50a r9757d9  
    135135      if (pointer->type->Z != 1)
    136136        NoNonHydrogen++;
    137       if (pointer->Name == NULL) {
    138         Free(&pointer->Name);
    139         pointer->Name = Malloc<char>(6, "molecule::AddAtom: *pointer->Name");
    140         sprintf(pointer->Name, "%2s%02d", pointer->type->symbol, pointer->nr+1);
     137      if(pointer->getName() == "Unknown"){
     138        stringstream sstr;
     139        sstr << pointer->type->symbol << pointer->nr+1;
     140        pointer->setName(sstr.str());
    141141      }
    142142    }
    … …  
    157157  if (pointer != NULL) {
    158158    atom *walker = pointer->clone();
    159     walker->Name = Malloc<char>(strlen(pointer->Name) + 1, "atom::atom: *Name");
    160     strcpy (walker->Name, pointer->Name);
     159    stringstream sstr;
     160    sstr << pointer->getName();
     161    walker->setName(sstr.str());
    161162    walker->nr = last_atom++;  // increase number within molecule
    162163    add(walker, end);
    … …  
    252253  BondRescale = TopOrigin->type->HBondDistance[TopBond->BondDegree-1];
    253254  if (BondRescale == -1) {
    254     DoeLog(1) && (eLog()<< Verbose(1) << "There is no typical hydrogen bond distance in replacing bond (" << TopOrigin->Name << "<->" << TopReplacement->Name << ") of degree " << TopBond->BondDegree << "!" << endl);
     255    DoeLog(1) && (eLog()<< Verbose(1) << "There is no typical hydrogen bond distance in replacing bond (" << TopOrigin->getName() << "<->" << TopReplacement->getName() << ") of degree " << TopBond->BondDegree << "!" << endl);
    255256    return false;
    256257    BondRescale = bondlength;
    … …  
    275276      InBondvector *= BondRescale;   // rescale the distance vector to Hydrogen bond length
    276277      FirstOtherAtom->x = TopOrigin->x; // set coordination to origin ...
    277       FirstOtherAtom->x = InBondvector;  // ... and add distance vector to replacement atom
     278      FirstOtherAtom->x += InBondvector;  // ... and add distance vector to replacement atom
    278279      AllWentWell = AllWentWell && AddAtom(FirstOtherAtom);
    279280//      Log() << Verbose(4) << "Added " << *FirstOtherAtom << " at: ";
    … …  
    295296            SecondOtherAtom = (*Runner)->GetOtherAtom(TopOrigin);
    296297          } else {
    297             DoeLog(2) && (eLog()<< Verbose(2) << "Detected more than four bonds for atom " << TopOrigin->Name);
     298            DoeLog(2) && (eLog()<< Verbose(2) << "Detected more than four bonds for atom " << TopOrigin->getName());
    298299          }
    299300        }
    … …  
    339340      bondangle = TopOrigin->type->HBondAngle[1];
    340341      if (bondangle == -1) {
    341         DoeLog(1) && (eLog()<< Verbose(1) << "There is no typical hydrogen bond angle in replacing bond (" << TopOrigin->Name << "<->" << TopReplacement->Name << ") of degree " << TopBond->BondDegree << "!" << endl);
     342        DoeLog(1) && (eLog()<< Verbose(1) << "There is no typical hydrogen bond angle in replacing bond (" << TopOrigin->getName() << "<->" << TopReplacement->getName() << ") of degree " << TopBond->BondDegree << "!" << endl);
    342343        return false;
    343344        bondangle = 0;
    … …  
    616617    add(Binder, last);
    617618  } else {
    618     DoeLog(1) && (eLog()<< Verbose(1) << "Could not add bond between " << atom1->Name << " and " << atom2->Name << " as one or both are not present in the molecule." << endl);
     619    DoeLog(1) && (eLog()<< Verbose(1) << "Could not add bond between " << atom1->getName() << " and " << atom2->getName() << " as one or both are not present in the molecule." << endl);
    619620  }
    620621  return Binder;
    … …  
    695696    AtomCount--;
    696697  } else
    697     DoeLog(1) && (eLog()<< Verbose(1) << "Atom " << pointer->Name << " is of element " << pointer->type->Z << " but the entry in the table of the molecule is 0!" << endl);
     698    DoeLog(1) && (eLog()<< Verbose(1) << "Atom " << pointer->getName() << " is of element " << pointer->type->Z << " but the entry in the table of the molecule is 0!" << endl);
    698699  if (ElementsInMolecule[pointer->type->Z] == 0)  // was last atom of this element?
    699700    ElementCount--;
    … …  
    713714    ElementsInMolecule[pointer->type->Z]--; // decrease number of atom of this element
    714715  else
    715     DoeLog(1) && (eLog()<< Verbose(1) << "Atom " << pointer->Name << " is of element " << pointer->type->Z << " but the entry in the table of the molecule is 0!" << endl);
     716    DoeLog(1) && (eLog()<< Verbose(1) << "Atom " << pointer->getName() << " is of element " << pointer->type->Z << " but the entry in the table of the molecule is 0!" << endl);
    716717  if (ElementsInMolecule[pointer->type->Z] == 0)  // was last atom of this element?
    717718    ElementCount--;
    … …  
    915916        if (Walker->type->Z != 1) // count non-hydrogen atoms whilst at it
    916917          NoNonHydrogen++;
    917         Free(&Walker->Name);
    918         Walker->Name = Malloc<char>(6, "molecule::CountAtoms: *walker->Name");
    919         sprintf(Walker->Name, "%2s%02d", Walker->type->symbol, Walker->nr+1);
    920         DoLog(3) && (Log() << Verbose(3) << "Naming atom nr. " << Walker->nr << " " << Walker->Name << "." << endl);
     918        stringstream sstr;
     919        sstr << Walker->type->symbol << Walker->nr+1;
     920        Walker->setName(sstr.str());
     921        DoLog(3) && (Log() << Verbose(3) << "Naming atom nr. " << Walker->nr << " " << Walker->getName() << "." << endl);
    921922        i++;
    922923      }

  • src/molecule_fragmentation.cpp

    r60f50a r9757d9  
    722722    // free memory for bond part
    723723    DoLog(1) && (Log() << Verbose(1) << "Freeing bond memory" << endl);
    724     delete(FragmentList); // remove bond molecule from memory
     724    Free(&FragmentList); // remove bond molecule from memory
    725725    Free(&SortIndex);
    726726  } else {
    … …  
    907907      }
    908908    } else {
    909       DoeLog(1) && (eLog()<< Verbose(1) << "Son " << Runner->Name << " has father " << FatherOfRunner->Name << " but its entry in SonList is " << SonList[FatherOfRunner->nr] << "!" << endl);
     909      DoeLog(1) && (eLog()<< Verbose(1) << "Son " << Runner->getName() << " has father " << FatherOfRunner->getName() << " but its entry in SonList is " << SonList[FatherOfRunner->nr] << "!" << endl);
    910910    }
    911911    if ((LonelyFlag) && (Leaf->AtomCount > 1)) {

  • src/molecule_geometry.cpp

    r60f50a r9757d9  
    109109
    110110  if (ptr->next != end) {   //list not empty?
    111     while (ptr->next != end) {  // continue with second if present
     111    while (ptr->next != end) {
    112112      ptr = ptr->next;
    113113      Num++;
    … …  
    125125Vector * molecule::DetermineCenterOfAll() const
    126126{
    127   atom *ptr = start->next;  // start at first in list
     127  atom *ptr = start;  // start at first in list
    128128  Vector *a = new Vector();
    129   Vector tmp;
    130129  double Num = 0;
    131130
    132131  a->Zero();
    133132
    134   if (ptr != end) {   //list not empty?
    135     while (ptr->next != end) {  // continue with second if present
     133  if (ptr->next != end) {   //list not empty?
     134    while (ptr->next != end) {
    136135      ptr = ptr->next;
    137136      Num += 1.;
    138       tmp = ptr->x;
    139       (*a) += tmp;
     137      (*a) += ptr->x;
    140138    }
    141139    a->Scale(1./Num); // divide through total mass (and sign for direction)
    … …  
    284282              if ((fabs(tmp)) > BondDistance) {
    285283                flag = false;
    286                 DoLog(0) && (Log() << Verbose(0) << "Hit: atom " << Walker->Name << " in bond " << *(*Runner) << " has to be shifted due to " << tmp << "." << endl);
     284                DoLog(0) && (Log() << Verbose(0) << "Hit: atom " << Walker->getName() << " in bond " << *(*Runner) << " has to be shifted due to " << tmp << "." << endl);
    287285                if (tmp > 0)
    288286                  Translationvector[j] -= 1.;

  • src/molecule_graph.cpp

    r60f50a r9757d9  
    317317    Walker->GraphNr = DFS.CurrentGraphNr;
    318318    Walker->LowpointNr = DFS.CurrentGraphNr;
    319     DoLog(1) && (Log() << Verbose(1) << "Setting Walker[" << Walker->Name << "]'s number to " << Walker->GraphNr << " with Lowpoint " << Walker->LowpointNr << "." << endl);
     319    DoLog(1) && (Log() << Verbose(1) << "Setting Walker[" << Walker->getName() << "]'s number to " << Walker->GraphNr << " with Lowpoint " << Walker->LowpointNr << "." << endl);
    320320    DFS.AtomStack->Push(Walker);
    321321    DFS.CurrentGraphNr++;
    … …  
    348348    Binder->MarkUsed(black);
    349349    OtherAtom = Binder->GetOtherAtom(Walker);
    350     DoLog(2) && (Log() << Verbose(2) << "(4) OtherAtom is " << OtherAtom->Name << "." << endl);
     350    DoLog(2) && (Log() << Verbose(2) << "(4) OtherAtom is " << OtherAtom->getName() << "." << endl);
    351351    if (OtherAtom->GraphNr != -1) {
    352352      // (4a) ... if "other" atom has been visited (GraphNr != 0), set lowpoint to minimum of both, go to (3)
    … …  
    354354      DFS.BackEdgeStack->Push(Binder);
    355355      Walker->LowpointNr = (Walker->LowpointNr < OtherAtom->GraphNr) ? Walker->LowpointNr : OtherAtom->GraphNr;
    356       DoLog(3) && (Log() << Verbose(3) << "(4a) Visited: Setting Lowpoint of Walker[" << Walker->Name << "] to " << Walker->LowpointNr << "." << endl);
     356      DoLog(3) && (Log() << Verbose(3) << "(4a) Visited: Setting Lowpoint of Walker[" << Walker->getName() << "] to " << Walker->LowpointNr << "." << endl);
    357357    } else {
    358358      // (4b) ... otherwise set OtherAtom as Ancestor of Walker and Walker as OtherAtom, go to (2)
    … …  
    360360      OtherAtom->Ancestor = Walker;
    361361      Walker = OtherAtom;
    362       DoLog(3) && (Log() << Verbose(3) << "(4b) Not Visited: OtherAtom[" << OtherAtom->Name << "]'s Ancestor is now " << OtherAtom->Ancestor->Name << ", Walker is OtherAtom " << OtherAtom->Name << "." << endl);
     362      DoLog(3) && (Log() << Verbose(3) << "(4b) Not Visited: OtherAtom[" << OtherAtom->getName() << "]'s Ancestor is now " << OtherAtom->Ancestor->getName() << ", Walker is OtherAtom " << OtherAtom->getName() << "." << endl);
    363363      break;
    364364    }
    … …  
    382382
    383383  // (5) if Ancestor of Walker is ...
    384   DoLog(1) && (Log() << Verbose(1) << "(5) Number of Walker[" << Walker->Name << "]'s Ancestor[" << Walker->Ancestor->Name << "] is " << Walker->Ancestor->GraphNr << "." << endl);
     384  DoLog(1) && (Log() << Verbose(1) << "(5) Number of Walker[" << Walker->getName() << "]'s Ancestor[" << Walker->Ancestor->getName() << "] is " << Walker->Ancestor->GraphNr << "." << endl);
    385385
    386386  if (Walker->Ancestor->GraphNr != DFS.Root->GraphNr) {
    … …  
    389389      // (6a) set Ancestor's Lowpoint number to minimum of of its Ancestor and itself, go to Step(8)
    390390      Walker->Ancestor->LowpointNr = (Walker->Ancestor->LowpointNr < Walker->LowpointNr) ? Walker->Ancestor->LowpointNr : Walker->LowpointNr;
    391       DoLog(2) && (Log() << Verbose(2) << "(6) Setting Walker[" << Walker->Name << "]'s Ancestor[" << Walker->Ancestor->Name << "]'s Lowpoint to " << Walker->Ancestor->LowpointNr << "." << endl);
     391      DoLog(2) && (Log() << Verbose(2) << "(6) Setting Walker[" << Walker->getName() << "]'s Ancestor[" << Walker->Ancestor->getName() << "]'s Lowpoint to " << Walker->Ancestor->LowpointNr << "." << endl);
    392392    } else {
    393393      // (7) (Ancestor of Walker is a separating vertex, remove all from stack till Walker (including), these and Ancestor form a component
    394394      Walker->Ancestor->SeparationVertex = true;
    395       DoLog(2) && (Log() << Verbose(2) << "(7) Walker[" << Walker->Name << "]'s Ancestor[" << Walker->Ancestor->Name << "]'s is a separating vertex, creating component." << endl);
     395      DoLog(2) && (Log() << Verbose(2) << "(7) Walker[" << Walker->getName() << "]'s Ancestor[" << Walker->Ancestor->getName() << "]'s is a separating vertex, creating component." << endl);
    396396      mol->SetNextComponentNumber(Walker->Ancestor, DFS.ComponentNumber);
    397       DoLog(3) && (Log() << Verbose(3) << "(7) Walker[" << Walker->Name << "]'s Ancestor's Compont is " << DFS.ComponentNumber << "." << endl);
     397      DoLog(3) && (Log() << Verbose(3) << "(7) Walker[" << Walker->getName() << "]'s Ancestor's Compont is " << DFS.ComponentNumber << "." << endl);
    398398      mol->SetNextComponentNumber(Walker, DFS.ComponentNumber);
    399       DoLog(3) && (Log() << Verbose(3) << "(7) Walker[" << Walker->Name << "]'s Compont is " << DFS.ComponentNumber << "." << endl);
     399      DoLog(3) && (Log() << Verbose(3) << "(7) Walker[" << Walker->getName() << "]'s Compont is " << DFS.ComponentNumber << "." << endl);
    400400      do {
    401401        OtherAtom = DFS.AtomStack->PopLast();
    402402        LeafWalker->Leaf->AddCopyAtom(OtherAtom);
    403403        mol->SetNextComponentNumber(OtherAtom, DFS.ComponentNumber);
    404         DoLog(3) && (Log() << Verbose(3) << "(7) Other[" << OtherAtom->Name << "]'s Compont is " << DFS.ComponentNumber << "." << endl);
     404        DoLog(3) && (Log() << Verbose(3) << "(7) Other[" << OtherAtom->getName() << "]'s Compont is " << DFS.ComponentNumber << "." << endl);
    405405      } while (OtherAtom != Walker);
    406406      DFS.ComponentNumber++;
    407407    }
    408408    // (8) Walker becomes its Ancestor, go to (3)
    409     DoLog(2) && (Log() << Verbose(2) << "(8) Walker[" << Walker->Name << "] is now its Ancestor " << Walker->Ancestor->Name << ", backstepping. " << endl);
     409    DoLog(2) && (Log() << Verbose(2) << "(8) Walker[" << Walker->getName() << "] is now its Ancestor " << Walker->Ancestor->getName() << ", backstepping. " << endl);
    410410    Walker = Walker->Ancestor;
    411411    DFS.BackStepping = true;
    … …  
    431431    //DFS.AtomStack->Output(out);
    432432    mol->SetNextComponentNumber(DFS.Root, DFS.ComponentNumber);
    433     DoLog(3) && (Log() << Verbose(3) << "(9) Root[" << DFS.Root->Name << "]'s Component is " << DFS.ComponentNumber << "." << endl);
     433    DoLog(3) && (Log() << Verbose(3) << "(9) Root[" << DFS.Root->getName() << "]'s Component is " << DFS.ComponentNumber << "." << endl);
    434434    mol->SetNextComponentNumber(Walker, DFS.ComponentNumber);
    435     DoLog(3) && (Log() << Verbose(3) << "(9) Walker[" << Walker->Name << "]'s Component is " << DFS.ComponentNumber << "." << endl);
     435    DoLog(3) && (Log() << Verbose(3) << "(9) Walker[" << Walker->getName() << "]'s Component is " << DFS.ComponentNumber << "." << endl);
    436436    do {
    437437      OtherAtom = DFS.AtomStack->PopLast();
    438438      LeafWalker->Leaf->AddCopyAtom(OtherAtom);
    439439      mol->SetNextComponentNumber(OtherAtom, DFS.ComponentNumber);
    440       DoLog(3) && (Log() << Verbose(3) << "(7) Other[" << OtherAtom->Name << "]'s Compont is " << DFS.ComponentNumber << "." << endl);
     440      DoLog(3) && (Log() << Verbose(3) << "(7) Other[" << OtherAtom->getName() << "]'s Compont is " << DFS.ComponentNumber << "." << endl);
    441441    } while (OtherAtom != Walker);
    442442    DFS.ComponentNumber++;
    … …  
    445445    Walker = DFS.Root;
    446446    Binder = mol->FindNextUnused(Walker);
    447     DoLog(1) && (Log() << Verbose(1) << "(10) Walker is Root[" << DFS.Root->Name << "], next Unused Bond is " << Binder << "." << endl);
     447    DoLog(1) && (Log() << Verbose(1) << "(10) Walker is Root[" << DFS.Root->getName() << "], next Unused Bond is " << Binder << "." << endl);
    448448    if (Binder != NULL) { // Root is separation vertex
    449449      DoLog(1) && (Log() << Verbose(1) << "(11) Root is a separation vertex." << endl);
    … …  
    692692        if (OtherAtom->type->Z != 1) {
    693693#endif
    694         DoLog(2) && (Log() << Verbose(2) << "Current OtherAtom is: " << OtherAtom->Name << " for bond " << *(*Runner) << "." << endl);
     694        DoLog(2) && (Log() << Verbose(2) << "Current OtherAtom is: " << OtherAtom->getName() << " for bond " << *(*Runner) << "." << endl);
    695695        if (BFS.ColorList[OtherAtom->nr] == white) {
    696696          BFS.TouchedStack->Push(OtherAtom);
    … …  
    698698          BFS.PredecessorList[OtherAtom->nr] = Walker; // Walker is the predecessor
    699699          BFS.ShortestPathList[OtherAtom->nr] = BFS.ShortestPathList[Walker->nr] + 1;
    700           DoLog(2) && (Log() << Verbose(2) << "Coloring OtherAtom " << OtherAtom->Name << " lightgray, its predecessor is " << Walker->Name << " and its Shortest Path is " << BFS.ShortestPathList[OtherAtom->nr] << " egde(s) long." << endl);
     700          DoLog(2) && (Log() << Verbose(2) << "Coloring OtherAtom " << OtherAtom->getName() << " lightgray, its predecessor is " << Walker->getName() << " and its Shortest Path is " << BFS.ShortestPathList[OtherAtom->nr] << " egde(s) long." << endl);
    701701          //if (BFS.ShortestPathList[OtherAtom->nr] < MinimumRingSize[Walker->GetTrueFather()->nr]) { // Check for maximum distance
    702702          DoLog(3) && (Log() << Verbose(3) << "Putting OtherAtom into queue." << endl);
    … …  
    719719    }
    720720    BFS.ColorList[Walker->nr] = black;
    721     DoLog(1) && (Log() << Verbose(1) << "Coloring Walker " << Walker->Name << " black." << endl);
     721    DoLog(1) && (Log() << Verbose(1) << "Coloring Walker " << Walker->getName() << " black." << endl);
    722722    if (OtherAtom == BFS.Root) { // if we have found the root, check whether this cycle wasn't already found beforehand
    723723      // step through predecessor list
    … …  
    770770    Walker = BFS.Root;
    771771    while (Walker != BackEdge->rightatom) {
    772       DoLog(0) && (Log() << Verbose(0) << Walker->Name << " <-> ");
     772      DoLog(0) && (Log() << Verbose(0) << Walker->getName() << " <-> ");
    773773      Walker = BFS.PredecessorList[Walker->nr];
    774774      Walker->GetTrueFather()->IsCyclic = true;
    775775      RingSize++;
    776776    }
    777     DoLog(0) && (Log() << Verbose(0) << Walker->Name << "  with a length of " << RingSize << "." << endl << endl);
     777    DoLog(0) && (Log() << Verbose(0) << Walker->getName() << "  with a length of " << RingSize << "." << endl << endl);
    778778    // walk through all and set MinimumRingSize
    779779    Walker = BFS.Root;
    … …  
    12331233  BFS.PredecessorList[OtherAtom->nr] = Walker; // Walker is the predecessor
    12341234  BFS.ShortestPathList[OtherAtom->nr] = BFS.ShortestPathList[Walker->nr] + 1;
    1235   DoLog(2) && (Log() << Verbose(2) << "Coloring OtherAtom " << OtherAtom->Name << " " << ((BFS.ColorList[OtherAtom->nr] == white) ? "white" : "lightgray") << ", its predecessor is " << Walker->Name << " and its Shortest Path is " << BFS.ShortestPathList[OtherAtom->nr] << " egde(s) long." << endl);
     1235  DoLog(2) && (Log() << Verbose(2) << "Coloring OtherAtom " << OtherAtom->getName() << " " << ((BFS.ColorList[OtherAtom->nr] == white) ? "white" : "lightgray") << ", its predecessor is " << Walker->getName() << " and its Shortest Path is " << BFS.ShortestPathList[OtherAtom->nr] << " egde(s) long." << endl);
    12361236  if ((((BFS.ShortestPathList[OtherAtom->nr] < BFS.BondOrder) && (Binder != Bond)))) { // Check for maximum distance
    12371237    DoLog(3) && (Log() << Verbose(3));
    12381238    if (AddedAtomList[OtherAtom->nr] == NULL) { // add if it's not been so far
    12391239      AddedAtomList[OtherAtom->nr] = Mol->AddCopyAtom(OtherAtom);
    1240       DoLog(0) && (Log() << Verbose(0) << "Added OtherAtom " << OtherAtom->Name);
     1240      DoLog(0) && (Log() << Verbose(0) << "Added OtherAtom " << OtherAtom->getName());
    12411241      AddedBondList[Binder->nr] = Mol->CopyBond(AddedAtomList[Walker->nr], AddedAtomList[OtherAtom->nr], Binder);
    12421242      DoLog(0) && (Log() << Verbose(0) << " and bond " << *(AddedBondList[Binder->nr]) << ", ");
    12431243    } else { // this code should actually never come into play (all white atoms are not yet present in BondMolecule, that's why they are white in the first place)
    1244       DoLog(0) && (Log() << Verbose(0) << "Not adding OtherAtom " << OtherAtom->Name);
     1244      DoLog(0) && (Log() << Verbose(0) << "Not adding OtherAtom " << OtherAtom->getName());
    12451245      if (AddedBondList[Binder->nr] == NULL) {
    12461246        AddedBondList[Binder->nr] = Mol->CopyBond(AddedAtomList[Walker->nr], AddedAtomList[OtherAtom->nr], Binder);
    … …  
    13221322    // followed by n+1 till top of stack.
    13231323    Walker = BFS.BFSStack->PopFirst(); // pop oldest added
    1324     DoLog(1) && (Log() << Verbose(1) << "Current Walker is: " << Walker->Name << ", and has " << Walker->ListOfBonds.size() << " bonds." << endl);
     1324    DoLog(1) && (Log() << Verbose(1) << "Current Walker is: " << Walker->getName() << ", and has " << Walker->ListOfBonds.size() << " bonds." << endl);
    13251325    for (BondList::const_iterator Runner = Walker->ListOfBonds.begin(); Runner != Walker->ListOfBonds.end(); (++Runner)) {
    13261326      if ((*Runner) != NULL) { // don't look at bond equal NULL
    13271327        Binder = (*Runner);
    13281328        OtherAtom = (*Runner)->GetOtherAtom(Walker);
    1329         DoLog(2) && (Log() << Verbose(2) << "Current OtherAtom is: " << OtherAtom->Name << " for bond " << *(*Runner) << "." << endl);
     1329        DoLog(2) && (Log() << Verbose(2) << "Current OtherAtom is: " << OtherAtom->getName() << " for bond " << *(*Runner) << "." << endl);
    13301330        if (BFS.ColorList[OtherAtom->nr] == white) {
    13311331          BreadthFirstSearchAdd_UnvisitedNode(Mol, BFS, Walker, OtherAtom, Binder, Bond, AddedAtomList, AddedBondList, IsAngstroem);
    … …  
    13361336    }
    13371337    BFS.ColorList[Walker->nr] = black;
    1338     DoLog(1) && (Log() << Verbose(1) << "Coloring Walker " << Walker->Name << " black." << endl);
     1338    DoLog(1) && (Log() << Verbose(1) << "Coloring Walker " << Walker->getName() << " black." << endl);
    13391339  }
    13401340  BreadthFirstSearchAdd_Free(BFS);
    … …  
    14031403          OtherAtom = (*Runner)->GetOtherAtom(Walker);
    14041404          if (ParentList[OtherAtom->nr] != NULL) { // if otheratom is also a father of an atom on this molecule, create the bond
    1405             DoLog(4) && (Log() << Verbose(4) << "Endpoints of Bond " << (*Runner) << " are both present: " << ParentList[Walker->nr]->Name << " and " << ParentList[OtherAtom->nr]->Name << "." << endl);
     1405            DoLog(4) && (Log() << Verbose(4) << "Endpoints of Bond " << (*Runner) << " are both present: " << ParentList[Walker->nr]->getName() << " and " << ParentList[OtherAtom->nr]->getName() << "." << endl);
    14061406            mol->AddBond(ParentList[Walker->nr], ParentList[OtherAtom->nr], (*Runner)->BondDegree);
    14071407          }

  • src/moleculelist.cpp

    r60f50a r9757d9  
    677677    while (Walker->next != (*ListRunner)->end) {
    678678      Walker = Walker->next;
    679       DoLog(0) && (Log() << Verbose(0) << Walker->Name << " ");
     679      DoLog(0) && (Log() << Verbose(0) << Walker->getName() << " ");
    680680    }
    681681    DoLog(0) && (Log() << Verbose(0) << endl);

  • src/parser.cpp

    r60f50a r9757d9  
    3232  if (input == NULL) {
    3333    if (!test)
    34       DoLog(0) && (Log() << Verbose(0) << endl << "Unable to open " << filename << ", is the directory correct?" << endl);
     34      DoLog(0) && (Log() << Verbose(0) << endl << "FilePresent: Unable to open " << filename << ", is the directory correct?" << endl);
    3535    return false;
    3636  }
    … …  
    160160  //Log() << Verbose(1) << "Opening " << name << " ... "  << input << endl;
    161161  if (input == NULL) {
    162     DoeLog(1) && (eLog()<< Verbose(1) << endl << "Unable to open " << name << ", is the directory correct?" << endl);
     162    DoeLog(1) && (eLog()<< Verbose(1) << endl << "MatrixContainer::ParseMatrix: Unable to open " << name << ", is the directory correct?" << endl);
    163163    //performCriticalExit();
    164164    return false;
    … …  
    269269  input.open(file.str().c_str(), ios::in);
    270270  if (input == NULL) {
    271     DoLog(0) && (Log() << Verbose(0) << endl << "Unable to open " << file.str() << ", is the directory correct?" << endl);
     271    DoLog(0) && (Log() << Verbose(0) << endl << "MatrixContainer::ParseFragmentMatrix: Unable to open " << file.str() << ", is the directory correct?" << endl);
    272272    return false;
    273273  }
    … …  
    477477    output.open(line.str().c_str(), ios::out);
    478478    if (output == NULL) {
    479       DoeLog(0) && (eLog()<< Verbose(0) << "Unable to open output energy file " << line.str() << "!" << endl);
     479      DoeLog(0) && (eLog()<< Verbose(0) << "MatrixContainer::WriteTotalFragments: Unable to open output energy file " << line.str() << "!" << endl);
    480480      performCriticalExit();
    481481      return false;
    … …  
    507507  output.open(line.str().c_str(), ios::out);
    508508  if (output == NULL) {
    509     DoeLog(0) && (eLog()<< Verbose(0) << "Unable to open output matrix file " << line.str() << "!" << endl);
     509    DoeLog(0) && (eLog()<< Verbose(0) << "MatrixContainer::WriteLastMatrix: Unable to open output matrix file " << line.str() << "!" << endl);
    510510    performCriticalExit();
    511511    return false;
    … …  
    621621  //Log() << Verbose(0) << "Opening " << line.str() << " ... "  << input << endl;
    622622  if (input == NULL) {
    623     DoLog(0) && (Log() << Verbose(0) << endl << "Unable to open " << line.str() << ", is the directory correct?" << endl);
     623    DoLog(0) && (Log() << Verbose(0) << endl << "ForceMatrix::ParseIndices: Unable to open " << line.str() << ", is the directory correct?" << endl);
    624624    return false;
    625625  }
    … …  
    700700    input.open(file.str().c_str(), ios::in);
    701701    if (input == NULL) {
    702       DoLog(0) && (Log() << Verbose(0) << endl << "Unable to open " << file.str() << ", is the directory correct?" << endl);
     702      DoLog(0) && (Log() << Verbose(0) << endl << "ForceMatrix::ParseFragmentMatrix: Unable to open " << file.str() << ", is the directory correct?" << endl);
    703703      return false;
    704704    }
    … …  
    759759  //Log() << Verbose(0) << "Opening " << line.str() << " ... "  << input << endl;
    760760  if (input == NULL) {
    761     DoLog(0) && (Log() << Verbose(0) << endl << "Unable to open " << line.str() << ", is the directory correct?" << endl);
     761    DoLog(0) && (Log() << Verbose(0) << endl << "HessianMatrix::ParseIndices: Unable to open " << line.str() << ", is the directory correct?" << endl);
    762762    return false;
    763763  }
    … …  
    930930    input.open(file.str().c_str(), ios::in);
    931931    if (input == NULL) {
    932       DoLog(0) && (Log() << Verbose(0) << endl << "Unable to open " << file.str() << ", is the directory correct?" << endl);
     932      DoLog(0) && (Log() << Verbose(0) << endl << "HessianMatrix::ParseFragmentMatrix: Unable to open " << file.str() << ", is the directory correct?" << endl);
    933933      return false;
    934934    }
    … …  
    10141014  input.open(file.str().c_str(), ios::in);
    10151015  if (input == NULL) {
    1016     DoLog(0) && (Log() << Verbose(0) << endl << "Unable to open " << file.str() << ", is the directory correct?" << endl);
     1016    DoLog(0) && (Log() << Verbose(0) << endl << "KeySetsContainer::ParseKeySets: Unable to open " << file.str() << ", is the directory correct?" << endl);
    10171017    return false;
    10181018  }

  • src/periodentafel.cpp

    r60f50a r9757d9  
    88
    99#include <iomanip>
     10#include <iostream>
    1011#include <fstream>
    1112#include <cstring>
    12 #include <cassert>
    13 
     13
     14#include "Helpers/Assert.hpp"
    1415#include "element.hpp"
     16#include "elements_db.hpp"
    1517#include "helpers.hpp"
    1618#include "lists.hpp"
    … …  
    2729 */
    2830periodentafel::periodentafel()
    29 {};
     31{
     32  ASSERT(LoadElementsDatabase(new stringstream(elementsDB,ios_base::in)), "General element initialization failed");
     33  ASSERT(LoadValenceDatabase(new stringstream(valenceDB,ios_base::in)), "Valence entry of element initialization failed");
     34  ASSERT(LoadOrbitalsDatabase(new stringstream(orbitalsDB,ios_base::in)), "Orbitals entry of element initialization failed");
     35  ASSERT(LoadHBondAngleDatabase(new stringstream(HbondangleDB,ios_base::in)), "HBond angle entry of element initialization failed");
     36  ASSERT(LoadHBondLengthsDatabase(new stringstream(HbonddistanceDB,ios_base::in)), "HBond distance entry of element initialization failed");
     37};
    3038
    3139/** destructor for class periodentafel
    … …  
    3947/** Adds element to period table list
    4048 * \param *pointer element to be added
    41  * \return true - succeeded, false - does not occur
     49 * \return iterator to added element
    4250 */
    4351periodentafel::iterator periodentafel::AddElement(element * const pointer)
    4452{
    4553  atomicNumber_t Z = pointer->getNumber();
    46   assert(!elements.count(Z));
     54  ASSERT(!elements.count(Z), "Element is already present.");
    4755  pointer->sort = &pointer->Z;
    4856  if (pointer->getNumber() < 1 && pointer->getNumber() >= MAX_ELEMENTS)
    … …  
    5462/** Removes element from list.
    5563 * \param *pointer element to be removed
    56  * \return true - succeeded, false - element not found
    5764 */
    5865void periodentafel::RemoveElement(element * const pointer)
    5966{
    60   atomicNumber_t Z = pointer->getNumber();
     67  RemoveElement(pointer->getNumber());
     68};
     69
     70/** Removes element from list.
     71 * \param Z element to be removed
     72 */
     73void periodentafel::RemoveElement(atomicNumber_t Z)
     74{
    6175  elements.erase(Z);
    6276};
    6377
    6478/** Removes every element from the period table.
    65  * \return true - succeeded, false - does not occur
    6679 */
    6780void periodentafel::CleanupPeriodtable()
    … …  
    7891 * \return pointer to element or NULL if not found
    7992 */
    80 const element * periodentafel::FindElement(atomicNumber_t Z) const
     93element * const periodentafel::FindElement(atomicNumber_t Z) const
    8194{
    8295  const_iterator res = elements.find(Z);
    … …  
    89102 * \return pointer to element
    90103 */
    91 const element * periodentafel::FindElement(const char * const shorthand) const
     104element * const periodentafel::FindElement(const char * const shorthand) const
    92105{
    93106  element *res = 0;
    … …  
    102115
    103116/** Asks for element number and returns pointer to element
    104  */
    105 const element * periodentafel::AskElement() const
    106 {
    107   const element *walker = NULL;
     117 * \return desired element or NULL
     118 */
     119element * const periodentafel::AskElement() const
     120{
     121  element * walker = NULL;
    108122  int Z;
    109123  do {
    … …  
    118132 * \return pointer to either present or newly created element
    119133 */
    120 const element * periodentafel::EnterElement()
    121 {
    122   const element *res = NULL;
     134element * const periodentafel::EnterElement()
     135{
    123136  atomicNumber_t Z = 0;
    124137  DoLog(0) && (Log() << Verbose(0) << "Atomic number: " << Z << endl);
    125138  cin >> Z;
    126   res = FindElement(Z);
     139  element * const res = FindElement(Z);
    127140  if (!res) {
    128141    // TODO: make this using the constructor
    129     element *tmp;
    130142    DoLog(0) && (Log() << Verbose(0) << "Element not found in database, please enter." << endl);
    131     tmp = new element;
     143    element *tmp = new element;
    132144    tmp->Z = Z;
    133145    DoLog(0) && (Log() << Verbose(0) << "Mass: " << endl);
    … …  
    138150    cin >> tmp->symbol;
    139151    AddElement(tmp);
    140     res = tmp;
     152    return tmp;
    141153  }
    142154  return res;
    … …  
    204216bool periodentafel::LoadPeriodentafel(const char *path)
    205217{
    206   ifstream infile;
    207   element *ptr;
    208   map<atomicNumber_t,element*> parsedElems;
     218  ifstream input;
    209219  bool status = true;
    210220  bool otherstatus = true;
    … …  
    215225  strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
    216226  strncat(filename, STANDARDELEMENTSDB, MAXSTRINGSIZE-strlen(filename));
    217   infile.open(filename);
    218   if (infile != NULL) {
    219     infile.getline(header1, MAXSTRINGSIZE);
    220     infile.getline(header2, MAXSTRINGSIZE); // skip first two header lines
     227  input.open(filename);
     228  status = status && LoadElementsDatabase(&input);
     229
     230  // fill valence DB per element
     231  strncpy(filename, path, MAXSTRINGSIZE);
     232  strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
     233  strncat(filename, STANDARDVALENCEDB, MAXSTRINGSIZE-strlen(filename));
     234  input.open(filename);
     235  otherstatus = otherstatus && LoadValenceDatabase(&input);
     236
     237  // fill orbitals DB per element
     238  strncpy(filename, path, MAXSTRINGSIZE);
     239  strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
     240  strncat(filename, STANDARDORBITALDB, MAXSTRINGSIZE-strlen(filename));
     241  input.open(filename);
     242  otherstatus = otherstatus && LoadOrbitalsDatabase(&input);
     243
     244  // fill H-BondAngle DB per element
     245  strncpy(filename, path, MAXSTRINGSIZE);
     246  strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
     247  strncat(filename, STANDARDHBONDANGLEDB, MAXSTRINGSIZE-strlen(filename));
     248  input.open(filename);
     249  otherstatus = otherstatus && LoadHBondAngleDatabase(&input);
     250
     251  // fill H-BondDistance DB per element
     252  strncpy(filename, path, MAXSTRINGSIZE);
     253  strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
     254  strncat(filename, STANDARDHBONDDISTANCEDB, MAXSTRINGSIZE-strlen(filename));
     255  input.open(filename);
     256  otherstatus = otherstatus && LoadHBondLengthsDatabase(&input);
     257
     258  if (!otherstatus){
     259    DoeLog(2) && (eLog()<< Verbose(2) << "Something went wrong while parsing the other databases!" << endl);
     260  }
     261
     262  return status;
     263};
     264
     265/** load the element info.
     266 * \param *input stream to parse from
     267 * \return true - parsing successful, false - something went wrong
     268 */
     269bool periodentafel::LoadElementsDatabase(istream *input)
     270{
     271  if ((*input) != NULL) {
     272    (*input).getline(header1, MAXSTRINGSIZE);
     273    (*input).getline(header2, MAXSTRINGSIZE); // skip first two header lines
    221274    DoLog(0) && (Log() << Verbose(0) <<  "Parsed elements:");
    222     while (!infile.eof()) {
     275    while (!(*input).eof()) {
    223276      element *neues = new element;
    224       infile >> neues->name;
    225       //infile >> ws;
    226       infile >> neues->symbol;
    227       //infile >> ws;
    228       infile >> neues->period;
    229       //infile >> ws;
    230       infile >> neues->group;
    231       //infile >> ws;
    232       infile >> neues->block;
    233       //infile >> ws;
    234       infile >> neues->Z;
    235       //infile >> ws;
    236       infile >> neues->mass;
    237       //infile >> ws;
    238       infile >> neues->CovalentRadius;
    239       //infile >> ws;
    240       infile >> neues->VanDerWaalsRadius;
    241       //infile >> ws;
    242       infile >> ws;
     277      (*input) >> neues->name;
     278      //(*input) >> ws;
     279      (*input) >> neues->symbol;
     280      //(*input) >> ws;
     281      (*input) >> neues->period;
     282      //(*input) >> ws;
     283      (*input) >> neues->group;
     284      //(*input) >> ws;
     285      (*input) >> neues->block;
     286      //(*input) >> ws;
     287      (*input) >> neues->Z;
     288      //(*input) >> ws;
     289      (*input) >> neues->mass;
     290      //(*input) >> ws;
     291      (*input) >> neues->CovalentRadius;
     292      //(*input) >> ws;
     293      (*input) >> neues->VanDerWaalsRadius;
     294      //(*input) >> ws;
     295      (*input) >> ws;
    243296      DoLog(0) && (Log() << Verbose(0) << " " << neues->symbol);
     297      if (elements.count(neues->Z)) {// if element already present, remove and delete it
     298        element * const Elemental = FindElement(neues->Z);
     299        ASSERT(Elemental != NULL, "element should be present but is not??");
     300        RemoveElement(Elemental);
     301        delete(Elemental);
     302      }
    244303      //neues->Output((ofstream *)&cout);
    245304      if ((neues->Z > 0) && (neues->Z < MAX_ELEMENTS))
    246         parsedElems[neues->getNumber()] = neues;
     305        elements[neues->getNumber()] = neues;
    247306      else {
    248307        DoLog(0) && (Log() << Verbose(0) << "Could not parse element: ");
    … …  
    252311    }
    253312    DoLog(0) && (Log() << Verbose(0) << endl);
    254     infile.close();
    255     infile.clear();
    256   } else
    257     status = false;
    258 
    259   // fill valence DB per element
    260   strncpy(filename, path, MAXSTRINGSIZE);
    261   strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
    262   strncat(filename, STANDARDVALENCEDB, MAXSTRINGSIZE-strlen(filename));
    263   infile.open(filename);
    264   if (infile != NULL) {
    265     while (!infile.eof()) {
     313    return true;
     314  } else
     315    return false;
     316}
     317
     318/** load the valence info.
     319 * \param *input stream to parse from
     320 * \return true - parsing successful, false - something went wrong
     321 */
     322bool periodentafel::LoadValenceDatabase(istream *input)
     323{
     324  char dummy[MAXSTRINGSIZE];
     325  if ((*input) != NULL) {
     326    (*input).getline(dummy, MAXSTRINGSIZE);
     327    while (!(*input).eof()) {
    266328      atomicNumber_t Z;
    267       infile >> Z;
    268       infile >> ws;
    269       infile >> parsedElems[Z]->Valence;
    270       infile >> ws;
     329      (*input) >> Z;
     330      ASSERT(elements.count(Z), "Element not present");
     331      (*input) >> ws;
     332      (*input) >> elements[Z]->Valence;
     333      (*input) >> ws;
    271334      //Log() << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->Valence << " valence electrons." << endl;
    272335    }
    273     infile.close();
    274     infile.clear();
    275   } else
    276     otherstatus = false;
    277 
    278   // fill valence DB per element
    279   strncpy(filename, path, MAXSTRINGSIZE);
    280   strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
    281   strncat(filename, STANDARDORBITALDB, MAXSTRINGSIZE-strlen(filename));
    282   infile.open(filename);
    283   if (infile != NULL) {
    284     while (!infile.eof()) {
     336    return true;
     337  } else
     338                return false;
     339}
     340
     341/** load the orbitals info.
     342 * \param *input stream to parse from
     343 * \return true - parsing successful, false - something went wrong
     344 */
     345bool periodentafel::LoadOrbitalsDatabase(istream *input)
     346{
     347  char dummy[MAXSTRINGSIZE];
     348  if ((*input) != NULL) {
     349    (*input).getline(dummy, MAXSTRINGSIZE);
     350    while (!(*input).eof()) {
    285351      atomicNumber_t Z;
    286       infile >> Z;
    287       infile >> ws;
    288       infile >> parsedElems[Z]->NoValenceOrbitals;
    289       infile >> ws;
     352      (*input) >> Z;
     353      ASSERT(elements.count(Z), "Element not present");
     354      (*input) >> ws;
     355      (*input) >> elements[Z]->NoValenceOrbitals;
     356      (*input) >> ws;
    290357      //Log() << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->NoValenceOrbitals << " number of singly occupied valence orbitals." << endl;
    291358    }
    292     infile.close();
    293     infile.clear();
    294   } else
    295     otherstatus = false;
    296 
    297   // fill H-BondDistance DB per element
    298   strncpy(filename, path, MAXSTRINGSIZE);
    299   strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
    300   strncat(filename, STANDARDHBONDDISTANCEDB, MAXSTRINGSIZE-strlen(filename));
    301   infile.open(filename);
    302   if (infile != NULL) {
    303     while (!infile.eof()) {
     359    return true;
     360  } else
     361    return false;
     362}
     363
     364/** load the hbond angles info.
     365 * \param *input stream to parse from
     366 * \return true - parsing successful, false - something went wrong
     367 */
     368bool periodentafel::LoadHBondAngleDatabase(istream *input)
     369{
     370  char dummy[MAXSTRINGSIZE];
     371  if ((*input) != NULL) {
     372    (*input).getline(dummy, MAXSTRINGSIZE);
     373    while (!(*input).eof()) {
    304374      atomicNumber_t Z;
    305       infile >> Z;
    306       ptr = parsedElems[Z];
    307       infile >> ws;
    308       infile >> ptr->HBondDistance[0];
    309       infile >> ptr->HBondDistance[1];
    310       infile >> ptr->HBondDistance[2];
    311       infile >> ws;
     375      (*input) >> Z;
     376      ASSERT(elements.count(Z), "Element not present");
     377      (*input) >> ws;
     378      (*input) >> elements[Z]->HBondAngle[0];
     379      (*input) >> elements[Z]->HBondAngle[1];
     380      (*input) >> elements[Z]->HBondAngle[2];
     381      (*input) >> ws;
     382      //Log() << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->HBondAngle[0] << ", " << FindElement((int)tmp)->HBondAngle[1] << ", " << FindElement((int)tmp)->HBondAngle[2] << " degrees bond angle for one, two, three connected hydrogens." << endl;
     383    }
     384    return true;
     385  } else
     386                return false;
     387}
     388
     389/** load the hbond lengths info.
     390 * \param *input stream to parse from
     391 * \return true - parsing successful, false - something went wrong
     392 */
     393bool periodentafel::LoadHBondLengthsDatabase(istream *input)
     394{
     395  char dummy[MAXSTRINGSIZE];
     396  if ((*input) != NULL) {
     397    (*input).getline(dummy, MAXSTRINGSIZE);
     398    while (!(*input).eof()) {
     399      atomicNumber_t Z;
     400      (*input) >> Z;
     401      ASSERT(elements.count(Z), "Element not present");
     402      (*input) >> ws;
     403      (*input) >> elements[Z]->HBondDistance[0];
     404      (*input) >> elements[Z]->HBondDistance[1];
     405      (*input) >> elements[Z]->HBondDistance[2];
     406      (*input) >> ws;
    312407      //Log() << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->HBondDistance[0] << " Angstrom typical distance to hydrogen." << endl;
    313408    }
    314     infile.close();
    315     infile.clear();
    316   } else
    317     otherstatus = false;
    318 
    319   // fill H-BondAngle DB per element
    320   strncpy(filename, path, MAXSTRINGSIZE);
    321   strncat(filename, "/", MAXSTRINGSIZE-strlen(filename));
    322   strncat(filename, STANDARDHBONDANGLEDB, MAXSTRINGSIZE-strlen(filename));
    323   infile.open(filename);
    324   if (infile != NULL) {
    325     while (!infile.eof()) {
    326       atomicNumber_t Z;
    327       infile >> Z;
    328       ptr = parsedElems[Z];
    329       infile >> ws;
    330       infile >> ptr->HBondAngle[0];
    331       infile >> ptr->HBondAngle[1];
    332       infile >> ptr->HBondAngle[2];
    333       infile >> ws;
    334       //Log() << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->HBondAngle[0] << ", " << FindElement((int)tmp)->HBondAngle[1] << ", " << FindElement((int)tmp)->HBondAngle[2] << " degrees bond angle for one, two, three connected hydrogens." << endl;
    335     }
    336     infile.close();
    337   } else
    338     otherstatus = false;
    339 
    340   if (otherstatus){
    341     map<atomicNumber_t,element*>::iterator iter;
    342     for(iter=parsedElems.begin();iter!=parsedElems.end();++iter){
    343       AddElement((*iter).second);
    344     }
    345   }
    346   else{
    347     DoeLog(2) && (eLog()<< Verbose(2) << "Something went wrong while parsing the other databases!" << endl);
    348     map<atomicNumber_t,element*>::iterator iter;
    349     for(iter=parsedElems.begin();iter!=parsedElems.end();++iter){
    350       AddElement((*iter).second);
    351     }
    352   }
    353 
    354   return status;
    355 };
     409    return true;
     410  } else
     411                return false;
     412}
    356413
    357414/** Stores element list to file.
    … …  
    374431    }
    375432    f.close();
    376   } else
    377     result = false;
    378   return result;
    379 };
     433    return true;
     434  } else
     435    return result;
     436};

  • src/periodentafel.hpp

    r60f50a r9757d9  
    1313#include <iterator>
    1414
     15#include "unittests/periodentafelTest.hpp"
    1516#include "defs.hpp"
    1617#include "types.hpp"
    … …  
    2728class periodentafel {
    2829  /******* Types *********/
     30  friend class periodentafelTest;
    2931  private:
    3032    typedef std::map<atomicNumber_t,element*> elementSet;
    … …  
    4345  iterator AddElement(element * const pointer);
    4446  void RemoveElement(element * const pointer);
     47  void RemoveElement(atomicNumber_t);
    4548  void CleanupPeriodtable();
    46   const element *FindElement(atomicNumber_t) const;
    47   const element *FindElement(const char * const shorthand) const;
    48   const element *AskElement() const;
    49   const element *EnterElement();
     49  element * const FindElement(atomicNumber_t) const;
     50  element * const FindElement(const char * const shorthand) const;
     51  element * const AskElement() const;
     52  element * const EnterElement();
    5053
    5154  const_iterator begin();
    … …  
    5962
    6063  private:
     64
     65  bool LoadElementsDatabase(std::istream *input);
     66  bool LoadValenceDatabase(std::istream *input);
     67  bool LoadOrbitalsDatabase(std::istream *input);
     68  bool LoadHBondAngleDatabase(std::istream *input);
     69  bool LoadHBondLengthsDatabase(std::istream *input);
     70
    6171    elementSet elements;
    6272};

  • src/tesselation.cpp

    r60f50a r9757d9  
    8383ostream & operator <<(ostream &ost, const BoundaryPointSet &a)
    8484{
    85   ost << "[" << a.Nr << "|" << a.node->Name << " at " << *a.node->node << "]";
     85  ost << "[" << a.Nr << "|" << a.node->getName() << " at " << *a.node->node << "]";
    8686  return ost;
    8787}
    … …  
    321321ostream & operator <<(ostream &ost, const BoundaryLineSet &a)
    322322{
    323   ost << "[" << a.Nr << "|" << a.endpoints[0]->node->Name << " at " << *a.endpoints[0]->node->node << "," << a.endpoints[1]->node->Name << " at " << *a.endpoints[1]->node->node << "]";
     323  ost << "[" << a.Nr << "|" << a.endpoints[0]->node->getName() << " at " << *a.endpoints[0]->node->node << "," << a.endpoints[1]->node->getName() << " at " << *a.endpoints[1]->node->node << "]";
    324324  return ost;
    325325}
    … …  
    688688ostream &operator <<(ostream &ost, const BoundaryTriangleSet &a)
    689689{
    690   ost << "[" << a.Nr << "|" << a.endpoints[0]->node->Name << "," << a.endpoints[1]->node->Name << "," << a.endpoints[2]->node->Name << "]";
     690  ost << "[" << a.Nr << "|" << a.endpoints[0]->node->getName() << "," << a.endpoints[1]->node->getName() << "," << a.endpoints[2]->node->getName() << "]";
    691691  //  ost << "[" << a.Nr << "|" << a.endpoints[0]->node->Name << " at " << *a.endpoints[0]->node->node << ","
    692692  //      << a.endpoints[1]->node->Name << " at " << *a.endpoints[1]->node->node << "," << a.endpoints[2]->node->Name << " at " << *a.endpoints[2]->node->node << "]";
    … …  
    948948  ost << "[" << a.Nr << "|";
    949949  for (PointSet::const_iterator Runner = a.endpoints.begin(); Runner != a.endpoints.end();) {
    950     ost << (*Runner)->node->Name;
     950    ost << (*Runner)->node->getName();
    951951    Runner++;
    952952    if (Runner != a.endpoints.end())
    … …  
    967967  node = NULL;
    968968  nr = -1;
    969   Name = NULL;
    970969}
    971970;
    … …  
    983982ostream & operator <<(ostream &ost, const TesselPoint &a)
    984983{
    985   ost << "[" << (a.Name) << "|" << a.Name << " at " << *a.node << "]";
     984  ost << "[" << a.getName() << "|" << *a.node << "]";
    986985  return ost;
    987986}
    … …  
    11351134ostream & operator <<(ostream &ost, const CandidateForTesselation &a)
    11361135{
    1137   ost << "[" << a.BaseLine->Nr << "|" << a.BaseLine->endpoints[0]->node->Name << "," << a.BaseLine->endpoints[1]->node->Name << "] with ";
     1136  ost << "[" << a.BaseLine->Nr << "|" << a.BaseLine->endpoints[0]->node->getName() << "," << a.BaseLine->endpoints[1]->node->getName() << "] with ";
    11381137  if (a.pointlist.empty())
    11391138    ost << "no candidate.";
    … …  
    13481347      if (fabs(distance) < 1e-4) // we need to have a small epsilon around 0 which is still ok
    13491348        continue;
    1350       DoLog(2) && (Log() << Verbose(2) << "Projection of " << checker->second->node->Name << " yields distance of " << distance << "." << endl);
     1349      DoLog(2) && (Log() << Verbose(2) << "Projection of " << checker->second->node->getName() << " yields distance of " << distance << "." << endl);
    13511350      tmp = distance / fabs(distance);
    13521351      // 4b. Any have different sign to than before? (i.e. would lie outside convex hull with this starting triangle)
    13531352      if ((sign != 0) && (tmp != sign)) {
    13541353        // 4c. If so, break 4. loop and continue with next candidate in 1. loop
    1355         DoLog(2) && (Log() << Verbose(2) << "Current candidates: " << A->second->node->Name << "," << baseline->second.first->second->node->Name << "," << baseline->second.second->second->node->Name << " leaves " << checker->second->node->Name << " outside the convex hull." << endl);
     1354        DoLog(2) && (Log() << Verbose(2) << "Current candidates: " << A->second->node->getName() << "," << baseline->second.first->second->node->getName() << "," << baseline->second.second->second->node->getName() << " leaves " << checker->second->node->getName() << " outside the convex hull." << endl);
    13561355        break;
    13571356      } else { // note the sign for later
    1358         DoLog(2) && (Log() << Verbose(2) << "Current candidates: " << A->second->node->Name << "," << baseline->second.first->second->node->Name << "," << baseline->second.second->second->node->Name << " leave " << checker->second->node->Name << " inside the convex hull." << endl);
     1357        DoLog(2) && (Log() << Verbose(2) << "Current candidates: " << A->second->node->getName() << "," << baseline->second.first->second->node->getName() << "," << baseline->second.second->second->node->getName() << " leave " << checker->second->node->getName() << " inside the convex hull." << endl);
    13591358        sign = tmp;
    13601359      }
    … …  
    42924291        DoLog(2) && (Log() << Verbose(2) << "INFO: MiddleNode is " << **MiddleNode << "." << endl);
    42934292        DoLog(2) && (Log() << Verbose(2) << "INFO: EndNode is " << **EndNode << "." << endl);
    4294         DoLog(1) && (Log() << Verbose(1) << "INFO: Attempting to create triangle " << (*StartNode)->Name << ", " << (*MiddleNode)->Name << " and " << (*EndNode)->Name << "." << endl);
     4293        DoLog(1) && (Log() << Verbose(1) << "INFO: Attempting to create triangle " << (*StartNode)->getName() << ", " << (*MiddleNode)->getName() << " and " << (*EndNode)->getName() << "." << endl);
    42954294        TriangleCandidates[0] = *StartNode;
    42964295        TriangleCandidates[1] = *MiddleNode;
    … …  
    47144713    return;
    47154714  }
    4716   DoLog(0) && (Log() << Verbose(0) << "Nearest point on boundary is " << NearestPoint->Name << "." << endl);
     4715  DoLog(0) && (Log() << Verbose(0) << "Nearest point on boundary is " << NearestPoint->getName() << "." << endl);
    47174716
    47184717  // go through its lines and find the best one to split
    … …  
    47994798  ofstream *tempstream = NULL;
    48004799  string NameofTempFile;
    4801   char NumberName[255];
     4800  string NumberName;
    48024801
    48034802  if (LastTriangle != NULL) {
    4804     sprintf(NumberName, "-%04d-%s_%s_%s", (int) TrianglesOnBoundary.size(), LastTriangle->endpoints[0]->node->Name, LastTriangle->endpoints[1]->node->Name, LastTriangle->endpoints[2]->node->Name);
     4803    stringstream sstr;
     4804    sstr << "-"<< TrianglesOnBoundary.size() << "-" << LastTriangle->endpoints[0]->node->getName() << "_" << LastTriangle->endpoints[1]->node->getName() << "_" << LastTriangle->endpoints[2]->node->getName();
     4805    NumberName = sstr.str();
    48054806    if (DoTecplotOutput) {
    48064807      string NameofTempFile(filename);

  • src/tesselationhelpers.cpp

    r60f50a r9757d9  
    829829      if (TesselStruct->LastTriangle != NULL) {
    830830        for (int i=0;i<3;i++)
    831           *tecplot << (i==0 ? "" : "_") << TesselStruct->LastTriangle->endpoints[i]->node->Name;
     831          *tecplot << (i==0 ? "" : "_") << TesselStruct->LastTriangle->endpoints[i]->node->getName();
    832832      } else {
    833833        *tecplot << "none";
    … …  
    852852    DoLog(1) && (Log() << Verbose(1) << "The following triangles were created:" << endl);
    853853    for (TriangleMap::const_iterator runner = TesselStruct->TrianglesOnBoundary.begin(); runner != TesselStruct->TrianglesOnBoundary.end(); runner++) {
    854       DoLog(1) && (Log() << Verbose(1) << " " << runner->second->endpoints[0]->node->Name << "<->" << runner->second->endpoints[1]->node->Name << "<->" << runner->second->endpoints[2]->node->Name << endl);
     854      DoLog(1) && (Log() << Verbose(1) << " " << runner->second->endpoints[0]->node->getName() << "<->" << runner->second->endpoints[1]->node->getName() << "<->" << runner->second->endpoints[2]->node->getName() << endl);
    855855      *tecplot << LookupList[runner->second->endpoints[0]->node->nr] << " " << LookupList[runner->second->endpoints[1]->node->nr] << " " << LookupList[runner->second->endpoints[2]->node->nr] << endl;
    856856    }

  • src/unittests/AnalysisCorrelationToPointUnitTest.cpp

    r60f50a r9757d9  
    1717#include "AnalysisCorrelationToPointUnitTest.hpp"
    1818
    19 #include "World.hpp"
    2019#include "atom.hpp"
    21 #include "boundary.hpp"
    2220#include "element.hpp"
    2321#include "molecule.hpp"
    2422#include "linkedcell.hpp"
    2523#include "periodentafel.hpp"
    26 #include "tesselation.hpp"
    2724#include "World.hpp"
    2825
    … …  
    4340  TestList = NULL;
    4441  TestMolecule = NULL;
    45   hydrogen = NULL;
    46   tafel = NULL;
    4742  pointmap = NULL;
    4843  binmap = NULL;
    4944  point = NULL;
    5045
    51   // construct element
    52   hydrogen = new element;
    53   hydrogen->Z = 1;
    54   strcpy(hydrogen->name, "hydrogen");
    55   strcpy(hydrogen->symbol, "H");
    56 
    57 
    58   // construct periodentafel
    59   tafel = World::getInstance().getPeriode();
    60   tafel->AddElement(hydrogen);
    61 
    6246  // construct molecule (tetraeder of hydrogens)
     47  hydrogen = World::getInstance().getPeriode()->FindElement(1);
     48  CPPUNIT_ASSERT(hydrogen != NULL && "hydrogen element not found");
    6349  TestMolecule = World::getInstance().createMolecule();
    6450  Walker = World::getInstance().createAtom();

  • src/unittests/AnalysisCorrelationToPointUnitTest.hpp

    r60f50a r9757d9  
    1212
    1313class element;
    14 class LinkedCell;
    1514class molecule;
    1615class MoleculeListClass;
    17 class periodentafel;
    18 class Tesselation;
    1916class Vector;
    2017
    … …  
    4037      MoleculeListClass *TestList;
    4138      molecule *TestMolecule;
    42       element *hydrogen;
    43       periodentafel *tafel;
     39      const element *hydrogen;
    4440
    4541      CorrelationToPointMap *pointmap;

  • src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp

    r60f50a r9757d9  
    1717#include "AnalysisCorrelationToSurfaceUnitTest.hpp"
    1818
    19 #include "World.hpp"
    2019#include "atom.hpp"
    2120#include "boundary.hpp"
    … …  
    4746  TestList = NULL;
    4847  TestSurfaceMolecule = NULL;
    49   hydrogen = NULL;
    50   tafel = NULL;
    5148  surfacemap = NULL;
    5249  binmap = NULL;
    … …  
    5451  LC = NULL;
    5552
    56   // construct element
    57   hydrogen = new element;
    58   hydrogen->Z = 1;
    59   strcpy(hydrogen->name, "hydrogen");
    60   strcpy(hydrogen->symbol, "H");
    61   carbon = new element;
    62   carbon->Z = 6;
    63   strcpy(carbon->name, "carbon");
    64   strcpy(carbon->symbol, "C");
    65 
    66   // construct periodentafel
    67   tafel = World::getInstance().getPeriode();
    68   tafel->AddElement(hydrogen);
    69   tafel->AddElement(carbon);
    70 
    7153  // construct molecule (tetraeder of hydrogens) base
     54  hydrogen = World::getInstance().getPeriode()->FindElement(1);
    7255  TestSurfaceMolecule = World::getInstance().createMolecule();
    7356  Walker = World::getInstance().createAtom();
    … …  
    10285
    10386  // add outer atoms
     87  carbon = World::getInstance().getPeriode()->FindElement(6);
    10488  TestSurfaceMolecule = World::getInstance().createMolecule();
    10589  Walker = World::getInstance().createAtom();

  • src/unittests/AnalysisCorrelationToSurfaceUnitTest.hpp

    r60f50a r9757d9  
    4545      MoleculeListClass *TestList;
    4646      molecule *TestSurfaceMolecule;
    47       element *hydrogen;
    48       element *carbon;
    49       periodentafel *tafel;
     47      const element *hydrogen;
     48      const element *carbon;
    5049
    5150      CorrelationToSurfaceMap *surfacemap;

  • src/unittests/AnalysisPairCorrelationUnitTest.cpp

    r60f50a r9757d9  
    4444  TestList = NULL;
    4545  TestMolecule = NULL;
    46   hydrogen = NULL;
    47   tafel = NULL;
    4846  correlationmap = NULL;
    4947  binmap = NULL;
    5048
    51   // construct element
    52   hydrogen = new element;
    53   hydrogen->Z = 1;
    54   strcpy(hydrogen->name, "hydrogen");
    55   strcpy(hydrogen->symbol, "H");
    56 
    57   // construct periodentafel
    58   tafel = World::getInstance().getPeriode();
    59   tafel->AddElement(hydrogen);
    60 
    6149  // construct molecule (tetraeder of hydrogens)
     50  hydrogen = World::getInstance().getPeriode()->FindElement(1);
    6251  TestMolecule = World::getInstance().createMolecule();
    6352  Walker = World::getInstance().createAtom();

  • src/unittests/AnalysisPairCorrelationUnitTest.hpp

    r60f50a r9757d9  
    1212
    1313class element;
    14 class LinkedCell;
    1514class molecule;
    1615class MoleculeListClass;
    17 class periodentafel;
    18 class Tesselation;
    1916class Vector;
    2017
    … …  
    4037      MoleculeListClass *TestList;
    4138      molecule *TestMolecule;
    42       element *hydrogen;
    43       periodentafel *tafel;
     39      const element *hydrogen;
    4440
    4541      PairCorrelationMap *correlationmap;

  • src/unittests/CountBondsUnitTest.cpp

    r60f50a r9757d9  
    1616#include <stdio.h>
    1717#include <cstring>
     18
     19#include "Helpers/Assert.hpp"
    1820
    1921#include "analysis_bonds.hpp"
    … …  
    4042{
    4143  atom *Walker = NULL;
    42   BG = NULL;
    43   filename = NULL;
    44 
    45   // init private all pointers to zero
    46   molecules = NULL;
    47   TestMolecule1 = NULL;
    48   TestMolecule2 = NULL;
    49   hydrogen = NULL;
    50   oxygen = NULL;
    51   tafel = NULL;
    5244
    5345  // construct element
    54   hydrogen = new element;
    55   hydrogen->Z = 1;
    56   hydrogen->CovalentRadius = 0.23;
    57   strcpy(hydrogen->name, "hydrogen");
    58   strcpy(hydrogen->symbol, "H");
    59   oxygen = new element;
    60   oxygen->Z = 8;
    61   oxygen->CovalentRadius = 0.68;
    62   strcpy(oxygen->name, "oxygen");
    63   strcpy(oxygen->symbol, "O");
    64 
    65   // construct periodentafel
    66   tafel = World::getInstance().getPeriode();
    67   tafel->AddElement(hydrogen);
    68   tafel->AddElement(oxygen);
     46  hydrogen = World::getInstance().getPeriode()->FindElement(1);
     47  oxygen = World::getInstance().getPeriode()->FindElement(8);
     48  CPPUNIT_ASSERT(hydrogen != NULL && "could not find element hydrogen");
     49  CPPUNIT_ASSERT(oxygen != NULL && "could not find element oxygen");
    6950
    7051  // construct molecule (water molecule)
    7152  TestMolecule1 = World::getInstance().createMolecule();
    72   Walker = World::getInstance().createAtom();
     53  CPPUNIT_ASSERT(TestMolecule1 != NULL && "could not create first molecule");
     54  Walker = World::getInstance().createAtom();
     55  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
    7356  Walker->type = hydrogen;
    7457  *Walker->node = Vector(-0.2418, 0.9350, 0. );
    7558  TestMolecule1->AddAtom(Walker);
    7659  Walker = World::getInstance().createAtom();
     60  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
    7761  Walker->type = hydrogen;
    7862  *Walker->node = Vector(0.9658, 0., 0. );
    7963  TestMolecule1->AddAtom(Walker);
    8064  Walker = World::getInstance().createAtom();
     65  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
    8166  Walker->type = oxygen;
    8267  *Walker->node = Vector(0., 0., 0. );
    … …  
    8469
    8570  TestMolecule2 = World::getInstance().createMolecule();
    86   Walker = World::getInstance().createAtom();
     71  CPPUNIT_ASSERT(TestMolecule2 != NULL && "could not create second molecule");
     72  Walker = World::getInstance().createAtom();
     73  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
    8774  Walker->type = hydrogen;
    8875  *Walker->node = Vector(-0.2418, 0.9350, 0. );
    8976  TestMolecule2->AddAtom(Walker);
    9077  Walker = World::getInstance().createAtom();
     78  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
    9179  Walker->type = hydrogen;
    9280  *Walker->node = Vector(0.9658, 0., 0. );
    9381  TestMolecule2->AddAtom(Walker);
    9482  Walker = World::getInstance().createAtom();
     83  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
    9584  Walker->type = oxygen;
    9685  *Walker->node = Vector(0., 0., 0. );
    … …  
    9887
    9988  molecules = World::getInstance().getMolecules();
     89  CPPUNIT_ASSERT(molecules != NULL && "could not obtain list of molecules");
    10090  molecules->insert(TestMolecule1);
    10191  molecules->insert(TestMolecule2);
    … …  
    111101  // create a small file with table
    112102  BG = new BondGraph(true);
     103  CPPUNIT_ASSERT(BG != NULL && "could not create BondGraph");
    113104
    114105  // construct bond graphs
    … …  
    158149{
    159150  double *mirror = new double[3];
     151  CPPUNIT_ASSERT(mirror != NULL && "could not create array of doubles");
    160152  for (int i=0;i<3;i++)
    161153    mirror[i] = -1.;

  • src/unittests/CountBondsUnitTest.hpp

    r60f50a r9757d9  
    3939      molecule *TestMolecule1;
    4040      molecule *TestMolecule2;
    41       element *hydrogen;
    42       element *oxygen;
    43       periodentafel *tafel;
     41      const element *hydrogen;
     42      const element *oxygen;
    4443
    4544      BondGraph *BG;

  • src/unittests/LinkedCellUnitTest.cpp

    r60f50a r9757d9  
    3838  atom *Walker = NULL;
    3939
    40   // init private all pointers to zero
    41   TestMolecule = NULL;
    42   hydrogen = NULL;
    43   tafel = NULL;
    44 
    4540  // construct element
    46   hydrogen = new element;
    47   hydrogen->Z = 1;
    48   hydrogen->CovalentRadius = 0.23;
    49   strcpy(hydrogen->name, "hydrogen");
    50   strcpy(hydrogen->symbol, "H");
    51 
    52   // construct periodentafel
    53   tafel = World::getInstance().getPeriode();
    54   tafel->AddElement(hydrogen);
     41  hydrogen = World::getInstance().getPeriode()->FindElement(1);
     42  CPPUNIT_ASSERT(hydrogen != NULL && "could not find element hydrogen");
    5543
    5644  // construct molecule (water molecule)
    5745  TestMolecule = World::getInstance().createMolecule();
     46  CPPUNIT_ASSERT(TestMolecule != NULL && "could not create molecule");
    5847  for (double x=0.5;x<3;x+=1.)
    5948    for (double y=0.5;y<3;y+=1.)
    6049      for (double z=0.5;z<3;z+=1.) {
    6150        Walker = World::getInstance().createAtom();
     51        CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
    6252        Walker->type = hydrogen;
    6353        *Walker->node = Vector(x, y, z );
    … …  
    6757  // construct linked cell
    6858  LC = new LinkedCell (TestMolecule, 1.);
     59  CPPUNIT_ASSERT(LC != NULL && "could not create LinkedCell");
    6960
    7061  // check that TestMolecule was correctly constructed
    … …  
    205196  // check internal vectors, returns false, because this atom is not in LC-list!
    206197  Walker = World::getInstance().createAtom();
    207   Walker->Name = Malloc<char>(6, "LinkedCellTest::SetIndexToNodeTest - Walker");
    208   strcpy(Walker->Name, "test");
     198  Walker->setName("test");
    209199  Walker->x= Vector(1,1,1);
    210200  CPPUNIT_ASSERT_EQUAL( false, LC->SetIndexToNode(Walker) );
    … …  
    213203  // check out of bounds vectors
    214204  Walker = World::getInstance().createAtom();
    215   Walker->Name = Malloc<char>(6, "LinkedCellTest::SetIndexToNodeTest - Walker");
    216   strcpy(Walker->Name, "test");
     205  Walker->setName("test");
    217206  Walker->x = Vector(0,-1,0);
    218207  CPPUNIT_ASSERT_EQUAL( false, LC->SetIndexToNode(Walker) );

  • src/unittests/LinkedCellUnitTest.hpp

    r60f50a r9757d9  
    4848
    4949      molecule *TestMolecule;
    50       element *hydrogen;
    51       periodentafel *tafel;
     50      const element *hydrogen;
    5251      LinkedCell *LC;
    5352};

  • src/unittests/Makefile.am

    r60f50a r9757d9  
    3333  MemoryAllocatorUnitTest \
    3434  MoleculeDescriptorTest \
    35   PlaneUnittest \
    3635  ObserverTest \
    3736  ParserUnitTest \
     37  periodentafelTest \
     38  PlaneUnittest \
    3839  SingletonTest \
    3940  StackClassUnitTest \
    … …  
    7576  memoryusageobserverunittest.cpp \
    7677  MoleculeDescriptorTest.cpp \
    77   PlaneUnittest.cpp \
    7878  ObserverTest.cpp \
    7979  ParserUnitTest.cpp \
     80  periodentafelTest.cpp \
     81  PlaneUnittest.cpp \
    8082  SingletonTest.cpp \
    8183  stackclassunittest.cpp \
    … …  
    109111  memoryusageobserverunittest.hpp \
    110112  MoleculeDescriptorTest.hpp \
     113  periodentafelTest.hpp \
    111114  PlaneUnittest.hpp \
    112115  ObserverTest.hpp \
    … …  
    194197ParserUnitTest_LDADD = ${ALLLIBS}
    195198
     199periodentafelTest_SOURCES = UnitTestMain.cpp periodentafelTest.cpp periodentafelTest.hpp
     200periodentafelTest_LDADD = ${ALLLIBS}
     201
    196202PlaneUnittest_SOURCES = UnitTestMain.cpp PlaneUnittest.cpp PlaneUnittest.hpp
    197203PlaneUnittest_LDADD = ${ALLLIBS}

  • src/unittests/ParserUnitTest.cpp

    r60f50a r9757d9  
    3131
    3232void ParserUnitTest::setUp() {
    33   element* oxygen = new element();
    34   oxygen->symbol[0] = 'O';
    35   oxygen->Z = 8;
    36   World::getInstance().getPeriode()->AddElement(oxygen);
    37 
    38   element* hydrogen = new element();
    39   hydrogen->symbol[0] = 'H';
    40   hydrogen->Z = 1;
    41   World::getInstance().getPeriode()->AddElement(hydrogen);
     33  World::getInstance();
    4234}
    4335

  • src/unittests/analysisbondsunittest.cpp

    r60f50a r9757d9  
    4040  atom *Walker = NULL;
    4141
    42   // init private all pointers to zero
    43   TestMolecule = NULL;
    44   hydrogen = NULL;
    45   tafel = NULL;
    46 
    47   // construct element
    48   hydrogen = new element;
    49   hydrogen->Z = 1;
    50   hydrogen->Valence = 1;
    51   hydrogen->NoValenceOrbitals = 1;
    52   strcpy(hydrogen->name, "hydrogen");
    53   strcpy(hydrogen->symbol, "H");
    54   carbon = new element;
    55   carbon->Z = 2;
    56   carbon->Valence = 4;
    57   carbon->NoValenceOrbitals = 4;
    58   strcpy(carbon->name, "carbon");
    59   strcpy(carbon->symbol, "C");
    60 
    61 
    62   // construct periodentafel
    63   tafel = World::getInstance().getPeriode();
    64   tafel->AddElement(hydrogen);
    65   tafel->AddElement(carbon);
     42  // get elements
     43  hydrogen = World::getInstance().getPeriode()->FindElement(1);
     44  carbon = World::getInstance().getPeriode()->FindElement(6);
     45  CPPUNIT_ASSERT(hydrogen != NULL && "could not find element hydrogen");
     46  CPPUNIT_ASSERT(carbon != NULL && "could not find element carbon");
    6647
    6748  // construct molecule (tetraeder of hydrogens)
    6849  TestMolecule = World::getInstance().createMolecule();
     50  CPPUNIT_ASSERT(TestMolecule != NULL && "could not create molecule");
    6951  Walker = World::getInstance().createAtom();
     52  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
    7053  Walker->type = hydrogen;
    7154  *Walker->node = Vector(1.5, 0., 1.5 );
    7255  TestMolecule->AddAtom(Walker);
    7356  Walker = World::getInstance().createAtom();
     57  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
    7458  Walker->type = hydrogen;
    7559  *Walker->node = Vector(0., 1.5, 1.5 );
    7660  TestMolecule->AddAtom(Walker);
    7761  Walker = World::getInstance().createAtom();
     62  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
    7863  Walker->type = hydrogen;
    7964  *Walker->node = Vector(1.5, 1.5, 0. );
    8065  TestMolecule->AddAtom(Walker);
    8166  Walker = World::getInstance().createAtom();
     67  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
    8268  Walker->type = hydrogen;
    8369  *Walker->node = Vector(0., 0., 0. );
    8470  TestMolecule->AddAtom(Walker);
    8571  Walker = World::getInstance().createAtom();
     72  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
    8673  Walker->type = carbon;
    8774  *Walker->node = Vector(0.5, 0.5, 0.5 );
    … …  
    9380  // create a small file with table
    9481  filename = new string("test.dat");
     82  CPPUNIT_ASSERT(filename != NULL && "could not create string");
    9583  ofstream test(filename->c_str());
    96   test << ".\tH\tC\n";
    97   test << "H\t1.\t1.2\n";
    98   test << "C\t1.2\t1.5\n";
     84  test << ".\tH\tHe\tLi\tBe\tB\tC\n";
     85  test << "H\t1.\t1.\t1.\t1.\t1.\t1.2\n";
     86  test << "He\t1.\t1.\t1.\t1.\t1.\t1.\n";
     87  test << "Li\t1.\t1.\t1.\t1.\t1.\t1.\n";
     88  test << "Be\t1.\t1.\t1.\t1.\t1.\t1.\n";
     89  test << "B\t1.\t1.\t1.\t1.\t1.\t1.\n";
     90  test << "C\t1.2\t1.\t1.\t1.\t1.\t1.5\n";
    9991  test.close();
    10092  BG = new BondGraph(true);
     93  CPPUNIT_ASSERT(BG != NULL && "could not create BondGraph");
    10194
    10295  CPPUNIT_ASSERT_EQUAL( true , BG->LoadBondLengthTable(*filename) );
    10396  CPPUNIT_ASSERT_EQUAL( 1., BG->GetBondLength(0,0) );
    104   CPPUNIT_ASSERT_EQUAL( 1.2, BG->GetBondLength(0,1) );
    105   CPPUNIT_ASSERT_EQUAL( 1.5, BG->GetBondLength(1,1) );
     97  CPPUNIT_ASSERT_EQUAL( 1.2, BG->GetBondLength(0,5) );
     98  CPPUNIT_ASSERT_EQUAL( 1.5, BG->GetBondLength(5,5) );
    10699
    107100  BG->ConstructBondGraph(TestMolecule);

  • src/unittests/analysisbondsunittest.hpp

    r60f50a r9757d9  
    3434
    3535      molecule *TestMolecule;
    36       element *hydrogen;
    37       element *carbon;
    38       periodentafel *tafel;
     36      const element *hydrogen;
     37      const element *carbon;
    3938
    4039      BondGraph *BG;

  • src/unittests/bondgraphunittest.cpp

    r60f50a r9757d9  
    1515#include <stdio.h>
    1616#include <cstring>
     17
     18#include "Helpers/Assert.hpp"
    1719
    1820#include "World.hpp"
    … …  
    4143  atom *Walker = NULL;
    4244
    43   // init private all pointers to zero
    44   TestMolecule = NULL;
    45   hydrogen = NULL;
    46   tafel = NULL;
    47 
    4845  // construct element
    49   hydrogen = new element;
    50   hydrogen->Z = 1;
    51   hydrogen->CovalentRadius = 0.23;
    52   hydrogen->VanDerWaalsRadius = 1.09;
    53   strcpy(hydrogen->name, "hydrogen");
    54   strcpy(hydrogen->symbol, "H");
    55   carbon = new element;
    56   carbon->Z = 2;
    57   carbon->CovalentRadius = 0.68;
    58   carbon->VanDerWaalsRadius = 1.7;
    59   strcpy(carbon->name, "carbon");
    60   strcpy(carbon->symbol, "C");
    61 
    62 
    63   // construct periodentafel
    64   tafel = World::getInstance().getPeriode();
    65   tafel->AddElement(hydrogen);
    66   tafel->AddElement(carbon);
     46  hydrogen = World::getInstance().getPeriode()->FindElement(1);
     47  carbon = World::getInstance().getPeriode()->FindElement(6);
     48  CPPUNIT_ASSERT(hydrogen != NULL && "could not find element hydrogen");
     49  CPPUNIT_ASSERT(carbon != NULL && "could not find element carbon");
    6750
    6851  // construct molecule (tetraeder of hydrogens)
    6952  TestMolecule = World::getInstance().createMolecule();
     53  CPPUNIT_ASSERT(TestMolecule != NULL && "could not create molecule");
    7054  Walker = World::getInstance().createAtom();
     55  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
    7156  Walker->type = carbon;
    7257  *Walker->node = Vector(1., 0., 1. );
    … …  
    7459
    7560  Walker = World::getInstance().createAtom();
     61  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
    7662  Walker->type = carbon;
    7763  *Walker->node = Vector(0., 1., 1. );
    … …  
    7965
    8066  Walker = World::getInstance().createAtom();
     67  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
    8168  Walker->type = carbon;
    8269  *Walker->node = Vector(1., 1., 0. );
    … …  
    8471
    8572  Walker = World::getInstance().createAtom();
     73  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
    8674  Walker->type = carbon;
    8775  *Walker->node = Vector(0., 0., 0. );
    … …  
    9381  // create a small file with table
    9482  dummyname = new string("dummy.dat");
     83  CPPUNIT_ASSERT(dummyname != NULL && "could not create string");
    9584  filename = new string("test.dat");
     85  CPPUNIT_ASSERT(filename != NULL && "could not create string");
    9686  ofstream test(filename->c_str());
    97   test << ".\tH\tC\n";
    98   test << "H\t1.\t1.2\n";
    99   test << "C\t1.2\t1.5\n";
     87  test << ".\tH\tHe\tLi\tBe\tB\tC\n";
     88  test << "H\t1.\t1.\t1.\t1.\t1.\t1.2\n";
     89  test << "He\t1.\t1.\t1.\t1.\t1.\t1.\n";
     90  test << "Li\t1.\t1.\t1.\t1.\t1.\t1.\n";
     91  test << "Be\t1.\t1.\t1.\t1.\t1.\t1.\n";
     92  test << "B\t1.\t1.\t1.\t1.\t1.\t1.\n";
     93  test << "C\t1.2\t1.\t1.\t1.\t1.\t1.5\n";
    10094  test.close();
    10195  BG = new BondGraph(true);
     96  CPPUNIT_ASSERT(BG != NULL && "could not create BondGraph");
    10297};
    10398
    … …  
    126121  CPPUNIT_ASSERT_EQUAL( true , BG->LoadBondLengthTable(*filename) );
    127122  CPPUNIT_ASSERT_EQUAL( 1., BG->GetBondLength(0,0) );
    128   CPPUNIT_ASSERT_EQUAL( 1.2, BG->GetBondLength(0,1) );
    129   CPPUNIT_ASSERT_EQUAL( 1.5, BG->GetBondLength(1,1) );
     123  CPPUNIT_ASSERT_EQUAL( 1.2, BG->GetBondLength(0,5) );
     124  CPPUNIT_ASSERT_EQUAL( 1.5, BG->GetBondLength(5,5) );
    130125};
    131126

  • src/unittests/bondgraphunittest.hpp

    r60f50a r9757d9  
    3737
    3838      molecule *TestMolecule;
    39       element *hydrogen;
    40       element *carbon;
    41       periodentafel *tafel;
     39      const element *hydrogen;
     40      const element *carbon;
    4241
    4342      BondGraph *BG;

  • src/unittests/listofbondsunittest.cpp

    r60f50a r9757d9  
    3838  atom *Walker = NULL;
    3939
    40   // init private all pointers to zero
    41   TestMolecule = NULL;
    42   hydrogen = NULL;
    43   tafel = NULL;
    44 
    4540  // construct element
    46   hydrogen = new element;
    47   hydrogen->Z = 1;
    48   strcpy(hydrogen->name, "hydrogen");
    49   strcpy(hydrogen->symbol, "H");
    50 
    51 
    52   // construct periodentafel
    53   tafel = World::getInstance().getPeriode();
    54   tafel->AddElement(hydrogen);
     41  hydrogen = World::getInstance().getPeriode()->FindElement(1);
     42  CPPUNIT_ASSERT(hydrogen != NULL && "could not find element hydrogen");
    5543
    5644  // construct molecule (tetraeder of hydrogens)
    5745  TestMolecule = World::getInstance().createMolecule();
    58   Walker = World::getInstance().createAtom();
     46  CPPUNIT_ASSERT(TestMolecule != NULL && "could not create molecule");
     47  Walker = World::getInstance().createAtom();
     48  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
    5949  Walker->type = hydrogen;
    6050  *Walker->node = Vector(1., 0., 1. );
    6151  TestMolecule->AddAtom(Walker);
    6252  Walker = World::getInstance().createAtom();
     53  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
    6354  Walker->type = hydrogen;
    6455  *Walker->node = Vector(0., 1., 1. );
    6556  TestMolecule->AddAtom(Walker);
    6657  Walker = World::getInstance().createAtom();
     58  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
    6759  Walker->type = hydrogen;
    6860  *Walker->node = Vector(1., 1., 0. );
    6961  TestMolecule->AddAtom(Walker);
    7062  Walker = World::getInstance().createAtom();
     63  CPPUNIT_ASSERT(Walker != NULL && "could not create atom");
    7164  Walker->type = hydrogen;
    7265  *Walker->node = Vector(0., 0., 0. );
    … …  
    7568  // check that TestMolecule was correctly constructed
    7669  CPPUNIT_ASSERT_EQUAL( TestMolecule->AtomCount, 4 );
    77 
    7870};
    7971

  • src/unittests/listofbondsunittest.hpp

    r60f50a r9757d9  
    4141
    4242      molecule *TestMolecule;
    43       element *hydrogen;
    44       periodentafel *tafel;
     43      const element *hydrogen;
    4544};
    4645

  • src/unittests/tesselation_boundarytriangleunittest.cpp

    r60f50a r9757d9  
    3737  tesselpoints[0] = new TesselPoint;
    3838  tesselpoints[0]->node = new Vector(0., 0., 0.);
    39   tesselpoints[0]->Name = Malloc<char>(3, "TesselationBoundaryTriangleTest::setUp - *Name");
    40   strcpy(tesselpoints[0]->Name, "1");
     39  tesselpoints[0]->setName("1");
    4140  tesselpoints[0]->nr = 1;
    4241  points[0] = new BoundaryPointSet(tesselpoints[0]);
    4342  tesselpoints[1] = new TesselPoint;
    4443  tesselpoints[1]->node = new Vector(0., 1., 0.);
    45   tesselpoints[1]->Name = Malloc<char>(3, "TesselationBoundaryTriangleTest::setUp - *Name");
    46   strcpy(tesselpoints[1]->Name, "2");
     44  tesselpoints[1]->setName("2");
    4745  tesselpoints[1]->nr = 2;
    4846  points[1] = new BoundaryPointSet(tesselpoints[1]);
    4947  tesselpoints[2] = new TesselPoint;
    50   tesselpoints[2] ->node = new Vector(1., 0., 0.);
    51   tesselpoints[2] ->Name = Malloc<char>(3, "TesselationBoundaryTriangleTest::setUp - *Name");
    52   strcpy(tesselpoints[2] ->Name, "3");
    53   tesselpoints[2] ->nr = 3;
     48  tesselpoints[2]->node = new Vector(1., 0., 0.);
     49  tesselpoints[2]->setName("3");
     50  tesselpoints[2]->nr = 3;
    5451  points[2] = new BoundaryPointSet(tesselpoints[2] );
    5552

  • src/unittests/tesselation_insideoutsideunittest.cpp

    r60f50a r9757d9  
    3838  Walker = new TesselPoint;
    3939  Walker->node = new Vector(0., 0., 0.);
    40   Walker->Name = Malloc<char>(3, "TesselationInOutsideTest::setUp - *Name");
    41   strcpy(Walker->Name, "1");
     40  Walker->setName("1");
    4241  Walker->nr = 1;
    4342  Corners.push_back(Walker);
    4443  Walker = new TesselPoint;
    4544  Walker->node = new Vector(0., 1., 0.);
    46   Walker->Name = Malloc<char>(3, "TesselationInOutsideTest::setUp - *Name");
    47   strcpy(Walker->Name, "2");
     45  Walker->setName("2");
    4846  Walker->nr = 2;
    4947  Corners.push_back(Walker);
    5048  Walker = new TesselPoint;
    5149  Walker->node = new Vector(1., 0., 0.);
    52   Walker->Name = Malloc<char>(3, "TesselationInOutsideTest::setUp - *Name");
    53   strcpy(Walker->Name, "3");
     50  Walker->setName("3");
    5451  Walker->nr = 3;
    5552  Corners.push_back(Walker);
    5653  Walker = new TesselPoint;
    5754  Walker->node = new Vector(1., 1., 0.);
    58   Walker->Name = Malloc<char>(3, "TesselationInOutsideTest::setUp - *Name");
    59   strcpy(Walker->Name, "4");
     55  Walker->setName("4");
    6056  Walker->nr = 4;
    6157  Corners.push_back(Walker);
    6258  Walker = new TesselPoint;
    6359  Walker->node = new Vector(0., 0., 1.);
    64   Walker->Name = Malloc<char>(3, "TesselationInOutsideTest::setUp - *Name");
    65   strcpy(Walker->Name, "5");
     60  Walker->setName("5");
    6661  Walker->nr = 5;
    6762  Corners.push_back(Walker);
    6863  Walker = new TesselPoint;
    6964  Walker->node = new Vector(0., 1., 1.);
    70   Walker->Name = Malloc<char>(3, "TesselationInOutsideTest::setUp - *Name");
    71   strcpy(Walker->Name, "6");
     65  Walker->setName("6");
    7266  Walker->nr = 6;
    7367  Corners.push_back(Walker);
    7468  Walker = new TesselPoint;
    7569  Walker->node = new Vector(1., 0., 1.);
    76   Walker->Name = Malloc<char>(3, "TesselationInOutsideTest::setUp - *Name");
    77   strcpy(Walker->Name, "7");
     70  Walker->setName("7");
    7871  Walker->nr = 7;
    7972  Corners.push_back(Walker);
    8073  Walker = new TesselPoint;
    8174  Walker->node = new Vector(1., 1., 1.);
    82   Walker->Name = Malloc<char>(3, "TesselationInOutsideTest::setUp - *Name");
    83   strcpy(Walker->Name, "8");
     75  Walker->setName("8");
    8476  Walker->nr = 8;
    8577  Corners.push_back(Walker);

  • src/unittests/tesselationunittest.cpp

    r60f50a r9757d9  
    3737  Walker = new TesselPoint;
    3838  Walker->node = new Vector(1., 0., -1.);
    39   Walker->Name = Malloc<char>(3, "TesselationTest::setUp");
    40   strcpy(Walker->Name, "1");
     39  Walker->setName("1");
    4140  Walker->nr = 1;
    4241  Corners.push_back(Walker);
    4342  Walker = new TesselPoint;
    4443  Walker->node = new Vector(-1., 1., -1.);
    45   Walker->Name = Malloc<char>(3, "TesselationTest::setUp");
    46   strcpy(Walker->Name, "2");
     44  Walker->setName("2");
    4745  Walker->nr = 2;
    4846  Corners.push_back(Walker);
    4947  Walker = new TesselPoint;
    5048  Walker->node = new Vector(-1., -1., -1.);
    51   Walker->Name = Malloc<char>(3, "TesselationTest::setUp");
    52   strcpy(Walker->Name, "3");
     49  Walker->setName("3");
    5350  Walker->nr = 3;
    5451  Corners.push_back(Walker);
    5552  Walker = new TesselPoint;
    5653  Walker->node = new Vector(-1., 0., 1.);
    57   Walker->Name = Malloc<char>(3, "TesselationTest::setUp");
    58   strcpy(Walker->Name, "4");
     54  Walker->setName("4");
    5955  Walker->nr = 4;
    6056  Corners.push_back(Walker);

  • tests/testsuite.at

    r60f50a r9757d9  
    1111AT_KEYWORDS([options])
    1212AT_CHECK([pwd],[ignore],[ignore])
    13 AT_CHECK([../../molecuilder -v], 0, [stdout], [ignore])
     13AT_CHECK([../../molecuilder -v 1], 0, [stdout], [ignore])
    1414AT_CHECK([fgrep olecuilder stdout], 0, [ignore], [ignore])
    1515AT_CHECK([../../molecuilder -h], 0, [stdout], [ignore])
    … …  
    1717AT_CHECK([../../molecuilder -e], 255, [ignore], [stderr])
    1818AT_CHECK([fgrep "Not enough or invalid arguments" stderr], 0, [ignore], [ignore])
    19 AT_CHECK([../../molecuilder test.conf], 0, [stdout], [stderr])
    20 AT_CHECK([fgrep "Element list loading failed" stdout], 0, [ignore], [ignore])
    2119AT_CLEANUP
    2220
    … …  
    105103AT_KEYWORDS([graph])
    106104AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/regression/Graph/1/pre/test.conf .], 0)
    107 AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -vvv -D 2.], 0, [stdout], [stderr])
     105AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -D 2.], 0, [stdout], [stderr])
    108106AT_CHECK([fgrep -c "No rings were detected in the molecular structure." stdout], 0, [1
    109107], [ignore])
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