Changes in / [c14c78:0bfe73]


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Files:
384 added
265 deleted
77 edited

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  • .gitignore

    rc14c78 r0bfe73  
    1313*.in
    1414build*
     15config/*
    1516debug*
    1617aclocal.m4

  • configure.ac

    rc14c78 r0bfe73  
    206206        tests/CodeChecks/Makefile])
    207207AC_CONFIG_FILES([
     208        tests/Fragmentations/Makefile
     209        tests/Fragmentations/defs])
     210AC_CONFIG_FILES([
    208211        tests/Tesselations/Makefile
    209212        tests/Tesselations/defs])

  • src/Actions/AtomAction/RotateAroundOriginByAngleAction.def

    rc14c78 r0bfe73  
    1313// "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
    1414#define paramtypes (double)(Vector)
    15 #define paramtokens ("rotate-origin")("position")
     15#define paramtokens ("rotate-around-origin")("position")
    1616#define paramdescriptions ("rotation angle")("position in R^3 space")
    1717#undef paramdefaults
    … …  
    2626#define MENUPOSITION 5
    2727#define ACTIONNAME RotateAroundOriginByAngle
    28 #define TOKEN "rotate-origin"
     28#define TOKEN "rotate-around-origin"
    2929
    3030

  • src/Actions/CommandAction/BondLengthTableAction.cpp

    rc14c78 r0bfe73  
    4545  DoLog(0) && (Log() << Verbose(0) << "Using " << params.BondGraphFileName << " as bond length table." << endl);
    4646  config *configuration = World::getInstance().getConfig();
    47   if (configuration->BG == NULL) {
    48     configuration->BG = new BondGraph(configuration->GetIsAngstroem());
    49     if ((!params.BondGraphFileName.empty())
    50         && boost::filesystem::exists(params.BondGraphFileName)
    51         && (configuration->BG->LoadBondLengthTable(params.BondGraphFileName.string()))) {
    52       DoLog(0) && (Log() << Verbose(0) << "Bond length table loaded successfully." << endl);
    53       return Action::success;
     47  BondGraph *OldBG;
     48  if (configuration->BG != NULL) {
     49    OldBG = configuration->BG;
     50    DoLog(0) && (Log() << Verbose(0) << "There is a bond length table already present." << endl);
     51  }
     52  configuration->BG = new BondGraph(configuration->GetIsAngstroem());
     53  if ((!params.BondGraphFileName.empty())
     54      && boost::filesystem::exists(params.BondGraphFileName)) {
     55    std::ifstream input(params.BondGraphFileName.string().c_str());
     56    if ((input.good()) && (configuration->BG->LoadBondLengthTable(input))) {
     57      DoLog(0) && (Log() << Verbose(0) << "Bond length table parsed successfully." << endl);
     58      input.close();
     59      return Action::state_ptr(new CommandBondLengthTableState(*OldBG, params));
    5460    } else {
    55       DoeLog(1) && (eLog()<< Verbose(1) << "Bond length table loading failed." << endl);
     61      DoeLog(1) && (eLog()<< Verbose(1) << "Bond length table parsing failed." << endl);
     62      input.close();
     63      configuration->BG = new BondGraph(*OldBG);
    5664      return Action::failure;
    5765    }
    5866  } else {
    59     DoLog(0) && (Log() << Verbose(0) << "Bond length table already present." << endl);
     67    DoeLog(1) && (eLog()<< Verbose(1) << "Bond length table loading failed." << endl);
     68    configuration->BG = new BondGraph(*OldBG);
    6069    return Action::failure;
    6170  }
    … …  
    6372
    6473Action::state_ptr CommandBondLengthTableAction::performUndo(Action::state_ptr _state) {
    65 //  ParserLoadXyzState *state = assert_cast<ParserLoadXyzState*>(_state.get());
     74  CommandBondLengthTableState *state = assert_cast<CommandBondLengthTableState*>(_state.get());
    6675
    67   return Action::failure;
    68 //  string newName = state->mol->getName();
    69 //  state->mol->setName(state->lastName);
    70 //
    71 //  return Action::state_ptr(new ParserLoadXyzState(state->mol,newName));
     76  config *configuration = World::getInstance().getConfig();
     77  BondGraph *OldBG = new BondGraph(*configuration->BG);
     78  configuration->BG = new BondGraph(state->OldBG);
     79
     80  return Action::state_ptr(new CommandBondLengthTableState(*OldBG,params));
    7281}
    7382
    7483Action::state_ptr CommandBondLengthTableAction::performRedo(Action::state_ptr _state){
    75   return Action::failure;
     84  CommandBondLengthTableState *state = assert_cast<CommandBondLengthTableState*>(_state.get());
     85
     86  config *configuration = World::getInstance().getConfig();
     87  BondGraph *OldBG = new BondGraph(*configuration->BG);
     88  configuration->BG = new BondGraph(state->OldBG);
     89
     90  return Action::state_ptr(new CommandBondLengthTableState(*OldBG,params));
    7691}
    7792

  • src/Actions/CommandAction/BondLengthTableAction.def

    rc14c78 r0bfe73  
    88// all includes and forward declarations necessary for non-integral types below
    99
     10#include "bondgraph.hpp"
    1011
    1112// i.e. there is an integer with variable name Z that can be found in
    … …  
    1819#define paramreferences (BondGraphFileName)
    1920
    20 #undef statetypes
    21 #undef statereferences
     21#define statetypes (BondGraph)
     22#define statereferences (OldBG)
    2223
    2324// some defines for all the names, you may use ACTION, STATE and PARAMS

  • src/Actions/FragmentationAction/DepthFirstSearchAction.cpp

    rc14c78 r0bfe73  
    5252  std::deque<bond *> *BackEdgeStack = NULL;
    5353  std::deque<bond *> *LocalBackEdgeStack = NULL;
    54   mol->CreateAdjacencyList(params.distance, World::getInstance().getConfig()->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, NULL);
     54  BondGraph *BG = World::getInstance().getConfig()->BG;
     55  if (BG != NULL)
     56    mol->CreateAdjacencyList(params.distance, World::getInstance().getConfig()->GetIsAngstroem(), &BondGraph::BondLengthMatrixMinMaxDistance, BG);
     57  else
     58    mol->CreateAdjacencyList(params.distance, World::getInstance().getConfig()->GetIsAngstroem(), &BondGraph::CovalentMinMaxDistance, BG);
    5559  Subgraphs = mol->DepthFirstSearchAnalysis(BackEdgeStack);
    5660  if (Subgraphs != NULL) {

  • src/Actions/FragmentationAction/FragmentationAction.def

    rc14c78 r0bfe73  
    1313// "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
    1414#define paramtypes (std::string)(double)(int)
    15 #define paramtokens ("fragment-mol")("distance")("order")
     15#define paramtokens ("fragment-molecule")("distance")("order")
    1616#define paramdescriptions ("path to where the fragment configurations shall be stored")("distance in space")("order of a discretization, dissection, ...")
    1717#undef paramdefaults
    … …  
    2626#define MENUPOSITION 3
    2727#define ACTIONNAME Fragmentation
    28 #define TOKEN "fragment-mol"
     28#define TOKEN "fragment-molecule"
    2929
    3030

  • src/Actions/FragmentationAction/SubgraphDissectionAction.def

    rc14c78 r0bfe73  
    2626#define MENUPOSITION 4
    2727#define ACTIONNAME SubgraphDissection
    28 #define TOKEN "subgraph-dissect"
     28#define TOKEN "subgraph-dissection"
    2929
    3030

  • src/Actions/Makefile.am

    rc14c78 r0bfe73  
    127127  MoleculeAction/VerletIntegrationAction.hpp
    128128
     129PARSERACTIONSOURCE = \
     130  ParserAction/ParseTremoloPotentialsAction.cpp \
     131  ParserAction/SetMpqcParametersAction.cpp \
     132  ParserAction/SetOutputFormatsAction.cpp
     133PARSERACTIONHEADER = \
     134  ParserAction/ParseTremoloPotentialsAction.hpp \
     135  ParserAction/SetMpqcParametersAction.hpp \
     136  ParserAction/SetOutputFormatsAction.hpp               
     137
    129138RANDONNUMBERSSOURCE =\
    130139        RandomNumbersAction/SetRandomNumbersDistributionAction.cpp \
    131140        RandomNumbersAction/SetRandomNumbersEngineAction.cpp
    132 
    133141RANDONNUMBERSHEADER =\
    134142        RandomNumbersAction/SetRandomNumbersDistributionAction.hpp \
    … …  
    210218  WorldAction/RepeatBoxAction.cpp \
    211219  WorldAction/ScaleBoxAction.cpp \
    212   WorldAction/SetDefaultNameAction.cpp \
    213   WorldAction/SetGaussianBasisAction.cpp \
    214   WorldAction/SetOutputFormatsAction.cpp
     220  WorldAction/SetDefaultNameAction.cpp
    215221WORLDACTIONHEADER = \
    216222  WorldAction/AddEmptyBoundaryAction.hpp \
    … …  
    223229  WorldAction/RepeatBoxAction.hpp \
    224230  WorldAction/ScaleBoxAction.hpp \
    225   WorldAction/SetDefaultNameAction.hpp \
    226   WorldAction/SetGaussianBasisAction.hpp \
    227   WorldAction/SetOutputFormatsAction.hpp               
     231  WorldAction/SetDefaultNameAction.hpp
    228232
    229233

  • src/Actions/MoleculeAction/LinearInterpolationofTrajectoriesAction.def

    rc14c78 r0bfe73  
    1313// "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
    1414#define paramtypes (boost::filesystem::path)(int)(int)(bool)
    15 #define paramtokens ("linear-interpolate")("start-step")("end-step")("id-mapping")
     15#define paramtokens ("linear-interpolation-of-trajectories")("start-step")("end-step")("id-mapping")
    1616#define paramdescriptions ("path where to store the intermediate configurations")("first or start step")("last or end step")("whether the identity shall be used in mapping atoms onto atoms or not")
    1717#undef paramdefaults
    … …  
    2626#define MENUPOSITION 6
    2727#define ACTIONNAME LinearInterpolationofTrajectories
    28 #define TOKEN "linear-interpolate"
     28#define TOKEN "linear-interpolation-of-trajectories"
    2929
    3030

  • src/Actions/MoleculeAction/LoadAction.cpp

    rc14c78 r0bfe73  
    7070    MoleculeList::const_reverse_iterator iter = World::getInstance().getMolecules()->ListOfMolecules.rbegin();
    7171    (*iter)->SetNameFromFilename(FilenamePrefix.c_str());
     72    DoLog(0) && (Log() << Verbose(0) << "Chemical formula is " << (*iter)->getFormula() << std::endl);
    7273  }
    7374  return Action::success;

  • src/Actions/MoleculeAction/RotateAroundSelfByAngleAction.def

    rc14c78 r0bfe73  
    1414// "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
    1515#define paramtypes (double)(Vector)
    16 #define paramtokens ("rotate-self")("axis")
     16#define paramtokens ("rotate-around-self")("axis")
    1717#define paramdescriptions ("rotation angle in degrees")("position in R^3 space")
    1818#undef paramdefaults
    … …  
    2727#define MENUPOSITION 8
    2828#define ACTIONNAME RotateAroundSelfByAngle
    29 #define TOKEN "rotate-self"
     29#define TOKEN "rotate-around-self"
    3030
    3131

  • src/Actions/MoleculeAction/RotateToPrincipalAxisSystemAction.def

    rc14c78 r0bfe73  
    1616// "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
    1717#define paramtypes (Vector)
    18 #define paramtokens ("rotate-to-pas")
     18#define paramtokens ("rotate-to-principal-axis-system")
    1919#define paramdescriptions ("vector to which to align the biggest eigenvector with")
    2020#undef paramdefaults
    … …  
    2929#define MENUPOSITION 9
    3030#define ACTIONNAME RotateToPrincipalAxisSystem
    31 #define TOKEN "rotate-to-pas"
     31#define TOKEN "rotate-to-principal-axis-system"
    3232
    3333

  • src/Actions/MoleculeAction/VerletIntegrationAction.def

    rc14c78 r0bfe73  
    1313// "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
    1414#define paramtypes (boost::filesystem::path)
    15 #define paramtokens ("verlet-integrate")
     15#define paramtokens ("verlet-integration")
    1616#define paramdescriptions ("perform verlet integration of a given force file")
    1717#undef paramdefaults
    … …  
    2626#define MENUPOSITION 14
    2727#define ACTIONNAME VerletIntegration
    28 #define TOKEN "verlet-integrate"
     28#define TOKEN "verlet-integration"
    2929
    3030

  • src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.def

    rc14c78 r0bfe73  
    1313// "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
    1414#define paramtypes (std::string)
    15 #define paramtokens ("select-molecule-by-formula")
     15#define paramtokens ("select-molecules-by-formula")
    1616#define paramdescriptions ("chemical formula")
    1717#undef paramdefaults
    … …  
    2626#define MENUPOSITION 10
    2727#define ACTIONNAME MoleculeByFormula
    28 #define TOKEN "select-molecule-by-formula"
     28#define TOKEN "select-molecules-by-formula"
    2929
    3030

  • src/Actions/SelectionAction/Molecules/MoleculeByNameAction.def

    rc14c78 r0bfe73  
    1515// "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
    1616#define paramtypes (std::string)
    17 #define paramtokens ("select-molecule-by-name")
     17#define paramtokens ("select-molecules-by-name")
    1818#define paramdescriptions ("molecule name")
    1919#undef paramdefaults
    … …  
    2828#define MENUPOSITION 9
    2929#define ACTIONNAME MoleculeByName
    30 #define TOKEN "select-molecule-by-name"
     30#define TOKEN "select-molecules-by-name"
    3131
    3232

  • src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.def

    rc14c78 r0bfe73  
    1313// "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
    1414#define paramtypes (std::string)
    15 #define paramtokens ("unselect-molecule-by-formula")
     15#define paramtokens ("unselect-molecules-by-formula")
    1616#define paramdescriptions ("chemical formula")
    1717#undef paramdefaults
    … …  
    2626#define MENUPOSITION 19
    2727#define ACTIONNAME NotMoleculeByFormula
    28 #define TOKEN "unselect-molecule-by-formula"
     28#define TOKEN "unselect-molecules-by-formula"
    2929
    3030

  • src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.def

    rc14c78 r0bfe73  
    1313// "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
    1414#define paramtypes (std::string)
    15 #define paramtokens ("unselect-molecule-by-name")
     15#define paramtokens ("unselect-molecules-by-name")
    1616#define paramdescriptions ("molecule name")
    1717#undef paramdefaults
    … …  
    2626#define MENUPOSITION 9
    2727#define ACTIONNAME NotMoleculeByName
    28 #define TOKEN "unselect-molecule-by-name"
     28#define TOKEN "unselect-molecules-by-name"
    2929
    3030

  • src/Actions/WorldAction/AddEmptyBoundaryAction.def

    rc14c78 r0bfe73  
    1414// "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
    1515#define paramtypes (Vector)
    16 #define paramtokens ("boundary")
     16#define paramtokens ("add-empty-boundary")
    1717#define paramdescriptions ("desired minimum distance to boundary for each axis over all atoms")
    1818#undef paramdefaults
    … …  
    2727#define MENUPOSITION 1
    2828#define ACTIONNAME AddEmptyBoundary
    29 #define TOKEN "boundary"
     29#define TOKEN "add-empty-boundary"
    3030
    3131

  • src/Actions/WorldAction/InputAction.cpp

    rc14c78 r0bfe73  
    7878    iter--;
    7979    (*iter)->SetNameFromFilename(FilenamePrefix.c_str());
     80    DoLog(0) && (Log() << Verbose(0) << "Chemical formula is " << (*iter)->getFormula() << std::endl);
    8081  }
    8182  return Action::success;

  • src/Descriptors/MoleculeFormulaDescriptor.cpp

    rc14c78 r0bfe73  
    4242}
    4343
    44 MoleculeDescriptor MoleculeByFormula(const std::string &_formula) throw(ParseError){
     44MoleculeDescriptor MoleculeByFormula(const std::string &_formula) throw(FormulaStringParseException){
    4545  Formula formula(_formula);
    4646  return MoleculeByFormula(formula);

  • src/Descriptors/MoleculeFormulaDescriptor.hpp

    rc14c78 r0bfe73  
    1616
    1717#include "Descriptors/MoleculeDescriptor.hpp"
    18 #include "Exceptions/ParseError.hpp"
     18#include "Exceptions/FormulaStringParseException.hpp"
    1919
    2020class Formula;
    2121
    2222MoleculeDescriptor MoleculeByFormula(const Formula&);
    23 MoleculeDescriptor MoleculeByFormula(const std::string&) throw(ParseError);
     23MoleculeDescriptor MoleculeByFormula(const std::string&) throw(FormulaStringParseException);
    2424
    2525#endif /* MOLECULEFORMULADESCRIPTOR_HPP_ */

  • src/Exceptions/Makefile.am

    rc14c78 r0bfe73  
    1616  NotOnSurfaceException.cpp \
    1717  ShapeException.cpp \
    18   ParseError.cpp \
     18  FormulaStringParseException.cpp \
    1919  SkewException.cpp \
    2020  ZeroVectorException.cpp
    … …  
    2929  NotInvertibleException.hpp \
    3030  NotOnSurfaceException.hpp \
    31   ParseError.hpp \
     31  FormulaStringParseException.hpp \
    3232  SkewException.hpp \
    3333  ZeroVectorException.hpp

  • src/Formula.cpp

    rc14c78 r0bfe73  
    6868}
    6969
    70 void Formula::fromString(const std::string &formula) throw(ParseError){
     70void Formula::fromString(const std::string &formula) throw(FormulaStringParseException){
    7171  // make this transactional, in case an error is thrown
    7272  Formula res;
    … …  
    7777}
    7878
    79 int Formula::parseMaybeNumber(string::const_iterator &it,string::const_iterator &end) throw(ParseError){
     79int Formula::parseMaybeNumber(string::const_iterator &it,string::const_iterator &end) throw(FormulaStringParseException){
    8080  static const range<char> Numbers = makeRange('0',static_cast<char>('9'+1));
    8181  int count = 0;
    … …  
    8787}
    8888
    89 void Formula::parseFromString(string::const_iterator &it,string::const_iterator &end,char delimiter) throw(ParseError){
     89void Formula::parseFromString(string::const_iterator &it,string::const_iterator &end,char delimiter) throw(FormulaStringParseException){
    9090  // some constants needed for parsing... Assumes ASCII, change if other encodings are used
    9191  static const range<char> CapitalLetters = makeRange('A',static_cast<char>('Z'+1));
    … …  
    103103      sub.parseFromString(++it,end,nextdelim);
    104104      if(!sub.getElementCount()){
    105         throw(ParseError(__FILE__,__LINE__));
     105        throw(FormulaStringParseException(__FILE__,__LINE__));
    106106      }
    107107      int count = parseMaybeNumber(++it,end);
    … …  
    112112    // Atom names start with a capital letter
    113113    if(!CapitalLetters.isInRange(*it))
    114       throw(ParseError(__FILE__,__LINE__));
     114      throw(FormulaStringParseException(__FILE__,__LINE__));
    115115    shorthand+=(*it++);
    116116    // the rest of the name follows
    … …  
    120120    // test if the shorthand exists
    121121    if(!World::getInstance().getPeriode()->FindElement(shorthand))
    122       throw(ParseError(__FILE__,__LINE__));
     122      throw(FormulaStringParseException(__FILE__,__LINE__));
    123123    // done, we can get the next one
    124124    addElements(shorthand,count);
    125125  }
    126126  if(it==end && delimiter!=0){
    127     throw(ParseError(__FILE__,__LINE__));
     127    throw(FormulaStringParseException(__FILE__,__LINE__));
    128128  }
    129129}

  • src/Formula.hpp

    rc14c78 r0bfe73  
    1919#include <iterator>
    2020
    21 #include "Exceptions/ParseError.hpp"
     21#include "Exceptions/FormulaStringParseException.hpp"
    2222
    2323#include "types.hpp"
    … …  
    7171
    7272  std::string toString() const;
    73   void fromString(const std::string&) throw(ParseError);
     73  void fromString(const std::string&) throw(FormulaStringParseException);
    7474  bool checkOut(std::ostream*) const;
    7575
    … …  
    112112
    113113private:
    114   void parseFromString(std::string::const_iterator&,std::string::const_iterator&,char) throw(ParseError);
    115   int parseMaybeNumber(std::string::const_iterator &it,std::string::const_iterator &end) throw(ParseError);
     114  void parseFromString(std::string::const_iterator&,std::string::const_iterator&,char) throw(FormulaStringParseException);
     115  int parseMaybeNumber(std::string::const_iterator &it,std::string::const_iterator &end) throw(FormulaStringParseException);
    116116  // this contains all counts of elements in the formula
    117117  // the size of the actual structure might be used in comparisons

  • src/LinearAlgebra/RealSpaceMatrix.cpp

    rc14c78 r0bfe73  
    2828#include "LinearAlgebra/Vector.hpp"
    2929#include "LinearAlgebra/VectorContent.hpp"
     30#include "RandomNumbers/RandomNumberGeneratorFactory.hpp"
     31#include "RandomNumbers/RandomNumberGenerator.hpp"
    3032
    3133#include <gsl/gsl_blas.h>
    … …  
    125127{
    126128  double phi[NDIM];
     129  RandomNumberGenerator &random = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
     130  const double rng_min = random.min();
     131  const double rng_max = random.max();
     132
    127133
    128134  for (int i=0;i<NDIM;i++) {
    129     phi[i] = rand()/(RAND_MAX/(2.*M_PI));
     135    phi[i] = (random()/(rng_max-rng_min))*(2.*M_PI);
     136    std::cout << "Random angle is " << phi[i] << std::endl;
    130137  }
    131138

  • src/Parser/Makefile.am

    rc14c78 r0bfe73  
    1212  FormatParserStorage.cpp \
    1313  MpqcParser.cpp \
     14  MpqcParser_Parameters.cpp \
     15  MpqcParser_Parameters_initBasis.cpp \
    1416  PcpParser.cpp \
    1517  PdbAtomInfoContainer.cpp \
    … …  
    2426  FormatParserStorage.hpp \
    2527  MpqcParser.hpp \
     28  MpqcParser_Parameters.hpp \
    2629  PcpParser.hpp \
    2730  PdbAtomInfoContainer.hpp \

  • src/Parser/MpqcParser.cpp

    rc14c78 r0bfe73  
    1818#endif
    1919
     20#include <iostream>
     21#include <boost/tokenizer.hpp>
     22#include <string>
     23
    2024#include "CodePatterns/MemDebug.hpp"
    2125
    … …  
    2529#include "config.hpp"
    2630#include "element.hpp"
     31#include "molecule.hpp"
    2732#include "CodePatterns/Log.hpp"
     33#include "CodePatterns/toString.hpp"
    2834#include "CodePatterns/Verbose.hpp"
    2935#include "LinearAlgebra/Vector.hpp"
    … …  
    3541 *
    3642 */
    37 MpqcParser::MpqcParser() : HessianPresent(false)
     43MpqcParser::MpqcParser()
    3844{}
    3945
    … …  
    4955void MpqcParser::load(istream *file)
    5056{
    51   // TODO: MpqcParser::load implementation
    52   ASSERT(false, "Not implemented yet");
     57  bool MpqcSection = false;
     58  bool MoleculeSection = false;
     59  bool GeometrySection = false;
     60  bool BasisSection = false;
     61  bool AuxBasisSection = false;
     62  char line[MAXSTRINGSIZE];
     63  typedef boost::tokenizer<boost::char_separator<char> > tokenizer;
     64  boost::char_separator<char> sep("[]");
     65  boost::char_separator<char> angularsep("<>");
     66  boost::char_separator<char> equalitysep("=");
     67  boost::char_separator<char> whitesep(" \t");
     68  ConvertTo<double> toDouble;
     69
     70  molecule *newmol = World::getInstance().createMolecule();
     71  newmol->ActiveFlag = true;
     72  // TODO: Remove the insertion into molecule when saving does not depend on them anymore. Also, remove molecule.hpp include
     73  World::getInstance().getMolecules()->insert(newmol);
     74  while (file->good()) {
     75    file->getline(line, MAXSTRINGSIZE-1);
     76    std::string linestring(line);
     77    if ((linestring.find("atoms geometry") == string::npos) && (linestring.find("}") != string::npos)) {
     78      GeometrySection = false;
     79    }
     80    if ((linestring.find(")") != string::npos)) { // ends a section which do not overlap
     81      MpqcSection = false;
     82      MoleculeSection = false;
     83      BasisSection = false;
     84      AuxBasisSection = false;
     85    }
     86    if (MoleculeSection) {
     87      if (GeometrySection) { // we have an atom
     88        tokenizer tokens(linestring, sep);
     89  //      if (tokens.size() != 2)
     90  //        throw MpqcParseException;
     91        tokenizer::iterator tok_iter = tokens.begin();
     92        std::stringstream whitespacefilter(*tok_iter++);
     93        std::string element;
     94        whitespacefilter >> element;
     95        std::string vector = *tok_iter;
     96        tokenizer vectorcomponents(vector, whitesep);
     97        Vector X;
     98  //      if (vectorcomponents.size() != NDIM)
     99  //        throw MpqcParseException;
     100        tok_iter = vectorcomponents.begin();
     101        for (int i=0; i<NDIM; ++i) {
     102          X[i] = toDouble(*tok_iter++);
     103        }
     104        // create atom
     105        atom *newAtom = World::getInstance().createAtom();
     106        newAtom->setType(World::getInstance().getPeriode()->FindElement(element));
     107        newAtom->setPosition(X);
     108        newmol->AddAtom(newAtom);
     109        DoLog(1) && (Log() << Verbose(1) << "Adding atom " << *newAtom << std::endl);
     110      }
     111    }
     112    if (MpqcSection) {
     113      tokenizer tokens(linestring, equalitysep);
     114      tokenizer::iterator tok_iter = tokens.begin();
     115      std::stringstream whitespacefilter(*tok_iter++);
     116      std::string key(*tok_iter++);
     117      if (params.haveParam(key)) {
     118        std::stringstream linestream(linestring);
     119        linestream >> params;
     120      } else if (linestring.find("mole<") != string::npos) { // get theory
     121        tokenizer tokens(linestring, angularsep);
     122        tokenizer::iterator tok_iter = tokens.begin();
     123        std::string value(*(++tok_iter));
     124        std::stringstream linestream("theory = "+value);
     125        linestream >> params;
     126      } else if (linestring.find("integrals<") != string::npos) { // get theory
     127        tokenizer tokens(linestring, angularsep);
     128        tokenizer::iterator tok_iter = tokens.begin();
     129        std::string value(*(++tok_iter));
     130        std::stringstream linestream("integration = "+value);
     131        linestream >> params;
     132      }
     133    }
     134    if (BasisSection) {
     135      tokenizer tokens(linestring, equalitysep);
     136      tokenizer::iterator tok_iter = tokens.begin();
     137      std::string key(*tok_iter++);
     138      std::string value(*tok_iter);
     139      // TODO: use exception instead of ASSERT
     140      ASSERT(tok_iter == tokens.end(),
     141          "MpqcParser::load() - more than (key = value) on line "+linestring+".");
     142      if (key == "name") {
     143        std::stringstream linestream("basis = "+value);
     144        linestream >> params;
     145      }
     146    }
     147    if (AuxBasisSection) {
     148      tokenizer tokens(linestring, equalitysep);
     149      tokenizer::iterator tok_iter = tokens.begin();
     150      std::string key(*tok_iter++);
     151      std::string value(*tok_iter);
     152      // TODO: use exception instead of ASSERT
     153      ASSERT(tok_iter == tokens.end(),
     154          "MpqcParser::load() - more than (key = value) on line "+linestring+".");
     155      if (key == "name") {
     156        std::stringstream linestream("aux_basis = "+value);
     157        linestream >> params;
     158      }
     159    }
     160    // set some scan flags
     161    if (linestring.find("mpqc:") != string::npos) {
     162      MpqcSection = true;
     163    }
     164    if (linestring.find("molecule<Molecule>:") != string::npos) {
     165      MoleculeSection = true;
     166    }
     167    if (linestring.find("atoms geometry") != string::npos) {
     168      GeometrySection = true;
     169    }
     170    if ((linestring.find("basis<GaussianBasisSet>:") != string::npos) && ((linestring.find("abasis<") == string::npos))) {
     171      BasisSection = true;
     172    }
     173    if (linestring.find("abasis<") != string::npos) {
     174      AuxBasisSection = true;
     175    }
     176  }
    53177}
    54178
    55 /**
    56  * Saves the \a atoms into as a MPQC file.
    57  *
    58  * \param file where to save the state
    59  * \param atoms atoms to store
    60  */
    61 void MpqcParser::save(ostream *file, const std::vector<atom *> &atoms)
    62 {
    63   DoLog(0) && (Log() << Verbose(0) << "Saving changes to MPQC ." << std::endl);
    64 
    65   if (HessianPresent)
    66     saveHessian(file, atoms);
    67   else
    68     saveSimple(file, atoms);
    69 }
    70 
    71 /** Saves all atoms and data into a MPQC config file without hessian.
     179/** Saves all atoms and data into a MPQC config file.
    72180 * \param *file output stream
    73181 * \param atoms atoms to store
    74182 */
    75 void MpqcParser::saveSimple(ostream *file, const std::vector<atom *> &atoms)
     183void MpqcParser::save(ostream *file, const std::vector<atom *> &atoms)
    76184{
    77185  Vector center;
    … …  
    81189  for (vector<atom *>::iterator runner = allatoms.begin();runner != allatoms.end(); ++runner)
    82190    center += (*runner)->getPosition();
    83   center.Scale(1./allatoms.size());
     191  center.Scale(1./(double)allatoms.size());
    84192
    85193  // first without hessian
    … …  
    89197    *file << "% Created by MoleCuilder" << endl;
    90198    *file << "mpqc: (" << endl;
    91     *file << "\tsavestate = no" << endl;
    92     *file << "\tdo_gradient = yes" << endl;
    93     *file << "\tmole<MBPT2>: (" << endl;
    94     *file << "\t\tmaxiter = 200" << endl;
    95     *file << "\t\tbasis = $:basis" << endl;
    96     *file << "\t\tmolecule = $:molecule" << endl;
    97     *file << "\t\treference<CLHF>: (" << endl;
    98     *file << "\t\t\tbasis = $:basis" << endl;
    99     *file << "\t\t\tmolecule = $:molecule" << endl;
    100     *file << "\t\t)" << endl;
    101     *file << "\t)" << endl;
     199    *file << "\tsavestate = " << params.getString(MpqcParser_Parameters::savestateParam) << endl;
     200    *file << "\tdo_gradient = " << params.getString(MpqcParser_Parameters::do_gradientParam) << endl;
     201    if (params.getBool(MpqcParser_Parameters::hessianParam)) {
     202      *file << "\tfreq<MolecularFrequencies>: (" << endl;
     203      *file << "\t\tmolecule=$:molecule" << endl;
     204      *file << "\t)" << endl;
     205    }
     206    switch (params.getTheory()) {
     207      case MpqcParser_Parameters::CLHF:
     208        *file << "\tmole<" << params.getString(MpqcParser_Parameters::theoryParam) << ">: (" << endl;
     209        *file << "\t\tmolecule = $:molecule" << endl;
     210        *file << "\t\tbasis = $:basis" << endl;
     211        *file << "\t\tmaxiter = " << toString(params.getInt(MpqcParser_Parameters::maxiterParam))<< endl;
     212        *file << "\t\tmemory = " << toString(params.getInt(MpqcParser_Parameters::memoryParam)) << endl;
     213        *file << "\t)" << endl;
     214        break;
     215      case MpqcParser_Parameters::CLKS:
     216        *file << "\tmole<" << params.getString(MpqcParser_Parameters::theoryParam) << ">: (" << endl;
     217        *file << "\t\tfunctional<StdDenFunctional>:(name=B3LYP)" << endl;
     218        *file << "\t\tmolecule = $:molecule" << endl;
     219        *file << "\t\tbasis = $:basis" << endl;
     220        *file << "\t\tmaxiter = " << toString(params.getInt(MpqcParser_Parameters::maxiterParam))<< endl;
     221        *file << "\t\tmemory = " << toString(params.getInt(MpqcParser_Parameters::memoryParam)) << endl;
     222        *file << "\t)" << endl;
     223        break;
     224      case MpqcParser_Parameters::MBPT2:
     225        *file << "\tmole<" << params.getString(MpqcParser_Parameters::theoryParam) << ">: (" << endl;
     226        *file << "\t\tbasis = $:basis" << endl;
     227        *file << "\t\tmolecule = $:molecule" << endl;
     228        *file << "\t\tmemory = " << toString(params.getInt(MpqcParser_Parameters::memoryParam)) << endl;
     229        *file << "\t\treference<CLHF>: (" << endl;
     230        *file << "\t\t\tmaxiter = " << toString(params.getInt(MpqcParser_Parameters::maxiterParam))<< endl;
     231        *file << "\t\t\tbasis = $:basis" << endl;
     232        *file << "\t\t\tmolecule = $:molecule" << endl;
     233        *file << "\t\t\tmemory = " << toString(params.getInt(MpqcParser_Parameters::memoryParam)) << endl;
     234        *file << "\t\t)" << endl;
     235        *file << "\t)" << endl;
     236        break;
     237      case MpqcParser_Parameters::MBPT2_R12:
     238        *file << "\tmole<" << params.getString(MpqcParser_Parameters::theoryParam) << ">: (" << endl;
     239        *file << "\t\tmolecule = $:molecule" << endl;
     240        *file << "\t\tbasis = $:basis" << endl;
     241        *file << "\t\taux_basis = $:abasis" << endl;
     242        *file << "\t\tstdapprox = \"" << params.getString(MpqcParser_Parameters::stdapproxParam) << "\"" << endl;
     243        *file << "\t\tnfzc = " << toString(params.getInt(MpqcParser_Parameters::nfzcParam)) << endl;
     244        *file << "\t\tmemory = " << toString(params.getInt(MpqcParser_Parameters::memoryParam)) << endl;
     245        *file << "\t\tintegrals<IntegralCints>:()" << endl;
     246        *file << "\t\treference<CLHF>: (" << endl;
     247        *file << "\t\t\tmolecule = $:molecule" << endl;
     248        *file << "\t\t\tbasis = $:basis" << endl;
     249        *file << "\t\t\tmaxiter = " << toString(params.getInt(MpqcParser_Parameters::maxiterParam)) << endl;
     250        *file << "\t\t\tmemory = " << toString(params.getInt(MpqcParser_Parameters::memoryParam)) << endl;
     251        *file << "\t\t\tintegrals<" << params.getString(MpqcParser_Parameters::integrationParam) << ">:()" << endl;
     252        *file << "\t\t)" << endl;
     253        *file << "\t)" << endl;
     254        break;
     255      default:
     256        DoeLog(0) && (eLog() << Verbose(0)
     257            << "Unknown level of theory requested for MPQC output file." << std::endl);
     258        break;
     259    }
    102260    *file << ")" << endl;
    103261    *file << "molecule<Molecule>: (" << endl;
    … …  
    111269    *file << ")" << endl;
    112270    *file << "basis<GaussianBasisSet>: (" << endl;
    113     *file << "\tname = \"" << World::getInstance().getConfig()->basis << "\"" << endl;
     271    *file << "\tname = \"" << params.getString(MpqcParser_Parameters::basisParam) << "\"" << endl;
    114272    *file << "\tmolecule = $:molecule" << endl;
    115273    *file << ")" << endl;
     274    if (params.getTheory() == MpqcParser_Parameters::MBPT2_R12) {
     275      *file << "% auxiliary basis set specification" << endl;
     276      *file << "\tabasis<GaussianBasisSet>: (" << endl;
     277      *file << "\tname = \"" << params.getString(MpqcParser_Parameters::aux_basisParam) << "\"" << endl;
     278      *file << "\tmolecule = $:molecule" << endl;
     279      *file << ")" << endl;
     280    }
    116281  }
    117282}
    118283
    119 /** Saves all atoms and data into a MPQC config file with hessian.
    120  * \param *file output stream
    121  * \param atoms atoms to store
    122  */
    123 void MpqcParser::saveHessian(ostream *file, const std::vector<atom *> &atoms)
     284MpqcParser_Parameters & MpqcParser::getParams()
    124285{
    125   Vector center;
    126   vector<atom *> allatoms = World::getInstance().getAllAtoms();
    127 
    128   // calculate center
    129   for (vector<atom *>::iterator runner = allatoms.begin();runner != allatoms.end(); ++runner)
    130     center += (*runner)->getPosition();
    131   center.Scale(1./allatoms.size());
    132 
    133   // with hessian
    134   if (file->fail()) {
    135     DoeLog(1) && (eLog()<< Verbose(1) << "Cannot open mpqc output file." << endl);
    136   } else {
    137     *file << "% Created by MoleCuilder" << endl;
    138     *file << "mpqc: (" << endl;
    139     *file << "\tsavestate = no" << endl;
    140     *file << "\tdo_gradient = yes" << endl;
    141     *file << "\tmole<CLHF>: (" << endl;
    142     *file << "\t\tmaxiter = 200" << endl;
    143     *file << "\t\tbasis = $:basis" << endl;
    144     *file << "\t\tmolecule = $:molecule" << endl;
    145     *file << "\t)" << endl;
    146     *file << "\tfreq<MolecularFrequencies>: (" << endl;
    147     *file << "\t\tmolecule=$:molecule" << endl;
    148     *file << "\t)" << endl;
    149     *file << ")" << endl;
    150     *file << "molecule<Molecule>: (" << endl;
    151     *file << "\tunit = " << (World::getInstance().getConfig()->GetIsAngstroem() ? "angstrom" : "bohr" ) << endl;
    152     *file << "\t{ atoms geometry } = {" << endl;
    153     // output of atoms
    154     for (vector<atom *>::iterator AtomRunner = allatoms.begin(); AtomRunner != allatoms.end(); ++AtomRunner) {
    155       (*AtomRunner)->OutputMPQCLine(file, &center);
    156     }
    157     *file << "\t}" << endl;
    158     *file << ")" << endl;
    159     *file << "basis<GaussianBasisSet>: (" << endl;
    160     *file << "\tname = \"" << World::getInstance().getConfig()->basis << "\"" << endl;
    161     *file << "\tmolecule = $:molecule" << endl;
    162     *file << ")" << endl;
    163   }
     286  return params;
    164287}
    165288
    166 /** Sets whether hessian is desired or not
    167  * \param hessian statement
    168  */
    169 void MpqcParser::setHessian(bool hessian)
    170 {
    171   HessianPresent = hessian;
    172 }

  • src/Parser/MpqcParser.hpp

    rc14c78 r0bfe73  
    1616
    1717#include "FormatParser.hpp"
     18#include "MpqcParser_Parameters.hpp"
    1819
    1920#include <iosfwd>
    … …  
    2425class MpqcParser : public FormatParser
    2526{
     27  friend class ParserMpqcUnitTest;
    2628public:
     29
    2730  MpqcParser();
    2831  ~MpqcParser();
    … …  
    3033  void save(std::ostream* file, const std::vector<atom *> &atoms);
    3134
    32   void setHessian(bool hessian);
     35  /** Getter for parameter set.
     36   *
     37   * @return reference to parameter class
     38   */
     39  MpqcParser_Parameters & getParams();
    3340
    3441private:
    35   // whether output with computing hessian is desired.
    36   bool HessianPresent;
    37 
    38   void saveSimple(std::ostream *file, const std::vector<atom *> &atoms);
    39   void saveHessian(std::ostream *file, const std::vector<atom *> &atoms);
     42  MpqcParser_Parameters params;
    4043};
    4144
     45
    4246#endif /* MPQCPARSER_HPP_ */

  • src/Parser/TremoloAtomInfoContainer.cpp

    rc14c78 r0bfe73  
    2020#include "CodePatterns/MemDebug.hpp"
    2121
     22#include "CodePatterns/toString.hpp"
     23
    2224#include <iostream>
    2325
    … …  
    3032  imprData("-"),
    3133  GroupMeasureTypeNo("0"),
     34  Type("-"),
    3235  extType("-"),
    3336  name("-"),
    … …  
    5962    case TremoloKey::GroupMeasureTypeNo :
    6063      GroupMeasureTypeNo = value;
     64      break;
     65    case TremoloKey::Type :
     66      Type = value;
    6167      break;
    6268    case TremoloKey::extType :
    … …  
    104110}
    105111
    106 std::string TremoloAtomInfoContainer::get(TremoloKey::atomDataKey key) {
     112std::string TremoloAtomInfoContainer::get(TremoloKey::atomDataKey key) const
     113{
    107114  switch (key) {
    108115    case TremoloKey::F :
    … …  
    114121    case TremoloKey::GroupMeasureTypeNo :
    115122      return GroupMeasureTypeNo;
     123    case TremoloKey::Type :
     124      return Type;
    116125    case TremoloKey::extType :
    117126      return extType;
    … …  
    146155}
    147156
     157std::ostream& operator<<(std::ostream& out, const TremoloAtomInfoContainer& info)
     158{
     159  out << info.get(TremoloKey::F) << "\t";
     160  out << info.get(TremoloKey::stress) << "\t";
     161  out << info.get(TremoloKey::imprData) << "\t";
     162  out << info.get(TremoloKey::GroupMeasureTypeNo) << "\t";
     163  out << info.get(TremoloKey::Type) << "\t";
     164  out << info.get(TremoloKey::extType) << "\t";
     165  out << info.get(TremoloKey::name) << "\t";
     166  out << info.get(TremoloKey::resName) << "\t";
     167  out << info.get(TremoloKey::chainID) << "\t";
     168  out << info.get(TremoloKey::resSeq) << "\t";
     169  out << info.get(TremoloKey::occupancy) << "\t";
     170  out << info.get(TremoloKey::tempFactor) << "\t";
     171  out << info.get(TremoloKey::segID) << "\t";
     172  out << info.get(TremoloKey::Charge) << "\t";
     173  out << info.get(TremoloKey::charge) << "\t";
     174  out << info.get(TremoloKey::GrpTypeNo) << "\t";
     175  out << info.get(TremoloKey::torsion) << "\t";
     176  out << info.neighbors << "\t";
     177  out << info.neighbors_processed;
     178
     179  return out;
     180}

  • src/Parser/TremoloAtomInfoContainer.hpp

    rc14c78 r0bfe73  
    2727  TremoloAtomInfoContainer();
    2828  void set(TremoloKey::atomDataKey key, std::string value);
    29   std::string get(TremoloKey::atomDataKey key);
     29  std::string get(TremoloKey::atomDataKey key) const;
    3030  std::string F;
    3131  std::string stress;
    3232  std::string imprData;
    3333  std::string GroupMeasureTypeNo;
     34  std::string Type;
    3435  std::string extType;
    3536  std::string name;
    … …  
    4849};
    4950
     51std::ostream& operator<<(std::ostream& out, const TremoloAtomInfoContainer&);
    5052
    5153#endif /* TREMOLOATOMINFOCONTAINER_HPP_ */

  • src/Parser/TremoloParser.cpp

    rc14c78 r0bfe73  
    2222#include "CodePatterns/Assert.hpp"
    2323#include "CodePatterns/Log.hpp"
     24#include "CodePatterns/toString.hpp"
    2425#include "CodePatterns/Verbose.hpp"
    2526#include "TremoloParser.hpp"
    … …  
    3435#include <vector>
    3536
     37#include <boost/tokenizer.hpp>
    3638#include <iostream>
    3739#include <iomanip>
    … …  
    6567  knownKeys["torsion"] = TremoloKey::torsion;
    6668
     69  createKnownTypesByIdentity();
     70
    6771  // default behavior: use all possible keys on output
    6872  for (std::map<std::string, TremoloKey::atomDataKey>::iterator iter = knownKeys.begin(); iter != knownKeys.end(); ++iter)
    … …  
    7175  // and noKey afterwards(!) such that it is not used in usedFields
    7276  knownKeys[" "] = TremoloKey::noKey; // with this we can detect invalid keys
     77
     78  // invert knownKeys for debug output
     79  for (std::map<std::string, TremoloKey::atomDataKey>::iterator iter = knownKeys.begin(); iter != knownKeys.end(); ++iter)
     80    knownKeyNames.insert( make_pair( iter->second, iter->first) );
     81
     82  additionalAtomData.clear();
    7383}
    7484
    … …  
    130140  vector<string>::iterator it;
    131141
     142  DoLog(3) && (Log() << Verbose(3) << "additionalAtomData contains: " << additionalAtomData << std::endl);
     143
    132144  *file << "# ATOMDATA";
    133145  for (it=usedFields.begin(); it < usedFields.end(); it++) {
    … …  
    161173  vector<string>::iterator it;
    162174  TremoloKey::atomDataKey currentField;
     175
     176  DoLog(4) && (Log() << Verbose(4) << "INFO: Saving atom " << *currentAtom << ", its father id is " << currentAtom->GetTrueFather()->getId() << std::endl);
    163177
    164178  for (it = usedFields.begin(); it != usedFields.end(); it++) {
    … …  
    167181      case TremoloKey::x :
    168182        // for the moment, assume there are always three dimensions
     183        DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << currentAtom->getPosition() << std::endl);
    169184        *file << currentAtom->at(0) << "\t";
    170185        *file << currentAtom->at(1) << "\t";
    … …  
    173188      case TremoloKey::u :
    174189        // for the moment, assume there are always three dimensions
     190        DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << currentAtom->AtomicVelocity << std::endl);
    175191        *file << currentAtom->AtomicVelocity[0] << "\t";
    176192        *file << currentAtom->AtomicVelocity[1] << "\t";
    … …  
    178194        break;
    179195      case TremoloKey::Type :
    180         *file << currentAtom->getType()->getSymbol() << "\t";
     196        if (additionalAtomData.count(currentAtom->getId())) {
     197          if (additionalAtomData[currentAtom->getId()].get(currentField) != "-") {
     198            DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << additionalAtomData[currentAtom->getId()].get(currentField) << std::endl);
     199            *file << additionalAtomData[currentAtom->getId()].get(currentField) << "\t";
     200          } else {
     201            DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " default value: " << currentAtom->getType()->getSymbol() << std::endl);
     202            *file << currentAtom->getType()->getSymbol() << "\t";
     203          }
     204        } else if (additionalAtomData.count(currentAtom->GetTrueFather()->getId())) {
     205          if (additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField) != "-") {
     206            DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " stuff from father: " << additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField) << std::endl);
     207            *file << additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField) << "\t";
     208          } else {
     209            DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " default value from father: " << currentAtom->GetTrueFather()->getType()->getSymbol() << std::endl);
     210            *file << currentAtom->GetTrueFather()->getType()->getSymbol() << "\t";
     211          }
     212        } else {
     213          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " its default value: " << currentAtom->getType()->getSymbol() << std::endl);
     214          *file << currentAtom->getType()->getSymbol() << "\t";
     215        }
    181216        break;
    182217      case TremoloKey::Id :
     218        DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << currentAtom->getId()+1 << std::endl);
    183219        *file << currentAtom->getId()+1 << "\t";
    184220        break;
    185221      case TremoloKey::neighbors :
     222        DoLog(3) && (Log() << Verbose(3) << "Writing type " << knownKeyNames[currentField] << std::endl);
    186223        writeNeighbors(file, atoi(it->substr(it->find("=") + 1, 1).c_str()), currentAtom);
    187224        break;
    188225      case TremoloKey::resSeq :
    189         if (additionalAtomData.find(currentAtom->getId()) != additionalAtomData.end()) {
     226        if (additionalAtomData.count(currentAtom->getId())) {
     227          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << additionalAtomData[currentAtom->getId()].get(currentField) << std::endl);
    190228          *file << additionalAtomData[currentAtom->getId()].get(currentField);
    191229        } else if (currentAtom->getMolecule() != NULL) {
     230          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " its own id: " << currentAtom->getMolecule()->getId()+1 << std::endl);
    192231          *file << setw(4) << currentAtom->getMolecule()->getId()+1;
    193232        } else {
     233          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " default value: " << defaultAdditionalData.get(currentField) << std::endl);
    194234          *file << defaultAdditionalData.get(currentField);
    195235        }
    196236        *file << "\t";
    197       break;
     237        break;
    198238      default :
    199         if (additionalAtomData.find(currentAtom->getId()) != additionalAtomData.end()) {
     239        if (additionalAtomData.count(currentAtom->getId())) {
     240          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << additionalAtomData[currentAtom->getId()].get(currentField) << std::endl);
    200241          *file << additionalAtomData[currentAtom->getId()].get(currentField);
    201         } else if (additionalAtomData.find(currentAtom->GetTrueFather()->getId()) != additionalAtomData.end()) {
     242        } else if (additionalAtomData.count(currentAtom->GetTrueFather()->getId())) {
     243          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " stuff from father: " << additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField) << std::endl);
    202244          *file << additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField);
    203245        } else {
     246          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " the default: " << defaultAdditionalData.get(currentField) << std::endl);
    204247          *file << defaultAdditionalData.get(currentField);
    205248        }
    … …  
    250293    usedFields.push_back(keyword);
    251294  }
     295  //DoLog(1) && (Log() << Verbose(1) << "INFO: " << usedFields << std::endl);
    252296}
    253297
    … …  
    267311  atomInfo = &additionalAtomData[newAtom->getId()];
    268312  TremoloKey::atomDataKey currentField;
    269   string word;
    270   int oldId;
    271   double tmp;
    272 
    273   lineStream << line;
     313  ConvertTo<double> toDouble;
     314  ConvertTo<int> toInt;
     315
     316  // setup tokenizer, splitting up white-spaced entries
     317  typedef boost::tokenizer<boost::char_separator<char> >
     318      tokenizer;
     319  boost::char_separator<char> whitespacesep(" \t");
     320  tokenizer tokens(line, whitespacesep);
     321  ASSERT(tokens.begin() != tokens.end(),
     322      "TremoloParser::readAtomDataLine - empty string, need at least ' '!");
     323  tokenizer::iterator tok_iter = tokens.begin();
     324  // then associate each token to each file
    274325  for (it = usedFields.begin(); it < usedFields.end(); it++) {
    275     currentField = knownKeys[it->substr(0, it->find("="))];
     326    const std::string keyName = it->substr(0, it->find("="));
     327    currentField = knownKeys[keyName];
     328    const string word = *tok_iter;
     329    //DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing key " << keyName << " with remaining data " << word << std::endl);
    276330    switch (currentField) {
    277331      case TremoloKey::x :
    278332        // for the moment, assume there are always three dimensions
    279333        for (int i=0;i<NDIM;i++) {
    280           lineStream >> tmp;
    281           newAtom->set(i, tmp);
     334          ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for x["+toString(i)+"]!");
     335          //DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
     336          newAtom->set(i, toDouble(*tok_iter));
     337          tok_iter++;
    282338        }
    283339        break;
    284340      case TremoloKey::u :
    285341        // for the moment, assume there are always three dimensions
    286         lineStream >> newAtom->AtomicVelocity[0];
    287         lineStream >> newAtom->AtomicVelocity[1];
    288         lineStream >> newAtom->AtomicVelocity[2];
     342        for (int i=0;i<NDIM;i++) {
     343          ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for u["+toString(i)+"]!");
     344          //DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
     345          newAtom->AtomicVelocity[i] = toDouble(*tok_iter);
     346          tok_iter++;
     347        }
    289348        break;
    290349      case TremoloKey::Type :
    291         char type[3];
    292         lineStream >> type;
    293         newAtom->setType(World::getInstance().getPeriode()->FindElement(type));
     350      {
     351        ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for "+keyName+"!");
     352        DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
     353        std::string element(knownTypes[(*tok_iter)]);
     354        // put type name into container for later use
     355        atomInfo->set(currentField, *tok_iter);
     356        DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing element " << (*tok_iter) << " as " << element << " according to KnownTypes." << std::endl);
     357        tok_iter++;
     358        newAtom->setType(World::getInstance().getPeriode()->FindElement(element));
    294359        ASSERT(newAtom->getType(), "Type was not set for this atom");
    295360        break;
     361      }
    296362      case TremoloKey::Id :
    297         lineStream >> oldId;
    298         atomIdMap[oldId] = newAtom->getId();
     363        ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for "+keyName+"!");
     364        //DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
     365        atomIdMap[toInt(*tok_iter)] = newAtom->getId();
     366        tok_iter++;
    299367        break;
    300368      case TremoloKey::neighbors :
     369        for (int i=0;i<atoi(it->substr(it->find("=") + 1, 1).c_str());i++) {
     370          ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for "+keyName+"!");
     371          //DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
     372          lineStream << *tok_iter << "\t";
     373          tok_iter++;
     374        }
    301375        readNeighbors(&lineStream,
    302376            atoi(it->substr(it->find("=") + 1, 1).c_str()), newAtom->getId());
    303377        break;
    304378      default :
    305         lineStream >> word;
    306         atomInfo->set(currentField, word);
    307         break;
    308     }
    309   }
    310   if (newmol != NULL)
     379        ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for "+keyName+"!");
     380        //DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
     381        atomInfo->set(currentField, *tok_iter);
     382        tok_iter++;
     383        break;
     384    }
     385  }
     386  if (newmol != NULL) {
     387    //DoLog(0) && (Log() << Verbose(0) << "New Atom: " << *newAtom << " with type " << newAtom->getType()->getName() << std::endl);
    311388    newmol->AddAtom(newAtom);
     389  }
    312390}
    313391
    … …  
    325403    // 0 is used to fill empty neighbor positions in the tremolo file.
    326404    if (neighborId > 0) {
    327 //      std::cout << "Atom with global id " << atomId << " has neighbour with serial " << neighborId << std::endl;
     405//      DoLog(1) && (Log() << Verbose(1)
     406//          << "Atom with global id " << atomId
     407//          << " has neighbour with serial " << neighborId
     408//          << std::endl);
    328409      additionalAtomData[atomId].neighbors.push_back(neighborId);
    329410    }
    … …  
    366447        neighbor != currentInfo->second.neighbors.end(); neighbor++
    367448      ) {
    368 //        std::cout << "Creating bond between ("
     449//        DoLog(1) && (Log() << Verbose(1) << "Creating bond between ("
    369450//            << currentInfo->first
    370451//            << ") and ("
    371 //            << atomIdMap[*neighbor] << "|" << *neighbor << ")" << std::endl;
     452//            << atomIdMap[*neighbor] << "|" << *neighbor << ")" << std::endl);
    372453        World::getInstance().getAtom(AtomById(currentInfo->first))
    373454            ->addBond(World::getInstance().getAtom(AtomById(atomIdMap[*neighbor])));
    … …  
    440521}
    441522
     523/** Creates knownTypes as the identity, e.g. H -> H, He -> He, ... .
     524 *
     525 */
     526void TremoloParser::createKnownTypesByIdentity()
     527{
     528  // remove old mapping
     529  knownTypes.clear();
     530  // make knownTypes the identity mapping
     531  const periodentafel *periode = World::getInstance().getPeriode();
     532  for (periodentafel::const_iterator iter = periode->begin();
     533      iter != periode->end();
     534      ++iter) {
     535    knownTypes.insert( make_pair(iter->second->getSymbol(), iter->second->getSymbol()) );
     536  }
     537}
     538
     539/** Parses a .potentials file and creates from it the knownTypes file.
     540 *
     541 * @param file input stream of .potentials file
     542 */
     543void TremoloParser::parseKnownTypes(std::istream &file)
     544{
     545  const periodentafel *periode = World::getInstance().getPeriode();
     546  // remove old mapping
     547  knownTypes.clear();
     548
     549  DoLog(3) && (Log() << Verbose(3) << "additionalAtomData contains: " << additionalAtomData << std::endl);
     550
     551  // parse in file
     552  typedef boost::tokenizer<boost::char_separator<char> >
     553      tokenizer;
     554  boost::char_separator<char> tokensep(":\t ,;");
     555  boost::char_separator<char> equalitysep("\t =");
     556  std::string line;
     557  while (file.good()) {
     558    std::getline( file, line );
     559    DoLog(4) && (Log() << Verbose(4) << "INFO: full line of parameters is '" << line << "'" << std::endl);
     560    if (line.find("particle:") != string::npos) {
     561      DoLog(3) && (Log() << Verbose(3) << "INFO: found line '" << line << "' containing keyword 'particle:'." << std::endl);
     562      tokenizer tokens(line, tokensep);
     563      ASSERT(tokens.begin() != tokens.end(),
     564          "TremoloParser::parseKnownTypes() - line with 'particle:' but no particles separated by comma.");
     565      // look for particle_type
     566      std::string particle_type("NULL");
     567      std::string element_type("NULL");
     568      for (tokenizer::iterator tok_iter = tokens.begin();
     569          tok_iter != tokens.end();
     570          ++tok_iter) {
     571        if ((*tok_iter).find("particle_type") != string::npos) {
     572          DoLog(3) && (Log() << Verbose(3) << "INFO: found line '" << line << "' containing keyword 'particle_type'." << std::endl);
     573          tokenizer token((*tok_iter), equalitysep);
     574          ASSERT(token.begin() != token.end(),
     575                    "TremoloParser::parseKnownTypes() - could not split particle_type by equality sign");
     576          tokenizer::iterator particle_iter = token.begin();
     577          particle_iter++;
     578          particle_type = *particle_iter;
     579        }
     580        if ((*tok_iter).find("element_name") != string::npos) {
     581          DoLog(3) && (Log() << Verbose(3) << "INFO: found line '" << line << "' containing keyword 'element_name'." << std::endl);
     582          tokenizer token((*tok_iter), equalitysep);
     583          ASSERT(token.begin() != token.end(),
     584                    "TremoloParser::parseKnownTypes() - could not split particle_type by equality sign");
     585          tokenizer::iterator element_iter = token.begin();
     586          element_iter++;
     587          element_type = *element_iter;
     588        }
     589      }
     590      if ((particle_type != "NULL") && (element_type != "NULL")) {
     591        if (periode->FindElement(element_type) != NULL) {
     592          DoLog(1) && (Log() << Verbose(1) << "INFO: Added Type " << particle_type << " as reference to element " << element_type << "." << std::endl);
     593          knownTypes.insert( make_pair (particle_type, element_type) );
     594        } else {
     595          DoeLog(1) && (Log() << Verbose(1) << "INFO: Either Type " << particle_type << " or " << element_type << " could not be recognized." << std::endl);
     596        }
     597      } else {
     598        DoeLog(1) && (Log() << Verbose(1) << "INFO: Desired element " << element_type << " is not known." << std::endl);
     599      }
     600    }
     601  }
     602
     603}

  • src/Parser/TremoloParser.hpp

    rc14c78 r0bfe73  
    3535  void setFieldsForSave(std::string atomDataLine);
    3636
     37  void parseKnownTypes(std::istream &file);
     38  void createKnownTypesByIdentity();
     39
    3740
    3841private:
    … …  
    5053
    5154  /**
     55   * Map to associate the elements with stuff in "Type", e.g. OC2 -> O.
     56   */
     57  std::map<std::string, std::string> knownTypes;
     58
     59  /**
    5260   * Map to associate the known keys with numbers.
    5361   */
    5462  std::map<std::string, TremoloKey::atomDataKey> knownKeys;
     63
     64  /**
     65   * Inverse Map to have a name to each known keys.
     66   */
     67  std::map<TremoloKey::atomDataKey, std::string> knownKeyNames;
    5568
    5669  /**

  • src/Parser/unittests/Makefile.am

    rc14c78 r0bfe73  
    88
    99TESTS = \
    10   ParserCommonUnitTest \
    11   ParserTremoloUnitTest
     10  ParserMpqcUnitTest \
     11  ParserPcpUnitTest \
     12  ParserPdbUnitTest \
     13  ParserTremoloUnitTest \
     14  ParserXyzUnitTest
    1215
    1316
    … …  
    3437UILIBS = ../../UIElements/libMolecuilderUI.la 
    3538
    36 ParserCommonUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    37         ParserCommonUnitTest.cpp \
    38         ParserCommonUnitTest.hpp
    39 ParserCommonUnitTest_LDADD = ${ALLLIBS}
     39ParserMpqcUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     40        ParserMpqcUnitTest.cpp \
     41        ParserMpqcUnitTest.hpp
     42ParserMpqcUnitTest_LDADD = ${ALLLIBS}
     43
     44ParserPcpUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     45        ParserPcpUnitTest.cpp \
     46        ParserPcpUnitTest.hpp
     47ParserPcpUnitTest_LDADD = ${ALLLIBS}
     48
     49ParserPdbUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     50        ParserPdbUnitTest.cpp \
     51        ParserPdbUnitTest.hpp
     52ParserPdbUnitTest_LDADD = ${ALLLIBS}
    4053
    4154ParserTremoloUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    … …  
    4457ParserTremoloUnitTest_LDADD = ${ALLLIBS}
    4558
     59ParserXyzUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     60        ParserXyzUnitTest.cpp \
     61        ParserXyzUnitTest.hpp
     62ParserXyzUnitTest_LDADD = ${ALLLIBS}
     63
    4664
    4765#AUTOMAKE_OPTIONS = parallel-tests

  • src/Parser/unittests/ParserTremoloUnitTest.cpp

    rc14c78 r0bfe73  
    4444CPPUNIT_TEST_SUITE_REGISTRATION( ParserTremoloUnitTest );
    4545
    46 static string Tremolo_Atomdata1 = "# ATOMDATA\tId\tname\tType\tx=3\n";
    47 static string Tremolo_Atomdata2 = "#\n#ATOMDATA Id name Type x=3\n1 hydrogen H 3.0 4.5 0.1\n\n";
    48 static string Tremolo_invalidkey = "#\n#ATOMDATA Id name foo Type x=3\n\n\n";
    49 static string Tremolo_velocity = "#\n#ATOMDATA Id name Type u=3\n1 hydrogen H 3.0 4.5 0.1\n\n";
    50 static string Tremolo_neighbours = "#\n#ATOMDATA Id Type neighbors=2\n1 H 3 0\n2 H 3 0\n3 O 1 2\n";
    51 static string Tremolo_improper = "#\n#ATOMDATA Id Type imprData\n8 H 9-10\n9 H 10-8,8-10\n10 O -\n";
    52 static string Tremolo_torsion = "#\n#ATOMDATA Id Type torsion\n8 H 9-10\n9 H 10-8,8-10\n10 O -\n";
    53 static string Tremolo_full = "# ATOMDATA\tx=3\tu=3\tF\tstress\tId\tneighbors=5\timprData\tGroupMeasureTypeNo\tType\textType\tname\tresName\tchainID\tresSeq\toccupancy\ttempFactor\tsegID\tCharge\tcharge\tGrpTypeNo\ttorsion\n0\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t-\t0\tH\t-\t-\t-\t0\t0\t0\t0\t0\t0\t0\t0\t-\t\n";
     46static string Tremolo_Atomdata1 = "\
     47# ATOMDATA\tId\tname\tType\tx=3\n";
     48static string Tremolo_Atomdata2 = "\
     49#\n\
     50#ATOMDATA Id name Type x=3\n\
     511 hydrogen H 3.0 4.5 0.1\n\
     52\n";
     53static string Tremolo_invalidkey = "\
     54#\n\
     55#ATOMDATA Id name foo Type x=3\n\
     56\n\n";
     57static string Tremolo_velocity = "\
     58#\n\
     59#ATOMDATA Id name Type u=3\n\
     601 hydrogen H 3.0 4.5 0.1\n\
     61\n";
     62static string Tremolo_neighbours = "#\n\
     63#ATOMDATA Id Type neighbors=2\n\
     641 H 3 0\n\
     652 H 3 0\n\
     663 O 1 2\n";
     67static string Tremolo_improper = "\
     68#\n\
     69#ATOMDATA Id Type imprData\n\
     708 H 9-10\n\
     719 H 10-8,8-10\n\
     7210 O -\n";
     73static string Tremolo_torsion = "\
     74#\n\
     75#ATOMDATA Id Type torsion\n\
     768 H 9-10\n\
     779 H 10-8,8-10\n\
     7810 O -\n";
     79static string Tremolo_full = "\
     80# ATOMDATA\tx=3\tu=3\tF\tstress\tId\tneighbors=5\timprData\tGroupMeasureTypeNo\tType\textType\tname\tresName\tchainID\tresSeq\toccupancy\ttempFactor\tsegID\tCharge\tcharge\tGrpTypeNo\ttorsion\n\
     810\t0\t0\t0\t0\t0\t0\t0\t1\t0\t0\t0\t0\t0\t-\t0\tH\t-\t-\t-\t0\t0\t0\t0\t0\t0\t0\t0\t-\t\n";
    5482
    5583void ParserTremoloUnitTest::setUp() {
    … …  
    79107    std::vector<atom *> atoms = World::getInstance().getAllAtoms();
    80108    testParser->save(&output, atoms);
     109//    std::cout << output.str() << std::endl;
     110//    std::cout << Tremolo_Atomdata1 << std::endl;
    81111    CPPUNIT_ASSERT(Tremolo_Atomdata1 == output.str());
    82112    input.clear();
    … …  
    90120    std::vector<atom *> atoms = World::getInstance().getAllAtoms();
    91121    testParser->save(&output, atoms);
     122    std::cout << output.str() << std::endl;
    92123    CPPUNIT_ASSERT(output.str().find("hydrogen") != string::npos);
    93124    input.clear();
    … …  
    149180    testParser->save(&output, atoms);
    150181    CPPUNIT_ASSERT_EQUAL(3, World::getInstance().numAtoms());
     182    std::cout << output.str() << std::endl;
    151183    CPPUNIT_ASSERT(output.str().find("2-0,0-2") != string::npos);
    152184    input.clear();
    … …  
    166198    testParser->save(&output, atoms);
    167199    CPPUNIT_ASSERT_EQUAL(3, World::getInstance().numAtoms());
     200    std::cout << output.str() << std::endl;
    168201    CPPUNIT_ASSERT(output.str().find("2-0,0-2") != string::npos);
    169202    input.clear();

  • src/RandomNumbers/RandomNumberDistribution_Encapsulation.cpp

    rc14c78 r0bfe73  
    2222#include "CodePatterns/MemDebug.hpp"
    2323
     24#include <limits>
     25
    2426#include "RandomNumberDistribution_Encapsulation.hpp"
    2527
    … …  
    130132}
    131133
    132 
     134template <>
     135double RandomNumberDistribution_Encapsulation< boost::bernoulli_distribution<> >::min() const
     136{
     137  return 0.;
     138}
     139
     140template <>
     141double RandomNumberDistribution_Encapsulation< boost::binomial_distribution<> >::min() const
     142{
     143  return 0.;
     144}
     145
     146template <>
     147double RandomNumberDistribution_Encapsulation< boost::cauchy_distribution<> >::min() const
     148{
     149  return std::numeric_limits<double>::min();
     150}
     151
     152template <>
     153double RandomNumberDistribution_Encapsulation< boost::gamma_distribution<> >::min() const
     154{
     155  return 0.;
     156}
     157
     158template <>
     159double RandomNumberDistribution_Encapsulation< boost::poisson_distribution<> >::min() const
     160{
     161  return 0.;
     162}
     163
     164template <>
     165double RandomNumberDistribution_Encapsulation< boost::geometric_distribution<> >::min() const
     166{
     167  return 0.;
     168}
     169
     170template <>
     171double RandomNumberDistribution_Encapsulation< boost::triangle_distribution<> >::min() const
     172{
     173  return distribution_type.a();
     174}
     175
     176template <>
     177double RandomNumberDistribution_Encapsulation< boost::exponential_distribution<> >::min() const
     178{
     179  return 0.;
     180}
     181
     182template <>
     183double RandomNumberDistribution_Encapsulation< boost::normal_distribution<> >::min() const
     184{
     185  return std::numeric_limits<double>::min();
     186}
     187
     188template <>
     189double RandomNumberDistribution_Encapsulation< boost::lognormal_distribution<> >::min() const
     190{
     191  return 0.;
     192}
    133193
    134194/* ===============  max() ======================= */
    … …  
    158218}
    159219
     220template <>
     221double RandomNumberDistribution_Encapsulation< boost::bernoulli_distribution<> >::max() const
     222{
     223  return 1.;
     224}
     225
     226template <>
     227double RandomNumberDistribution_Encapsulation< boost::binomial_distribution<> >::max() const
     228{
     229  return distribution_type.t();
     230}
     231
     232template <>
     233double RandomNumberDistribution_Encapsulation< boost::cauchy_distribution<> >::max() const
     234{
     235  return std::numeric_limits<double>::max();
     236}
     237
     238template <>
     239double RandomNumberDistribution_Encapsulation< boost::gamma_distribution<> >::max() const
     240{
     241  return std::numeric_limits<double>::max();
     242}
     243
     244template <>
     245double RandomNumberDistribution_Encapsulation< boost::poisson_distribution<> >::max() const
     246{
     247  return std::numeric_limits<double>::max();
     248}
     249
     250template <>
     251double RandomNumberDistribution_Encapsulation< boost::geometric_distribution<> >::max() const
     252{
     253  return std::numeric_limits<double>::max();
     254}
     255
     256template <>
     257double RandomNumberDistribution_Encapsulation< boost::triangle_distribution<> >::max() const
     258{
     259  return distribution_type.c();
     260}
     261
     262template <>
     263double RandomNumberDistribution_Encapsulation< boost::exponential_distribution<> >::max() const
     264{
     265  return std::numeric_limits<double>::max();
     266}
     267
     268template <>
     269double RandomNumberDistribution_Encapsulation< boost::normal_distribution<> >::max() const
     270{
     271  return std::numeric_limits<double>::max();
     272}
     273
     274template <>
     275double RandomNumberDistribution_Encapsulation< boost::lognormal_distribution<> >::max() const
     276{
     277  return std::numeric_limits<double>::max();
     278}
    160279
    161280/* ===============  p() ======================= */

  • src/RandomNumbers/RandomNumberGenerator.hpp

    rc14c78 r0bfe73  
    3939  virtual void seed(unsigned int _seed)=0;
    4040
     41  /** Getter for smallest possible random number
     42   *
     43   * @return smallest possible random number
     44   */
     45  virtual double min() const=0;
     46
     47  /** Getter for largest possible random number
     48   *
     49   * @return largest possible random number
     50   */
     51  virtual double max() const=0;
     52
    4153  /** Getter for the type name of the internal engine.
    4254   *
    4355   */
    44   virtual std::string EngineName()=0;
     56  virtual std::string EngineName() const=0;
    4557
    4658  /** Getter for the type name of the internal distribution.
    4759   *
    4860   */
    49   virtual std::string DistributionName()=0;
     61  virtual std::string DistributionName() const=0;
    5062
    5163  /** Destructor of class RandomNumberGenerator.

  • src/RandomNumbers/RandomNumberGeneratorFactory.cpp

    rc14c78 r0bfe73  
    5555      !GeneratorPrototypeTable.empty();
    5656      iter = GeneratorPrototypeTable.begin()) {
    57     EmptyPrototypeTable< std::map<RandomNumberDistributionFactory::TypeList,Clone<RandomNumberGenerator> *> > (iter->second);
     57    EmptyPrototypeTable< std::map<RandomNumberDistributionFactory::TypeList,RandomNumberGenerator*> > (iter->second);
    5858    GeneratorPrototypeTable.erase(iter);
    5959  }
    … …  
    100100}
    101101
    102 RandomNumberGenerator* RandomNumberGeneratorFactory::makeRandomNumberGenerator() const
     102RandomNumberGenerator& RandomNumberGeneratorFactory::makeRandomNumberGenerator() const
    103103{
    104104  // Instantiate and return (implicitly creates a copy of the stored prototype)
    105   return (GeneratorPrototypeTable[engine][distribution]->clone());
     105  RandomNumberEngineFactory::TypeList eng_type =
     106      RandomNumberEngineFactory::getInstance().getCurrentTypeEnum();
     107  RandomNumberDistributionFactory::TypeList dis_type =
     108      RandomNumberDistributionFactory::getInstance().getCurrentTypeEnum();
     109
     110  return (*GeneratorPrototypeTable[ eng_type ][ dis_type ]);
    106111}
    107112
    108 RandomNumberGenerator* RandomNumberGeneratorFactory::makeRandomNumberGenerator(
     113RandomNumberGenerator& RandomNumberGeneratorFactory::makeRandomNumberGenerator(
    109114    std::string engine_type,
    110115    std::string distribution_type
    … …  
    118123    eng_type = RandomNumberEngineFactory::getInstance().getEnum(engine_type);
    119124  } else
    120     eng_type = engine;
     125    eng_type = RandomNumberEngineFactory::getInstance().getCurrentTypeEnum();
    121126  if (!distribution_type.empty()) {
    122127    dis_type = RandomNumberDistributionFactory::getInstance().getEnum(distribution_type);
    123128  } else
    124     dis_type = distribution;
    125   return (GeneratorPrototypeTable[ eng_type ][ dis_type ]->clone());
     129    dis_type = RandomNumberDistributionFactory::getInstance().getCurrentTypeEnum();
     130  return (*GeneratorPrototypeTable[ eng_type ][ dis_type ]);
     131
     132  return (*GeneratorPrototypeTable[ eng_type ][ dis_type ]);
    126133}
    127134
    128135void RandomNumberGeneratorFactory::setEngine(std::string engine_type)
    129136{
    130   engine = RandomNumberEngineFactory::getInstance().getEnum(engine_type);
     137  RandomNumberEngineFactory::getInstance().setCurrentType(engine_type);
    131138}
    132139
    133140const std::string &RandomNumberGeneratorFactory::getEngineName() const
    134141{
    135   return RandomNumberEngineFactory::getInstance().getName(engine);
     142  return RandomNumberEngineFactory::getInstance().getCurrentTypeName();
    136143}
    137144
    138145void RandomNumberGeneratorFactory::setDistribution(std::string distribution_type)
    139146{
    140   distribution = RandomNumberDistributionFactory::getInstance().getEnum(distribution_type);
     147  RandomNumberDistributionFactory::getInstance().setCurrentType(distribution_type);
    141148}
    142149
    143150const std::string &RandomNumberGeneratorFactory::getDistributionName() const
    144151{
    145   return RandomNumberDistributionFactory::getInstance().getName(distribution);
     152  return RandomNumberDistributionFactory::getInstance().getCurrentTypeName();
    146153}
    147154

  • src/RandomNumbers/RandomNumberGeneratorFactory.def

    rc14c78 r0bfe73  
    2727 */
    2828#define engine_seq \
    29 (minstd_rand0)
     29(minstd_rand0) \
     30(mt19937)
     31
    3032/*
    3133(minstd_rand)\
    … …  
    3638(hellekalek1995)\
    3739(mt11213b)\
    38 (mt19937)
    3940*/
    4041

  • src/RandomNumbers/RandomNumberGeneratorFactory.hpp

    rc14c78 r0bfe73  
    4949   * \return random number generator instance
    5050   */
    51   RandomNumberGenerator* makeRandomNumberGenerator() const;
     51  RandomNumberGenerator& makeRandomNumberGenerator() const;
    5252
    5353  /** Create a Generator of desired combination of engine and distribution.
    … …  
    6161   * \return random number generator instance
    6262   */
    63   RandomNumberGenerator* makeRandomNumberGenerator(std::string engine_type, std::string distribution_type) const;
     63  RandomNumberGenerator& makeRandomNumberGenerator(std::string engine_type, std::string distribution_type) const;
    6464
    6565  /** Specify the precise type of the engine to build
    … …  
    9898      std::map<
    9999        RandomNumberDistributionFactory::TypeList,
    100         Clone<RandomNumberGenerator> *>
     100        RandomNumberGenerator *>
    101101  > EngineDistributionTable;
    102102

  • src/RandomNumbers/RandomNumberGenerator_Encapsulation.hpp

    rc14c78 r0bfe73  
    8787   */
    8888  double operator()() const {
    89     return (*randomgenerator)();
     89    const double value = (*randomgenerator)();
     90    //std::cout << "Current random value from (" << EngineName() << "," << DistributionName() << ") is " << value << std::endl;
     91    return value;
    9092  }
    9193
    … …  
    98100  }
    99101
     102  /** Getter for smallest possible random number
     103   *
     104   * @return smallest possible random number
     105   */
     106  double min() const {
     107    return distribution_type->min();
     108  }
     109
     110  /** Getter for largest possible random number
     111   *
     112   * @return largest possible random number
     113   */
     114  double max() const {
     115    return distribution_type->max();
     116  }
     117
    100118  /** Getter for the type name of the internal engine.
    101119   *
    102120   */
    103   std::string EngineName() {
     121  std::string EngineName() const {
    104122    return engine_type->name();
    105123  }
    … …  
    108126   *
    109127   */
    110   std::string DistributionName() {
     128  std::string DistributionName() const {
    111129    return distribution_type->name();
    112130  }

  • src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.cpp

    rc14c78 r0bfe73  
    7575void RandomNumberGeneratorFactoryTest::setUp()
    7676{
    77   rng = NULL;
    78 
    7977  RandomNumberGeneratorFactory::getInstance();
    8078}
    … …  
    8280void RandomNumberGeneratorFactoryTest::tearDown()
    8381{
    84   delete rng;
    8582
    8683  RandomNumberDistributionFactory::purgeInstance();
    … …  
    9289{
    9390  // check one of the engines and distributions
    94   rng = RandomNumberGeneratorFactory::getInstance().
     91  RandomNumberGenerator& rng = *(RandomNumberGeneratorFactory::getInstance().
    9592      GeneratorPrototypeTable[RandomNumberEngineFactory::minstd_rand0]
    96                               [RandomNumberDistributionFactory::uniform_smallint]->clone();
     93                              [RandomNumberDistributionFactory::uniform_smallint]);
    9794  CPPUNIT_ASSERT_EQUAL(
    9895      std::string(typeid(boost::minstd_rand0).name()),
    99       rng->EngineName()
     96      rng.EngineName()
    10097  );
    10198  CPPUNIT_ASSERT_EQUAL(
    10299      std::string(typeid(boost::uniform_smallint<> ).name()),
    103       rng->DistributionName()
     100      rng.DistributionName()
     101  );
     102
     103  // set types in lower factories
     104  RandomNumberEngineFactory::getInstance().setCurrentType(RandomNumberEngineFactory::minstd_rand0);
     105  RandomNumberDistributionFactory::getInstance().setCurrentType(RandomNumberDistributionFactory::uniform_int);
     106  // ... and check whether generator delivers those set types
     107  RandomNumberGenerator &rng_A = RandomNumberGeneratorFactory::getInstance().
     108      makeRandomNumberGenerator();
     109  CPPUNIT_ASSERT_EQUAL(
     110      std::string(typeid(boost::minstd_rand0).name()),
     111      rng_A.EngineName()
     112  );
     113  CPPUNIT_ASSERT_EQUAL(
     114      std::string(typeid(boost::uniform_int<> ).name()),
     115      rng_A.DistributionName()
    104116  );
    105117}

  • src/RandomNumbers/unittests/RandomNumberGeneratorFactoryUnitTest.hpp

    rc14c78 r0bfe73  
    2929
    3030  void GeneratorTest();
    31 
    32 private:
    33   RandomNumberGenerator *rng;
    3431};
    3532

  • src/RandomNumbers/unittests/RandomNumberGeneratorUnitTest.cpp

    rc14c78 r0bfe73  
    5050
    5151/** We check that the RandomNumberGenerator instance received
    52  * from the RandomNumberGeneratorFactory is truely a copy and
    53  * not the prototype instance.
     52 * from the RandomNumberGeneratorFactory is truely the prototype
     53 * itself.
    5454 */
    55 void RandomNumberGeneratorTest::PrototypeCopyTest()
     55void RandomNumberGeneratorTest::PrototypeNonCopyTest()
    5656{
    57   RandomNumberGenerator *rng1 = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
    58   RandomNumberGenerator *rng2 = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
     57  RandomNumberGenerator &rng1 = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
     58  RandomNumberGenerator &rng2 = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
    5959
    60   double random1_1 = (*rng1)();
    61   double random1_2 = (*rng1)();
    62   double random2_1 = (*rng2)();
    63   double random2_2 = (*rng2)();
    64 
    65   CPPUNIT_ASSERT(random1_1 == random2_1);
    66   CPPUNIT_ASSERT(random1_2 == random2_2);
    67 
    68   delete rng1;
    69   delete rng2;
     60  // compare addresses in memory, have to be the same
     61  CPPUNIT_ASSERT( &rng1 == &rng2 );
    7062}
    7163
    … …  
    7466  // obtain some random values for uniform_smallint
    7567  RandomNumberGeneratorFactory::getInstance().setDistribution("uniform_smallint");
    76   RandomNumberGenerator* rng = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
     68  RandomNumberGenerator& rng = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
    7769  for (size_t i=0; i < 1000; ++i) {
    78     const int testint = (*rng)();
     70    const int testint = rng();
    7971    CPPUNIT_ASSERT_MESSAGE("randon number from uniform_smallint is out of [0:9]!", testint >= 0);
    8072    CPPUNIT_ASSERT_MESSAGE("randon number from uniform_smallint is out of [0:9]!", testint <= 9);
    8173  }
    82   delete rng;
    8374}

  • src/RandomNumbers/unittests/RandomNumberGeneratorUnitTest.hpp

    rc14c78 r0bfe73  
    2020{
    2121  CPPUNIT_TEST_SUITE( RandomNumberGeneratorTest );
    22   CPPUNIT_TEST ( PrototypeCopyTest );
     22  CPPUNIT_TEST ( PrototypeNonCopyTest );
    2323  CPPUNIT_TEST ( Range_uniform_smallint_Test );
    2424  CPPUNIT_TEST_SUITE_END();
    … …  
    2828  void tearDown();
    2929
    30   void PrototypeCopyTest();
     30  void PrototypeNonCopyTest();
    3131  void Range_uniform_smallint_Test();
    3232

  • src/SubspaceFactorizer.cpp

    rc14c78 r0bfe73  
    3636#include "LinearAlgebra/Subspace.hpp"
    3737#include "LinearAlgebra/VectorContent.hpp"
     38
     39#include "RandomNumbers/RandomNumberGeneratorFactory.hpp"
     40#include "RandomNumbers/RandomNumberGenerator.hpp"
    3841
    3942typedef std::set<std::set<size_t> > SetofIndexSets;
    … …  
    203206  }
    204207
     208//  RandomNumberGenerator &random = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
     209//  const double rng_min = rng->min();
     210//  const double rng_max = rng->max();
    205211  MatrixContent *matrix = new MatrixContent(matrixdimension,matrixdimension);
    206212  matrix->setZero();
    207213  for (size_t i=0; i<matrixdimension ; i++) {
    208214    for (size_t j=0; j<= i; ++j) {
    209       //const double value = 10. * rand() / (double)RAND_MAX;
     215      //const double value = 10. * random() / (rng_max-rng_min);
    210216      //const double value = i==j ? 2. : 1.;
    211217      if (i==j)

  • src/Thermostats/Langevin.cpp

    rc14c78 r0bfe73  
    1919#include "CodePatterns/Log.hpp"
    2020#include "ThermoStatContainer.hpp"
     21
     22#include "RandomNumbers/RandomNumberGeneratorFactory.hpp"
     23#include "RandomNumbers/RandomNumberGenerator.hpp"
    2124
    2225Langevin::Langevin(double _TempFrequency,double _alpha) :
    … …  
    7376double Langevin::doScaleAtoms(unsigned int step,double ActualTemp,ForwardIterator begin, ForwardIterator end){
    7477  DoLog(2) && (Log() << Verbose(2) <<  "Applying Langevin thermostat..." << endl);
     78  RandomNumberGenerator &random = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
     79  const double rng_min = random.min();
     80  const double rng_max = random.max();
    7581  double ekin=0;
    7682  for(ForwardIterator iter=begin;iter!=end;++iter){
    … …  
    7985    if ((*iter)->FixedIon == 0) { // even FixedIon moves, only not by other's forces
    8086      // throw a dice to determine whether it gets hit by a heat bath particle
    81       if (((((rand()/(double)RAND_MAX))*TempFrequency) < 1.)) {
     87      if (((((random()/(rng_max-rng_min)))*TempFrequency) < 1.)) {
    8288        DoLog(3) && (Log() << Verbose(3) << "Particle " << (**iter) << " was hit (sigma " << sigma << "): " << U.Norm() << " -> ");
    8389        // pick three random numbers from a Boltzmann distribution around the desired temperature T for each momenta axis

  • src/bondgraph.cpp

    rc14c78 r0bfe73  
    5757 * Allocates \a MatrixContainer for BondGraph::BondLengthMatrix, using MatrixContainer::ParseMatrix(),
    5858 * but only if parsing is successful. Otherwise variable is left as NULL.
    59  * \param *out output stream for debugging
    60  * \param filename file with bond lengths to parse
     59 * \param &input input stream to parse table from
    6160 * \return true - success in parsing file, false - failed to parse the file
    6261 */
    63 bool BondGraph::LoadBondLengthTable(const string &filename)
     62bool BondGraph::LoadBondLengthTable(std::istream &input)
    6463{
    6564  Info FunctionInfo(__func__);
    … …  
    7574
    7675  // parse in matrix
    77   if ((status = TempContainer->ParseMatrix(filename.c_str(), 0, 1, 0))) {
     76  if ((input.good()) && (status = TempContainer->ParseMatrix(input, 0, 1, 0))) {
    7877    DoLog(1) && (Log() << Verbose(1) << "Parsing bond length matrix successful." << endl);
    7978  } else {
    8079    DoeLog(1) && (eLog()<< Verbose(1) << "Parsing bond length matrix failed." << endl);
     80    status = false;
    8181  }
    8282
    … …  
    129129double BondGraph::GetBondLength(int firstZ, int secondZ)
    130130{
    131   if (BondLengthMatrix == NULL)
     131  std::cout << "Request for length between " << firstZ << " and " << secondZ << ": ";
     132  if (BondLengthMatrix == NULL) {
     133    std::cout << "-1." << std::endl;
    132134    return( -1. );
    133   else
     135  } else {
     136    std::cout << BondLengthMatrix->Matrix[0][firstZ][secondZ] << std::endl;
    134137    return (BondLengthMatrix->Matrix[0][firstZ][secondZ]);
     138  }
    135139};
    136140

  • src/bondgraph.hpp

    rc14c78 r0bfe73  
    3636  BondGraph(bool IsA);
    3737  ~BondGraph();
    38   bool LoadBondLengthTable(const string &filename);
     38  bool LoadBondLengthTable(std::istream &input);
    3939  bool ConstructBondGraph(molecule * const mol);
    4040  double GetBondLength(int firstelement, int secondelement);

  • src/boundary.cpp

    rc14c78 r0bfe73  
    4040#include "LinearAlgebra/Plane.hpp"
    4141#include "LinearAlgebra/RealSpaceMatrix.hpp"
     42#include "RandomNumbers/RandomNumberGeneratorFactory.hpp"
     43#include "RandomNumbers/RandomNumberGenerator.hpp"
    4244#include "Box.hpp"
    4345
    … …  
    831833
    832834  // initialize seed of random number generator to current time
    833   srand ( time(NULL) );
     835  RandomNumberGenerator &random = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
     836  const double rng_min = random.min();
     837  const double rng_max = random.max();
     838  //srand ( time(NULL) );
    834839
    835840  // go over [0,1]^3 filler grid
    … …  
    841846        // create molecule random translation vector ...
    842847        for (int i=0;i<NDIM;i++)
    843           FillerTranslations[i] = RandomMolDisplacement*(rand()/(RAND_MAX/2.) - 1.);
     848          FillerTranslations[i] = RandomMolDisplacement*(random()/((rng_max-rng_min)/2.) - 1.);
    844849        DoLog(2) && (Log() << Verbose(2) << "INFO: Current Position is " << CurrentPosition << "+" << FillerTranslations << "." << endl);
    845850
    … …  
    851856        if (DoRandomRotation)
    852857          for (int i=0;i<NDIM;i++)
    853             phi[i] = (rand()/RAND_MAX)*(2.*M_PI);
     858            phi[i] = (random()/(rng_max-rng_min))*(2.*M_PI);
    854859
    855860        for(molecule::const_iterator iter = filler->begin(); iter !=filler->end();++iter){
    … …  
    857862          // create atomic random translation vector ...
    858863          for (int i=0;i<NDIM;i++)
    859             AtomTranslations[i] = RandomAtomDisplacement*(rand()/(RAND_MAX/2.) - 1.);
     864            AtomTranslations[i] = RandomAtomDisplacement*(random()/((rng_max-rng_min)/2.) - 1.);
    860865
    861866          // ... and rotation matrix
    … …  
    939944    molecule *&Filling,
    940945    double RandomAtomDisplacement,
    941     RealSpaceMatrix &Rotations
     946    RealSpaceMatrix &Rotations,
     947    RandomNumberGenerator &random
    942948    )
    943949{
     950  const double rng_min = random.min();
     951  const double rng_max = random.max();
     952
    944953  Vector AtomTranslations;
    945954  for(molecule::iterator miter = Filling->begin(); miter != Filling->end(); ++miter) {
    … …  
    949958    // create atomic random translation vector ...
    950959    for (int i=0;i<NDIM;i++)
    951       AtomTranslations[i] = RandomAtomDisplacement*(rand()/(RAND_MAX/2.) - 1.);
     960      AtomTranslations[i] = RandomAtomDisplacement*(random()/((rng_max-rng_min)/2.) - 1.);
    952961    (*miter)->setPosition((*miter)->getPosition() + AtomTranslations);
    953962  }
    … …  
    10901099
    10911100  // initialize seed of random number generator to current time
    1092   srand ( time(NULL) );
     1101  RandomNumberGenerator &random = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
     1102  const double rng_min = random.min();
     1103  const double rng_max = random.max();
     1104  //srand ( time(NULL) );
    10931105
    10941106  // go over [0,1]^3 filler grid
    … …  
    10991111        CurrentPosition = M * Vector((double)n[0]/(double)N[0], (double)n[1]/(double)N[1], (double)n[2]/(double)N[2]);
    11001112        // create molecule random translation vector ...
    1101         for (int i=0;i<NDIM;i++)
    1102           FillerTranslations[i] = RandomMolDisplacement*(rand()/(RAND_MAX/2.) - 1.);
     1113        for (int i=0;i<NDIM;i++) // have the random values [-1,1]*RandomMolDisplacement
     1114          FillerTranslations[i] = RandomMolDisplacement*(random()/((rng_max-rng_min)/2.) - 1.);
    11031115        DoLog(2) && (Log() << Verbose(2) << "INFO: Current Position is " << CurrentPosition << "+" << FillerTranslations << "." << endl);
    11041116
    … …  
    11301142          // fill!
    11311143          Filling = filler->CopyMolecule();
    1132           RandomizeMoleculePositions(Filling, RandomAtomDisplacement, Rotations);
     1144          RandomizeMoleculePositions(Filling, RandomAtomDisplacement, Rotations, random);
    11331145          // translation
    11341146          Filling->Translate(&Inserter);
    … …  
    11681180    else
    11691181      Rotations.setIdentity();
    1170     RandomizeMoleculePositions(filler, RandomAtomDisplacement, Rotations);
     1182    RandomizeMoleculePositions(filler, RandomAtomDisplacement, Rotations, random);
    11711183    // translation
    11721184    filler->Translate(&firstInserter);

  • src/builder_init.cpp

    rc14c78 r0bfe73  
    1919
    2020#include "CodePatterns/MemDebug.hpp"
     21
     22#include <iostream>
    2123
    2224#include "bondgraph.hpp"
    … …  
    107109    World::getInstance().getConfig()->BG = new BondGraph(World::getInstance().getConfig()->GetIsAngstroem());
    108110    if (boost::filesystem::exists(BondGraphFileName)) {
    109       if (World::getInstance().getConfig()->BG->LoadBondLengthTable(BondGraphFileName)) {
     111      std::ifstream input(BondGraphFileName.c_str());
     112      if ((input.good()) && (World::getInstance().getConfig()->BG->LoadBondLengthTable(input))) {
    110113        DoLog(0) && (Log() << Verbose(0) << "Bond length table loaded successfully." << endl);
    111114      } else {
    112115        DoeLog(1) && (eLog()<< Verbose(1) << "Bond length table loading failed." << endl);
    113116      }
     117      input.close();
    114118    }
    115119  }

  • src/config.cpp

    rc14c78 r0bfe73  
    6060  FastParsing(false),
    6161  Deltat(0.01),
    62   basis(""),
    6362  databasepath(NULL),
    6463  DoConstrainedMD(0),
    … …  
    117116  strcpy(pseudopotpath,"not specified");
    118117  configname[0]='\0';
    119   basis = "3-21G";
    120118};
    121119
    … …  
    786784    *output << ")" << endl;
    787785    *output << "basis<GaussianBasisSet>: (" << endl;
    788     *output << "\tname = \"" << basis << "\"" << endl;
     786    *output << "\tname = \"3-21G\"" << endl;
    789787    *output << "\tmolecule = $:molecule" << endl;
    790788    *output << ")" << endl;

  • src/config.hpp

    rc14c78 r0bfe73  
    5050    bool FastParsing;
    5151    double Deltat;
    52     string basis;
    5352
    5453    char *databasepath;

  • src/ellipsoid.cpp

    rc14c78 r0bfe73  
    3636#include "LinearAlgebra/RealSpaceMatrix.hpp"
    3737#include "CodePatterns/Verbose.hpp"
     38
     39#include "RandomNumbers/RandomNumberGeneratorFactory.hpp"
     40#include "RandomNumbers/RandomNumberGenerator.hpp"
    3841
    3942/** Determines squared distance for a given point \a x to surface of ellipsoid.
    … …  
    258261  }
    259262
     263  RandomNumberGenerator &random = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator("mt19937", "uniform_int");
     264  // check that random number generator's bounds are ok
     265  ASSERT(random.min() == 0,
     266      "PickRandomNeighbouredPointSet: Chosen RandomNumberGenerator's min "
     267      +toString(random.min())+" is not 0!");
     268  ASSERT(random.max() >= LC->N[0],
     269      "PickRandomNeighbouredPointSet: Chosen RandomNumberGenerator's max "
     270      +toString(random.max())+" is too small"+toString(LC->N[0])
     271      +" for axis 0!");
     272  ASSERT(random.max() >= LC->N[1],
     273      "PickRandomNeighbouredPointSet: Chosen RandomNumberGenerator's max "
     274      +toString(random.max())+" is too small"+toString(LC->N[1])
     275      +" for axis 1!");
     276  ASSERT(random.max() >= LC->N[2],
     277      "PickRandomNeighbouredPointSet: Chosen RandomNumberGenerator's max "
     278      +toString(random.max())+" is too small"+toString(LC->N[2])
     279      +" for axis 2!");
     280
    260281  do {
    261282    for(int i=0;i<NDIM;i++) // pick three random indices
    262       LC->n[i] = (rand() % LC->N[i]);
     283      LC->n[i] = ((int)random() % LC->N[i]);
    263284    DoLog(2) && (Log() << Verbose(2) << "INFO: Center cell is " << LC->n[0] << ", " << LC->n[1] << ", " << LC->n[2] << " ... ");
    264285    // get random cell
    … …  
    293314    PickedAtomNrs.clear();
    294315    do {
    295       index = (rand() % PointsLeft);
     316      index = (((int)random()) % PointsLeft);
    296317      current = PickedAtomNrs.find(index);  // not present?
    297318      if (current == PickedAtomNrs.end()) {
    … …  
    358379  }
    359380
     381  RandomNumberGenerator &random = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator("mt19937", "uniform_int");
     382  const double rng_min = random.min();
     383  const double rng_max = random.max();
    360384  if (List != NULL)
    361385    for (PointMap::iterator Runner = List->begin(); Runner != List->end(); Runner++) {
    362386      threshold = 1. - (double)(PointsToPick - PointsPicked)/(double)PointsLeft;
    363       value = (double)rand()/(double)RAND_MAX;
     387      value = (double)random()/(double)(rng_max-rng_min);
    364388      //Log() << Verbose(3) << "Current node is " << *Runner->second->node << " with " << value << " ... " << threshold << ": ";
    365389      if (value > threshold) {

  • src/molecule.hpp

    rc14c78 r0bfe73  
    206206  void SetNameFromFilename(const char *filename);
    207207  void SetBoxDimension(Vector *dim);
    208   void ScanForPeriodicCorrection();
     208  bool ScanForPeriodicCorrection();
    209209  bool VerletForceIntegration(char *file, config &configuration, const size_t offset);
    210210  double VolumeOfConvexEnvelope(bool IsAngstroem);

  • src/molecule_dynamics.cpp

    rc14c78 r0bfe73  
    574574{
    575575  Info FunctionInfo(__func__);
    576   ifstream input(file);
    577576  string token;
    578577  stringstream item;
    … …  
    582581
    583582  const int AtomCount = getAtomCount();
    584   // check file
    585   if (input == NULL) {
     583  // parse file into ForceMatrix
     584  std::ifstream input(file);
     585  if ((input.good()) && (!Force.ParseMatrix(input, 0,0,0))) {
     586    DoeLog(0) && (eLog()<< Verbose(0) << "Could not parse Force Matrix file " << file << "." << endl);
     587    performCriticalExit();
    586588    return false;
    587   } else {
    588     // parse file into ForceMatrix
    589     if (!Force.ParseMatrix(file, 0,0,0)) {
    590       DoeLog(0) && (eLog()<< Verbose(0) << "Could not parse Force Matrix file " << file << "." << endl);
    591       performCriticalExit();
    592       return false;
    593     }
    594     if (Force.RowCounter[0] != AtomCount) {
    595       DoeLog(0) && (eLog()<< Verbose(0) << "Mismatch between number of atoms in file " << Force.RowCounter[0] << " and in molecule " << getAtomCount() << "." << endl);
    596       performCriticalExit();
    597       return false;
    598     }
    599     // correct Forces
    600     Velocity.Zero();
    601     for(int i=0;i<AtomCount;i++)
    602       for(int d=0;d<NDIM;d++) {
    603         Velocity[d] += Force.Matrix[0][i][d+offset];
    604       }
    605     for(int i=0;i<AtomCount;i++)
    606       for(int d=0;d<NDIM;d++) {
    607         Force.Matrix[0][i][d+offset] -= Velocity[d]/static_cast<double>(AtomCount);
    608       }
    609     // solve a constrained potential if we are meant to
    610     if (configuration.DoConstrainedMD) {
    611       // calculate forces and potential
    612       atom **PermutationMap = NULL;
    613       ConstrainedPotentialEnergy = MinimiseConstrainedPotential(PermutationMap,configuration.DoConstrainedMD, 0, configuration.GetIsAngstroem());
    614       EvaluateConstrainedForces(configuration.DoConstrainedMD, 0, PermutationMap, &Force);
    615       delete[](PermutationMap);
    616     }
    617 
    618     // and perform Verlet integration for each atom with position, velocity and force vector
    619     // check size of vectors
    620     for_each(atoms.begin(),
    621              atoms.end(),
    622              boost::bind(&atom::VelocityVerletUpdate,_1,MDSteps+1, &configuration, &Force, (const size_t) 0));
    623   }
     589  }
     590  input.close();
     591  if (Force.RowCounter[0] != AtomCount) {
     592    DoeLog(0) && (eLog()<< Verbose(0) << "Mismatch between number of atoms in file " << Force.RowCounter[0] << " and in molecule " << getAtomCount() << "." << endl);
     593    performCriticalExit();
     594    return false;
     595  }
     596  // correct Forces
     597  Velocity.Zero();
     598  for(int i=0;i<AtomCount;i++)
     599    for(int d=0;d<NDIM;d++) {
     600      Velocity[d] += Force.Matrix[0][i][d+offset];
     601    }
     602  for(int i=0;i<AtomCount;i++)
     603    for(int d=0;d<NDIM;d++) {
     604      Force.Matrix[0][i][d+offset] -= Velocity[d]/static_cast<double>(AtomCount);
     605    }
     606  // solve a constrained potential if we are meant to
     607  if (configuration.DoConstrainedMD) {
     608    // calculate forces and potential
     609    atom **PermutationMap = NULL;
     610    ConstrainedPotentialEnergy = MinimiseConstrainedPotential(PermutationMap,configuration.DoConstrainedMD, 0, configuration.GetIsAngstroem());
     611    EvaluateConstrainedForces(configuration.DoConstrainedMD, 0, PermutationMap, &Force);
     612    delete[](PermutationMap);
     613  }
     614
     615  // and perform Verlet integration for each atom with position, velocity and force vector
     616  // check size of vectors
     617  for_each(atoms.begin(),
     618           atoms.end(),
     619           boost::bind(&atom::VelocityVerletUpdate,_1,MDSteps+1, &configuration, &Force, (const size_t) 0));
     620
    624621  // correct velocities (rather momenta) so that center of mass remains motionless
    625622  Velocity = atoms.totalMomentumAtStep(MDSteps+1);

  • src/molecule_fragmentation.cpp

    rc14c78 r0bfe73  
    661661  FragmentationToDo = FragmentationToDo && CheckAdjacencyFileAgainstMolecule(prefix, ListOfAtoms);
    662662  delete[](ListOfAtoms);
     663
     664  // === reset bond degree and perform CorrectBondDegree ===
     665  for(World::MoleculeIterator iter = World::getInstance().getMoleculeIter();
     666      iter != World::getInstance().moleculeEnd();
     667      ++iter) {
     668      // reset bond degree to 1
     669    for (molecule::iterator atomiter = (*iter)->begin();
     670        atomiter != (*iter)->end();
     671        ++atomiter) {
     672      for (BondList::iterator bonditer = (*atomiter)->ListOfBonds.begin();
     673          bonditer != (*atomiter)->ListOfBonds.end();
     674          ++bonditer) {
     675        (*bonditer)->BondDegree = 1;
     676      }
     677    }
     678    // correct bond degree
     679    (*iter)->CorrectBondDegree();
     680  }
    663681
    664682  // ===== 2. perform a DFS analysis to gather info on cyclic structure and a list of disconnected subgraphs =====
    … …  
    752770  // free subgraph memory again
    753771  FragmentCounter = 0;
    754   if (Subgraphs != NULL) {
    755     while (Subgraphs->next != NULL) {
    756       Subgraphs = Subgraphs->next;
    757       delete(FragmentList[FragmentCounter++]);
    758       delete(Subgraphs->previous);
    759     }
     772  while (Subgraphs != NULL) {
     773    // remove entry in fragment list
     774    // remove subgraph fragment
     775    MolecularWalker = Subgraphs->next;
    760776    delete(Subgraphs);
    761   }
     777    Subgraphs = MolecularWalker;
     778  }
     779  // free fragment list
     780  for (int i=0; i< FragmentCounter; ++i )
     781    delete(FragmentList[i]);
    762782  delete[](FragmentList);
     783
     784  DoLog(0) && (Log() << Verbose(0) << FragmentCounter-1 << " subgraph fragments have been removed." << std::endl);
    763785
    764786  // ===== 8b. gather keyset lists (graphs) from all subgraphs and transform into MoleculeListClass =====
    … …  
    813835  } else {
    814836    DoLog(1) && (Log() << Verbose(1) << "FragmentList is zero on return, splitting failed." << endl);
     837  }
     838  // remove all create molecules again from the World including their atoms
     839  for (MoleculeList::iterator iter = BondFragments->ListOfMolecules.begin();
     840      !BondFragments->ListOfMolecules.empty();
     841      iter = BondFragments->ListOfMolecules.begin()) {
     842    // remove copied atoms and molecule again
     843    molecule *mol = *iter;
     844    mol->removeAtomsinMolecule();
     845    World::getInstance().destroyMolecule(mol);
     846    BondFragments->ListOfMolecules.erase(iter);
    815847  }
    816848  delete(BondFragments);
    … …  
    17541786 * \param *out ofstream for debugging messages
    17551787 */
    1756 void molecule::ScanForPeriodicCorrection()
     1788bool molecule::ScanForPeriodicCorrection()
    17571789{
    17581790  bond *Binder = NULL;
    … …  
    17631795  enum Shading *ColorList = NULL;
    17641796  double tmp;
     1797  bool LastBond = true; // only needed to due list construct
    17651798  Vector Translationvector;
    17661799  //std::deque<atom *> *CompStack = NULL;
    … …  
    17731806  for (int i=0;i<getAtomCount();i++)
    17741807    ColorList[i] = (enum Shading)0;
    1775   while (flag) {
     1808  if (flag) {
    17761809    // remove bonds that are beyond bonddistance
    17771810    Translationvector.Zero();
    … …  
    17851818          //Log() << Verbose(3) << "Checking " << i << "th distance of " << *Binder->leftatom << " to " << *Binder->rightatom << ": " << tmp << "." << endl;
    17861819          if (tmp > BondDistance) {
    1787             OtherBinder = Binder->next; // note down binding partner for later re-insertion
    1788             unlink(Binder);   // unlink bond
     1820//            OtherBinder = Binder->next; // note down binding partner for later re-insertion
     1821//            if (OtherBinder != NULL) {
     1822//              LastBond = false;
     1823//            } else {
     1824//              OtherBinder = Binder->previous;
     1825//              LastBond = true;
     1826//            }
     1827//            unlink(Binder);   // unlink bond
    17891828            DoLog(2) && (Log() << Verbose(2) << "Correcting at bond " << *Binder << "." << endl);
    17901829            flag = true;
    … …  
    17931832        }
    17941833      }
    1795     if (flag) {
     1834    //if (flag) {
     1835    if (0) {
    17961836      // create translation vector from their periodically modified distance
    17971837      for (int i=NDIM;i--;) {
    … …  
    18231863      }
    18241864      // re-add bond
    1825       link(Binder, OtherBinder);
     1865      if (OtherBinder == NULL) { // is the only bond?
     1866        //Do nothing
     1867      } else {
     1868        if (!LastBond) {
     1869          link(Binder, OtherBinder);
     1870        } else {
     1871          link(OtherBinder, Binder);
     1872        }
     1873      }
    18261874    } else {
    18271875      DoLog(3) && (Log() << Verbose(3) << "No corrections for this fragment." << endl);
    … …  
    18331881  delete[](ColorList);
    18341882  DoLog(2) && (Log() << Verbose(2) << "End of ScanForPeriodicCorrection." << endl);
    1835 };
     1883
     1884  return flag;
     1885};

  • src/molecule_graph.cpp

    rc14c78 r0bfe73  
    2626#include "bondgraph.hpp"
    2727#include "config.hpp"
     28#include "element.hpp"
    2829#include "Helpers/defs.hpp"
    29 #include "element.hpp"
     30#include "Helpers/fast_functions.hpp"
    3031#include "Helpers/helpers.hpp"
    31 #include "CodePatterns/Info.hpp"
     32#include "LinearAlgebra/RealSpaceMatrix.hpp"
    3233#include "linkedcell.hpp"
    3334#include "lists.hpp"
    34 #include "CodePatterns/Verbose.hpp"
    35 #include "CodePatterns/Log.hpp"
    3635#include "molecule.hpp"
    3736#include "World.hpp"
    38 #include "Helpers/fast_functions.hpp"
     37#include "Box.hpp"
     38
    3939#include "CodePatterns/Assert.hpp"
    40 #include "LinearAlgebra/RealSpaceMatrix.hpp"
    41 #include "Box.hpp"
     40#include "CodePatterns/Info.hpp"
     41#include "CodePatterns/Log.hpp"
     42#include "CodePatterns/Verbose.hpp"
     43
     44#define MAXBONDS 8
    4245
    4346struct BFSAccounting
    … …  
    174177        for (LC->n[2] = 0; LC->n[2] < LC->N[2]; LC->n[2]++) {
    175178          const LinkedCell::LinkedNodes *List = LC->GetCurrentCell();
    176 //          Log() << Verbose(2) << "Current cell is " << LC->n[0] << ", " << LC->n[1] << ", " << LC->n[2] << " with No. " << LC->index << " containing " << List->size() << " points." << endl;
     179          Log() << Verbose(2) << "Current cell is " << LC->n[0] << ", " << LC->n[1] << ", " << LC->n[2] << " with No. " << LC->index << " containing " << List->size() << " points." << endl;
    177180          if (List != NULL) {
    178181            for (LinkedCell::LinkedNodes::const_iterator Runner = List->begin(); Runner != List->end(); Runner++) {
    179182              Walker = dynamic_cast<atom*>(*Runner);
    180183              ASSERT(Walker,"Tesselpoint that was not an atom retrieved from LinkedNode");
    181               //Log() << Verbose(0) << "Current Atom is " << *Walker << "." << endl;
     184              Log() << Verbose(0) << "Current Atom is " << *Walker << "." << endl;
    182185              // 3c. check for possible bond between each atom in this and every one in the 27 cells
    183186              for (n[0] = -1; n[0] <= 1; n[0]++)
    … …  
    185188                  for (n[2] = -1; n[2] <= 1; n[2]++) {
    186189                    const LinkedCell::LinkedNodes *OtherList = LC->GetRelativeToCurrentCell(n);
    187 //                    Log() << Verbose(2) << "Current relative cell is " << LC->n[0] << ", " << LC->n[1] << ", " << LC->n[2] << " with No. " << LC->index << " containing " << List->size() << " points." << endl;
    188190                    if (OtherList != NULL) {
     191                      Log() << Verbose(2) << "Current relative cell is " << LC->n[0] << ", " << LC->n[1] << ", " << LC->n[2] << " with No. " << LC->index << " containing " << List->size() << " points." << endl;
    189192                      for (LinkedCell::LinkedNodes::const_iterator OtherRunner = OtherList->begin(); OtherRunner != OtherList->end(); OtherRunner++) {
    190193                        if ((*OtherRunner)->nr > Walker->nr) {
    191194                          OtherWalker = dynamic_cast<atom*>(*OtherRunner);
    192195                          ASSERT(OtherWalker,"TesselPoint that was not an atom retrieved from LinkedNode");
    193                           //Log() << Verbose(1) << "Checking distance " << OtherWalker->x.PeriodicDistanceSquared(&(Walker->x), cell_size) << " against typical bond length of " << bonddistance*bonddistance << "." << endl;
    194196                          (BG->*minmaxdistance)(Walker, OtherWalker, MinDistance, MaxDistance, IsAngstroem);
    195197                          const double distance = domain.periodicDistanceSquared(OtherWalker->getPosition(),Walker->getPosition());
     198                          Log() << Verbose(1) << "Checking distance " << distance << " against typical bond length of " << bonddistance*bonddistance << "." << endl;
    196199                          const bool status = (distance <= MaxDistance * MaxDistance) && (distance >= MinDistance * MinDistance);
    197 //                          Log() << Verbose(1) << "MinDistance is " << MinDistance << " and MaxDistance is " << MaxDistance << "." << endl;
     200                          Log() << Verbose(1) << "MinDistance is " << MinDistance << " and MaxDistance is " << MaxDistance << "." << endl;
    198201                          if (OtherWalker->father->nr > Walker->father->nr) {
    199202                            if (status) { // create bond if distance is smaller
    200 //                              Log() << Verbose(1) << "Adding Bond between " << *Walker << " and " << *OtherWalker << " in distance " << sqrt(distance) << "." << endl;
     203                              Log() << Verbose(1) << "Adding Bond between " << *Walker << " and " << *OtherWalker << " in distance " << sqrt(distance) << "." << endl;
    201204                              AddBond(Walker->father, OtherWalker->father, 1); // also increases molecule::BondCount
    202205                            } else {
    203 //                              Log() << Verbose(1) << "Not Adding: distance too great." << endl;
     206                              Log() << Verbose(1) << "Not Adding: distance too great." << endl;
    204207                            }
    205208                          } else {
    206 //                            Log() << Verbose(1) << "Not Adding: Wrong order of labels." << endl;
     209                            Log() << Verbose(1) << "Not Adding: Wrong order of labels." << endl;
    207210                          }
    208211                        }
    … …  
    11441147
    11451148  // allocate storage structure
    1146   CurrentBonds = new int[8]; // contains parsed bonds of current atom
    1147   for(int i=0;i<8;i++)
     1149  CurrentBonds = new int[MAXBONDS]; // contains parsed bonds of current atom
     1150  for(int i=0;i<MAXBONDS;i++)
    11481151    CurrentBonds[i] = 0;
    11491152  return true;
    … …  
    12101213
    12111214  char buffer[MAXSTRINGSIZE];
     1215  int tmp;
    12121216  // Parse the file line by line and count the bonds
    12131217  while (!File.eof()) {
    … …  
    12211225    if ((AtomNr >= 0) && (AtomNr < AtomCount)) {
    12221226      Walker = ListOfAtoms[AtomNr];
    1223       while (!line.eof())
    1224         line >> CurrentBonds[++CurrentBondsOfAtom];
     1227      while (line >> ws >> tmp) {
     1228        std::cout << "Recognized bond partner " << tmp << std::endl;
     1229        CurrentBonds[++CurrentBondsOfAtom] = tmp;
     1230        ASSERT(CurrentBondsOfAtom < MAXBONDS,
     1231            "molecule::CheckAdjacencyFileAgainstMolecule() - encountered more bonds than allowed: "
     1232            +toString(CurrentBondsOfAtom)+" >= "+toString(MAXBONDS)+"!");
     1233      }
    12251234      // compare against present bonds
    12261235      CheckAdjacencyFileAgainstMolecule_CompareBonds(status, NonMatchNumber, Walker, CurrentBondsOfAtom, AtomNr, CurrentBonds, ListOfAtoms);

  • src/moleculelist.cpp

    rc14c78 r0bfe73  
    506506  RealSpaceMatrix cell_size = World::getInstance().getDomain().getM();
    507507  RealSpaceMatrix cell_size_backup = cell_size;
     508  int count=0;
    508509
    509510  // store the fragments as config and as xyz
    … …  
    519520
    520521    // correct periodic
    521     (*ListRunner)->ScanForPeriodicCorrection();
     522    if ((*ListRunner)->ScanForPeriodicCorrection()) {
     523      count++;
     524    }
    522525
    523526    // output xyz file
    … …  
    543546    // center on edge
    544547    (*ListRunner)->CenterEdge(&BoxDimension);
     548    for (int k = 0; k < NDIM; k++)  // if one edge is to small, set at least to 1 angstroem
     549      if (BoxDimension[k] < 1.)
     550        BoxDimension[k] += 1.;
    545551    (*ListRunner)->SetBoxDimension(&BoxDimension); // update Box of atoms by boundary
    546552    for (int k = 0; k < NDIM; k++) {
    … …  
    591597  // printing final number
    592598  DoLog(2) && (Log() << Verbose(2) << "Final number of fragments: " << FragmentCounter << "." << endl);
     599
     600  // printing final number
     601  DoLog(0) && (Log() << Verbose(0) << "For " << count << " fragments periodic correction would have been necessary." << endl);
    593602
    594603  // restore cell_size
    … …  
    741750  // remove the leaf itself
    742751  if (Leaf != NULL) {
     752    Leaf->removeAtomsinMolecule();
    743753    World::getInstance().destroyMolecule(Leaf);
    744754    Leaf = NULL;

  • src/parser.cpp

    rc14c78 r0bfe73  
    2222
    2323#include <cstring>
     24#include <iomanip>
    2425
    2526#include "Helpers/helpers.hpp"
    … …  
    158159 *    -# allocate matrix
    159160 *    -# loop over found column and row counts and parse in each entry
    160  * \param *name directory with files
     161 * \param &input input stream
    161162 * \param skiplines number of inital lines to skip
    162163 * \param skiplines number of inital columns to skip
    … …  
    164165 * \return parsing successful
    165166 */
    166 bool MatrixContainer::ParseMatrix(const char *name, int skiplines, int skipcolumns, int MatrixNr)
    167 {
    168   ifstream input;
     167bool MatrixContainer::ParseMatrix(std::istream &input, int skiplines, int skipcolumns, int MatrixNr)
     168{
    169169  stringstream line;
    170170  string token;
    171171  char filename[1023];
    172172
    173   input.open(name, ios::in);
    174173  //Log() << Verbose(1) << "Opening " << name << " ... "  << input << endl;
    175   if (input == NULL) {
    176     DoeLog(1) && (eLog()<< Verbose(1) << endl << "MatrixContainer::ParseMatrix: Unable to open " << name << ", is the directory correct?" << endl);
     174  if (input.bad()) {
     175    DoeLog(1) && (eLog()<< Verbose(1) << endl << "MatrixContainer::ParseMatrix: Unable to parse istream." << endl);
    177176    //performCriticalExit();
    178177    return false;
    … …  
    190189  for(int k=skipcolumns;k--;)
    191190    line >> Header[MatrixNr];
    192   //Log() << Verbose(0) << line.str() << endl;
     191  Log() << Verbose(0) << line.str() << endl;
    193192  ColumnCounter[MatrixNr]=0;
    194193  while ( getline(line,token, '\t') ) {
    … …  
    196195      ColumnCounter[MatrixNr]++;
    197196  }
    198   //Log() << Verbose(0) << line.str() << endl;
    199   //Log() << Verbose(1) << "ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << "." << endl;
     197  Log() << Verbose(0) << line.str() << endl;
     198  Log() << Verbose(1) << "ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << "." << endl;
    200199  if (ColumnCounter[MatrixNr] == 0) {
    201     DoeLog(0) && (eLog()<< Verbose(0) << "ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << " from file " << name << ", this is probably an error!" << endl);
     200    DoeLog(0) && (eLog()<< Verbose(0) << "ColumnCounter[" << MatrixNr << "]: " << ColumnCounter[MatrixNr] << " from ostream." << endl);
    202201    performCriticalExit();
    203202  }
    … …  
    207206  while (!input.eof()) {
    208207    input.getline(filename, 1023);
    209     //Log() << Verbose(0) << "Comparing: " << strncmp(filename,"MeanForce",9) << endl;
     208    Log() << Verbose(0) << "Comparing: " << strncmp(filename,"MeanForce",9) << endl;
    210209    RowCounter[MatrixNr]++; // then line was not last MeanForce
    211210    if (strncmp(filename,"MeanForce", 9) == 0) {
    … …  
    213212    }
    214213  }
    215   //Log() << Verbose(1) << "RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from file " << name << "." << endl;
     214  Log() << Verbose(1) << "RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from input stream." << endl;
    216215  if (RowCounter[MatrixNr] == 0) {
    217     DoeLog(0) && (eLog()<< Verbose(0) << "RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from file " << name << ", this is probably an error!" << endl);
     216    DoeLog(0) && (eLog()<< Verbose(0) << "RowCounter[" << MatrixNr << "]: " << RowCounter[MatrixNr] << " from input stream." << endl);
    218217    performCriticalExit();
    219218  }
    … …  
    233232      input.getline(Header[MatrixNr], 1023);    // skip header
    234233    line.str(Header[MatrixNr]);
     234    Log() << Verbose(0) << "Header: " << line.str() << endl;
    235235    for(int k=skipcolumns;k--;)  // skip columns in header too
    236236      line >> filename;
    … …  
    245245      input.getline(filename, 1023);
    246246      stringstream lines(filename);
    247       //Log() << Verbose(2) << "Matrix at level " << j << ":";// << filename << endl;
     247      Log() << Verbose(2) << "Matrix at level " << j << ":";// << filename << endl;
    248248      for(int k=skipcolumns;k--;)
    249249        lines >> filename;
    250250      for(int k=0;(k<ColumnCounter[MatrixNr]) && (!lines.eof());k++) {
    251251        lines >> Matrix[MatrixNr][j][k];
    252         //Log() << Verbose(1) << " " << setprecision(2) << Matrix[MatrixNr][j][k] << endl;
     252        Log() << Verbose(1) << " " << setprecision(2) << Matrix[MatrixNr][j][k] << endl;
    253253      }
    254254      if (Matrix[MatrixNr][ RowCounter[MatrixNr] ] != NULL)
    … …  
    261261    DoeLog(1) && (eLog()<< Verbose(1) << "Matrix nr. " << MatrixNr << " has column and row count of (" << ColumnCounter[MatrixNr] << "," << RowCounter[MatrixNr] << "), could not allocate nor parse!" << endl);
    262262  }
    263   input.close();
    264263  return true;
    265264};
    … …  
    327326    file.str(" ");
    328327    file << name << FRAGMENTPREFIX << FragmentNumber << prefix << suffix;
    329     if (!ParseMatrix(file.str().c_str(), skiplines, skipcolumns, i))
     328    std::ifstream input(file.str().c_str());
     329    if (!ParseMatrix(input, skiplines, skipcolumns, i)) {
     330      input.close();
    330331      return false;
     332    }
     333    input.close();
    331334    delete[](FragmentNumber);
    332335  }
    … …  
    628631    strncat(filename, prefix, 1023-strlen(filename));
    629632    strncat(filename, suffix.c_str(), 1023-strlen(filename));
    630     ParseMatrix(filename, skiplines, skipcolumns, MatrixCounter);
     633    std::ifstream input(filename);
     634    ParseMatrix(input, skiplines, skipcolumns, MatrixCounter);
     635    input.close();
    631636  }
    632637  return status;
    … …  
    764769    strncat(filename, prefix, 1023-strlen(filename));
    765770    strncat(filename, suffix.c_str(), 1023-strlen(filename));
    766     ParseMatrix(filename, skiplines, skipcolumns, MatrixCounter);
     771    std::ifstream input(filename);
     772    ParseMatrix(input, skiplines, skipcolumns, MatrixCounter);
     773    input.close();
    767774  }
    768775 
    … …  
    992999    strncat(filename, prefix, 1023-strlen(filename));
    9931000    strncat(filename, suffix.c_str(), 1023-strlen(filename));
    994     ParseMatrix(filename, skiplines, skipcolumns, MatrixCounter);
     1001    std::ifstream input(filename);
     1002    ParseMatrix(input, skiplines, skipcolumns, MatrixCounter);
     1003    input.close();
    9951004  }
    9961005

  • src/parser.hpp

    rc14c78 r0bfe73  
    8686 
    8787  bool InitialiseIndices(class MatrixContainer *Matrix = NULL);
    88   bool ParseMatrix(const char *name, int skiplines, int skipcolumns, int MatrixNr);
     88  bool ParseMatrix(std::istream &input, int skiplines, int skipcolumns, int MatrixNr);
    8989  virtual bool ParseFragmentMatrix(const char *name, const char *prefix, string suffix, int skiplines, int skipcolumns);
    9090  bool AllocateMatrix(char **GivenHeader, int MCounter, int *RCounter, int *CCounter);

  • src/periodentafel.cpp

    rc14c78 r0bfe73  
    429429      input >> elements[Z]->Electronegativity;
    430430      input >> ws;
    431       DoLog(1) && (Log() << Verbose(1)
    432           << "Element " << Z << " has " << FindElement(Z)->Electronegativity << " valence electrons." << endl);
     431      //DoLog(1) && (Log() << Verbose(1)
     432        //  << "Element " << Z << " has " << FindElement(Z)->Electronegativity << " valence electrons." << endl);
    433433    }
    434434    return true;

  • src/unittests/AnalysisBondsUnitTest.cpp

    rc14c78 r0bfe73  
    9292  CPPUNIT_ASSERT_EQUAL( TestMolecule->getAtomCount(), 5 );
    9393
    94   // create a small file with table
    95   filename = new string("test.dat");
    96   CPPUNIT_ASSERT(filename != NULL && "could not create string");
    97   ofstream test(filename->c_str());
     94  // create stream with table
     95  std::stringstream test;
    9896  test << ".\tH\tHe\tLi\tBe\tB\tC\n";
    9997  test << "H\t1.\t1.\t1.\t1.\t1.\t1.2\n";
    … …  
    103101  test << "B\t1.\t1.\t1.\t1.\t1.\t1.\n";
    104102  test << "C\t1.2\t1.\t1.\t1.\t1.\t1.5\n";
    105   test.close();
    106103  BG = new BondGraph(true);
    107104  CPPUNIT_ASSERT(BG != NULL && "could not create BondGraph");
    108105
    109   CPPUNIT_ASSERT_EQUAL( true , BG->LoadBondLengthTable(*filename) );
     106  CPPUNIT_ASSERT_EQUAL( true , BG->LoadBondLengthTable(test) );
    110107  CPPUNIT_ASSERT_EQUAL( 1., BG->GetBondLength(0,0) );
    111108  CPPUNIT_ASSERT_EQUAL( 1.2, BG->GetBondLength(0,5) );
    … …  
    119116{
    120117  // remove the file
    121   remove(filename->c_str());
    122   delete(filename);
    123118  delete(BG);
    124119

  • src/unittests/BondGraphUnitTest.cpp

    rc14c78 r0bfe73  
    9292  CPPUNIT_ASSERT_EQUAL( TestMolecule->getAtomCount(), 4 );
    9393
    94   // create a small file with table
    95   dummyname = new string("dummy.dat");
    96   CPPUNIT_ASSERT(dummyname != NULL && "could not create string");
    97   filename = new string("test.dat");
    98   CPPUNIT_ASSERT(filename != NULL && "could not create string");
    99   ofstream test(filename->c_str());
     94  // create stream with table
    10095  test << ".\tH\tHe\tLi\tBe\tB\tC\n";
    10196  test << "H\t1.\t1.\t1.\t1.\t1.\t1.2\n";
    … …  
    105100  test << "B\t1.\t1.\t1.\t1.\t1.\t1.\n";
    106101  test << "C\t1.2\t1.\t1.\t1.\t1.\t1.5\n";
    107   test.close();
     102  // created bad stream (i.e. non-present file)
     103  dummy.setstate(ios::eofbit);
     104  CPPUNIT_ASSERT(dummy.eof());
    108105  BG = new BondGraph(true);
    109106  CPPUNIT_ASSERT(BG != NULL && "could not create BondGraph");
    … …  
    114111{
    115112  // remove the file
    116   remove(filename->c_str());
    117   delete(filename);
    118   delete(dummyname);
    119113  delete(BG);
    120114
    … …  
    139133void BondGraphTest::LoadTableTest()
    140134{
    141   CPPUNIT_ASSERT_EQUAL( true , BG->LoadBondLengthTable(*filename) );
     135  CPPUNIT_ASSERT_EQUAL( true , BG->LoadBondLengthTable(test) );
    142136  CPPUNIT_ASSERT_EQUAL( 1., BG->GetBondLength(0,0) );
    143137  CPPUNIT_ASSERT_EQUAL( 1.2, BG->GetBondLength(0,5) );
    … …  
    152146  molecule::iterator Runner = TestMolecule->begin();
    153147  Runner++;
    154   CPPUNIT_ASSERT_EQUAL( true , BG->LoadBondLengthTable(*filename) );
     148  CPPUNIT_ASSERT_EQUAL( true , BG->LoadBondLengthTable(test) );
    155149  CPPUNIT_ASSERT_EQUAL( true , BG->ConstructBondGraph(TestMolecule) );
    156150  CPPUNIT_ASSERT_EQUAL( true , (*Walker)->IsBondedTo((*Runner)) );
    … …  
    165159  //atom *Runner = TestMolecule->end->previous;
    166160  //CPPUNIT_ASSERT( TestMolecule->end != Walker );
    167   CPPUNIT_ASSERT_EQUAL( false , BG->LoadBondLengthTable(*dummyname) );
     161  CPPUNIT_ASSERT_EQUAL( false , BG->LoadBondLengthTable(dummy) );
    168162  CPPUNIT_ASSERT_EQUAL( true , BG->ConstructBondGraph(TestMolecule) );
    169163

  • src/unittests/BondGraphUnitTest.hpp

    rc14c78 r0bfe73  
    4949
    5050      BondGraph *BG;
    51       string *filename;
    52       string *dummyname;
     51      std::stringstream dummy;
     52      std::stringstream test;
    5353};
    5454

  • src/unittests/FormulaUnitTest.cpp

    rc14c78 r0bfe73  
    246246  }
    247247  {
    248     CPPUNIT_ASSERT_THROW(Formula formula("74107"),ParseError);
    249     CPPUNIT_ASSERT_THROW(Formula formula("  "),ParseError);
    250     CPPUNIT_ASSERT_THROW(Formula formula("nAcL"),ParseError);
    251     CPPUNIT_ASSERT_THROW(Formula formula("NAcL"),ParseError);
    252     CPPUNIT_ASSERT_THROW(Formula formula("Na Cl"),ParseError);
    253     CPPUNIT_ASSERT_THROW(Formula formula("1NaCl"),ParseError);
    254     CPPUNIT_ASSERT_THROW(Formula formula("Mag"),ParseError);
    255     CPPUNIT_ASSERT_THROW(Formula formula("AgCl)"),ParseError);
    256     CPPUNIT_ASSERT_THROW(Formula formula("(Na"),ParseError);
    257     CPPUNIT_ASSERT_THROW(Formula formula("(Mag)"),ParseError);
    258     CPPUNIT_ASSERT_THROW(Formula formula("MgCl2)"),ParseError);
    259     CPPUNIT_ASSERT_THROW(Formula formula("((MgCl2)"),ParseError);
    260     CPPUNIT_ASSERT_THROW(Formula formula("(MgCl2))"),ParseError);
    261     CPPUNIT_ASSERT_THROW(Formula formula("(MgCl2]"),ParseError);
    262     CPPUNIT_ASSERT_THROW(Formula formula("[MgCl2)"),ParseError);
    263     CPPUNIT_ASSERT_THROW(Formula formula("N(aCl"),ParseError);
    264     CPPUNIT_ASSERT_THROW(Formula formula("Na()Cl"),ParseError);
     248    CPPUNIT_ASSERT_THROW(Formula formula("74107"),FormulaStringParseException);
     249    CPPUNIT_ASSERT_THROW(Formula formula("  "),FormulaStringParseException);
     250    CPPUNIT_ASSERT_THROW(Formula formula("nAcL"),FormulaStringParseException);
     251    CPPUNIT_ASSERT_THROW(Formula formula("NAcL"),FormulaStringParseException);
     252    CPPUNIT_ASSERT_THROW(Formula formula("Na Cl"),FormulaStringParseException);
     253    CPPUNIT_ASSERT_THROW(Formula formula("1NaCl"),FormulaStringParseException);
     254    CPPUNIT_ASSERT_THROW(Formula formula("Mag"),FormulaStringParseException);
     255    CPPUNIT_ASSERT_THROW(Formula formula("AgCl)"),FormulaStringParseException);
     256    CPPUNIT_ASSERT_THROW(Formula formula("(Na"),FormulaStringParseException);
     257    CPPUNIT_ASSERT_THROW(Formula formula("(Mag)"),FormulaStringParseException);
     258    CPPUNIT_ASSERT_THROW(Formula formula("MgCl2)"),FormulaStringParseException);
     259    CPPUNIT_ASSERT_THROW(Formula formula("((MgCl2)"),FormulaStringParseException);
     260    CPPUNIT_ASSERT_THROW(Formula formula("(MgCl2))"),FormulaStringParseException);
     261    CPPUNIT_ASSERT_THROW(Formula formula("(MgCl2]"),FormulaStringParseException);
     262    CPPUNIT_ASSERT_THROW(Formula formula("[MgCl2)"),FormulaStringParseException);
     263    CPPUNIT_ASSERT_THROW(Formula formula("N(aCl"),FormulaStringParseException);
     264    CPPUNIT_ASSERT_THROW(Formula formula("Na()Cl"),FormulaStringParseException);
    265265  }
    266266

  • src/unittests/Makefile.am

    rc14c78 r0bfe73  
    7777  ../UIElements/Menu/unittests/MenuDescriptionUnitTest.cpp \
    7878  ../Descriptors/unittests/MoleculeDescriptorUnitTest.cpp \
    79   ../Parser/unittests/ParserCommonUnitTest.cpp \
     79  ../Parser/unittests/ParserMpqcUnitTest.cpp \
     80  ../Parser/unittests/ParserPcpUnitTest.cpp \
     81  ../Parser/unittests/ParserPdbUnitTest.cpp \
    8082  ../Parser/unittests/ParserTremoloUnitTest.cpp \
     83  ../Parser/unittests/ParserXyzUnitTest.cpp \
    8184  PeriodentafelUnitTest.cpp \
    8285  ../LinearAlgebra/unittests/PlaneUnitTest.cpp \
    … …  
    111114  ../UIElements/Menu/unittests/MenuDescriptionUnitTest.hpp \
    112115  ../Descriptors/unittests/MoleculeDescriptorUnitTest.hpp \
    113   ../Parser/unittests/ParserCommonUnitTest.hpp \
     116  ../Parser/unittests/ParserMpqcUnitTest.hpp \
     117  ../Parser/unittests/ParserPcpUnitTest.hpp \
     118  ../Parser/unittests/ParserPdbUnitTest.hpp \
    114119  ../Parser/unittests/ParserTremoloUnitTest.hpp \
     120  ../Parser/unittests/ParserXyzUnitTest.hpp \
    115121  PeriodentafelUnitTest.hpp \
    116122  ../LinearAlgebra/unittests/PlaneUnitTest.hpp \

  • src/unittests/SubspaceFactorizerUnitTest.cpp

    rc14c78 r0bfe73  
    3939#include "LinearAlgebra/VectorContent.hpp"
    4040
     41#include "RandomNumbers/RandomNumberGeneratorFactory.hpp"
     42#include "RandomNumbers/RandomNumberGenerator.hpp"
     43
    4144#include "SubspaceFactorizerUnitTest.hpp"
    4245
    … …  
    4952
    5053void SubspaceFactorizerUnittest::setUp(){
     54//  RandomNumberGenerator &random = RandomNumberGeneratorFactory::getInstance().makeRandomNumberGenerator();
     55//  const double rng_min = rng->min();
     56//  const double rng_max = rng->max();
    5157  matrix = new MatrixContent(matrixdimension,matrixdimension);
    5258  matrix->setZero();
    5359  for (size_t i=0; i<matrixdimension ; i++) {
    5460    for (size_t j=0; j<= i; ++j) {
    55       //const double value = 10. * rand() / (double)RAND_MAX;
     61      //const double value = 10. * random() / (rng_max-rng_min);
    5662      //const double value = i==j ? 2. : 1.;
    5763      if (i==j)

  • tests/Makefile.am

    rc14c78 r0bfe73  
    1 SUBDIRS = CodeChecks regression Tesselations
     1SUBDIRS = CodeChecks regression Fragmentations Tesselations
    22

  • tests/Tesselations/Makefile.am

    rc14c78 r0bfe73  
    1616
    1717#       heptan.test
     18
     19${TESTS}: defs

  • tests/Tesselations/defs.in

    rc14c78 r0bfe73  
    3030        CLEANUP="$CLEANUP; rm -rf $testdir"
    3131        cp -r @srcdir@/$testdir/* $testdir/
    32         CLEANUP="rm -f stderr stdout diffstderr diffstdout; cd ..; $CLEANUP"
     32        CLEANUP="rm -f stderr stdout diffstderr diffstdout; $CLEANUP"
    3333        CLEANUP="rm -f *.conf*; rm -f NonConvexEnvelope*; rm -f ${testdir}.xyz; rm -f ${testdir}.dbond; $CLEANUP"
    3434fi
    … …  
    3636# debug runs should keep results
    3737if $DEBUG; then :; else
    38         trap "eval \"$CLEANUP\"" 0 1 2 13 15
     38        trap 'eval "$CLEANUP"' 0 1 2 13 15
    3939fi
    4040
    … …  
    5252        exitcode=0
    5353        cd $testdir/$RADIUS
    54         #echo "Current dir is `pwd`, calling $MOLECUILDER $mol.conf -e $exec_prefix -p ../$mol.xyz -N $RADIUS $FILENAME."
     54        echo "Current dir is `pwd`, calling $MOLECUILDER $mol.conf -e $exec_prefix -p ../$mol.xyz -N $RADIUS $FILENAME."
    5555        if [ -e $mol.dbond ]; then
    5656                $MOLECUILDER -i ../$mol.xyz -A $mol.dbond --select-molecule-by-id 0 -N $RADIUS --nonconvex-file $FILENAME 2>stderr >stdout || exitcode=$?
    … …  
    5858                $MOLECUILDER -i ../$mol.xyz --select-molecule-by-id 0 -N $RADIUS --nonconvex-file $FILENAME 2>stderr >stdout || exitcode=$?
    5959        fi
    60         #echo "Molecuilder done with exitcode $exitcode."
     60        echo "Molecuilder done with exitcode $exitcode."
    6161        cd ../..
    62         #cat stderr
    63         #cat stdout
    64         grep -E "^[0-9]* [0-9]* [0-9]*$" @srcdir@/$mol/$2/${FILENAME}-$mol.dat | sort -n >$testdir/$RADIUS/reference-triangles.dat
    65         grep -E "^[0-9]* [0-9]* [0-9]*$" $testdir/$RADIUS/${FILENAME}.dat | sort -n >$testdir/$RADIUS/new-triangles.dat
    66         diff $testdir/$RADIUS/reference-triangles.dat $testdir/$RADIUS/new-triangles.dat 2>$testdir/$RADIUS/diffstderr >$testdir/$RADIUS/diffstdout || exitcode=$?
    67         #echo "Diff done with exitcode $exitcode."
    68         #cat diffstderr
    69         #cat diffstdout
    70         test $exitcode = $expected_exitcode || exit 1
     62        grep -E "^[0-9]* [0-9]* [0-9]*$" @srcdir@/$mol/$2/${FILENAME}-$mol.dat | sort -n >$testdir/$RADIUS/reference-triangles.dat
     63        grep -E "^[0-9]* [0-9]* [0-9]*$" $testdir/$RADIUS/${FILENAME}.dat | sort -n >$testdir/$RADIUS/new-triangles.dat
     64        diff $testdir/$RADIUS/reference-triangles.dat $testdir/$RADIUS/new-triangles.dat 2>$testdir/$RADIUS/diffstderr >$testdir/$RADIUS/diffstdout || exitcode=$?
     65
     66        if test $exitcode = $expected_exitcode; then
     67                :
     68        else
     69                CLEANUP=
     70                exit 1
     71        fi
    7172}
    7273

  • tests/regression/Analysis/PrincipalAxisSystem/testsuite-analysis-principal-axis-system.at

    rc14c78 r0bfe73  
    1 ### 5. principal axis system
     1### principal axis system
    22
    33AT_SETUP([Analysis - Principal Axis System])

  • tests/regression/Analysis/testsuite-analysis.at

    rc14c78 r0bfe73  
    11AT_BANNER([MoleCuilder - Analysis])
    22
    3 # 1. & 2. pair correlation analysis
    4 m4_include(Analysis/testsuite-analysis-pair-correlation.at)
     3# pair correlation analysis
     4m4_include(Analysis/PairCorrelation/testsuite-analysis-pair-correlation.at)
    55
    6 # 3. pair correlation analysis to point
    7 m4_include(Analysis/testsuite-analysis-point-correlation.at)
     6# pair correlation analysis - range test
     7m4_include(Analysis/PairCorrelation-RangeTest/testsuite-analysis-pair-correlation-range-test.at)
    88
    9 # 4. pair correlation analysis to surface
    10 m4_include(Analysis/testsuite-analysis-surface-correlation.at)
     9# pair correlation analysis to point
     10m4_include(Analysis/PointCorrelation/testsuite-analysis-point-correlation.at)
    1111
    12 # 5. principal axis system
     12# pair correlation analysis to surface
     13m4_include(Analysis/SurfaceCorrelation/testsuite-analysis-surface-correlation.at)
     14
     15# principal axis system
    1316m4_include(Analysis/PrincipalAxisSystem/testsuite-analysis-principal-axis-system.at)
    1417
    15 # 6. angular dipole correlation - empty
    16 m4_include(Analysis/testsuite-analysis-angular-dipole-correlation-empty.at)
     18# angular dipole correlation - empty
     19m4_include(Analysis/AngularDipoleCorrelation-Empty/testsuite-analysis-angular-dipole-correlation-empty.at)
    1720
    18 # 7. angular dipole correlation - discrete angles
    19 m4_include(Analysis/testsuite-analysis-angular-dipole-correlation-discrete-angles.at)
    20 
    21 # 8. angular dipole correlation - random distribution
    22 m4_include(Analysis/testsuite-analysis-angular-dipole-correlation-random-distribution.at)
     21# angular dipole correlation - discrete angles
     22m4_include(Analysis/AngularDipoleCorrelation-DiscreteAngles/testsuite-analysis-angular-dipole-correlation-discrete-angles.at)

  • tests/regression/Filling/testsuite-filling.at

    rc14c78 r0bfe73  
    11AT_BANNER([MoleCuilder - Filling in molecules])
    22
    3 # 1. filling box
    4 m4_include(Filling/testsuite-fill-with-molecule.at)
     3# filling box
     4m4_include(Filling/FillWithMolecule/testsuite-fill-with-molecule.at)
    55
    6 # 2. suspend in water with certain density
    7 m4_include(Filling/testsuite-suspend-in-water.at)
     6# suspend in water with certain density
     7m4_include(Filling/SuspendInWater/testsuite-suspend-in-water.at)
    88
    9 # 3. filling box
    10 m4_include(Filling/testsuite-fill-void-with-molecule.at)
     9# filling box
     10m4_include(Filling/FillVoidWithMolecule/testsuite-fill-void-with-molecule.at)

  • tests/regression/Makefile.am

    rc14c78 r0bfe73  
    66        molecuider.in \
    77        Analysis \
     8        Atoms \
    89        Domain \
    910        Filling \
    … …  
    1112        Graph \
    1213        Molecules \
     14        Options \
     15        Parser \
    1316        RandomNumbers \
    1417        Selection \
    15         Simple_configuration \
    1618        Tesselation
    1719TESTSUITE = $(srcdir)/testsuite
    1820
    1921TESTSCRIPTS = \
     22        $(srcdir)/Atoms/testsuite-atoms.at \
     23        $(srcdir)/Atoms/Add/testsuite-atoms-add.at \
     24        $(srcdir)/Atoms/ChangeElement/testsuite-atoms-change-element.at \
     25        $(srcdir)/Atoms/Remove/testsuite-atoms-remove.at \
     26        $(srcdir)/Atoms/RemoveInsideSphere/testsuite-atoms-remove-inside-sphere.at \
     27        $(srcdir)/Atoms/RemoveInsideCuboid/testsuite-atoms-remove-inside-cuboid.at \
     28        $(srcdir)/Atoms/Translation/testsuite-atoms-translation.at \
    2029        $(srcdir)/Analysis/testsuite-analysis.at \
    21         $(srcdir)/Analysis/testsuite-analysis-pair-correlation.at \
    22         $(srcdir)/Analysis/testsuite-analysis-point-correlation.at \
    23         $(srcdir)/Analysis/testsuite-analysis-surface-correlation.at \
     30        $(srcdir)/Analysis/PairCorrelation/testsuite-analysis-pair-correlation.at \
     31        $(srcdir)/Analysis/PairCorrelation-RangeTest/testsuite-analysis-pair-correlation-range-test.at \
     32        $(srcdir)/Analysis/PointCorrelation/testsuite-analysis-point-correlation.at \
     33        $(srcdir)/Analysis/SurfaceCorrelation/testsuite-analysis-surface-correlation.at \
    2434        $(srcdir)/Analysis/PrincipalAxisSystem/testsuite-analysis-principal-axis-system.at \
    25         $(srcdir)/Analysis/testsuite-analysis-angular-dipole-correlation-empty.at \
    26         $(srcdir)/Analysis/testsuite-analysis-angular-dipole-correlation-discrete-angles.at \
    27         $(srcdir)/Analysis/testsuite-analysis-angular-dipole-correlation-random-distribution.at \
    28         $(srcdir)/testsuite-domain.at \
     35        $(srcdir)/Analysis/AngularDipoleCorrelation-Empty/testsuite-analysis-angular-dipole-correlation-empty.at \
     36        $(srcdir)/Analysis/AngularDipoleCorrelation-DiscreteAngles/testsuite-analysis-angular-dipole-correlation-discrete-angles.at \
     37        $(srcdir)/Domain/testsuite-domain.at \
     38        $(srcdir)/Domain/ChangeBox/testsuite-domain-change-box.at \
     39        $(srcdir)/Domain/CenterInBox/testsuite-domain-center-in-box.at \
     40        $(srcdir)/Domain/AddEmptyBoundary/testsuite-domain-add-empty-boundary.at \
     41        $(srcdir)/Domain/CenterOnEdge/testsuite-domain-center-on-edge.at \
     42        $(srcdir)/Domain/ScaleBox/testsuite-domain-scale-box.at \
     43        $(srcdir)/Domain/RepeatBox/testsuite-domain-repeat-box.at \
    2944        $(srcdir)/Filling/testsuite-filling.at \
    30         $(srcdir)/Filling/testsuite-fill-with-molecule.at \
    31         $(srcdir)/Filling/testsuite-suspend-in-water.at \
    32         $(srcdir)/Filling/testsuite-fill-void-with-molecule.at \
    33         $(srcdir)/testsuite-fragmentation.at \
    34         $(srcdir)/testsuite-graph.at \
    35         $(srcdir)/testsuite-molecules.at \
    36         $(srcdir)/testsuite-simple_configuration.at \
     45        $(srcdir)/Filling/FillWithMolecule/testsuite-fill-with-molecule.at \
     46        $(srcdir)/Filling/SuspendInWater/testsuite-suspend-in-water.at \
     47        $(srcdir)/Filling/FillVoidWithMolecule/testsuite-fill-void-with-molecule.at \
     48        $(srcdir)/Fragmentation/testsuite-fragmentation.at \
     49        $(srcdir)/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at \
     50        $(srcdir)/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at \
     51        $(srcdir)/Graph/testsuite-graph.at \
     52        $(srcdir)/Graph/DepthFirstSearch/testsuite-graph-depth-first-search.at \
     53        $(srcdir)/Graph/SubgraphDissection/testsuite-graph-subgraph-dissection.at \
     54        $(srcdir)/Molecules/testsuite-molecules.at \
     55        $(srcdir)/Molecules/BondFile/testsuite-molecules-bond-file.at \
     56        $(srcdir)/Molecules/SaveAdjacency/testsuite-molecules-save-adjacency.at \
     57        $(srcdir)/Molecules/SaveBonds/testsuite-molecules-save-bonds.at \
     58        $(srcdir)/Molecules/SaveTemperature/testsuite-molecules-save-temperature.at \
     59        $(srcdir)/Molecules/LinearInterpolationofTrajectories/testsuite-molecules-linear-interpolation-of-trajectories.at \
     60        $(srcdir)/Molecules/VerletIntegration/testsuite-molecules-verlet-integration.at \
     61        $(srcdir)/Molecules/Translation/testsuite-molecules-translation.at \
     62        $(srcdir)/Molecules/Translation-Periodic/testsuite-molecules-translation-periodic.at \
     63        $(srcdir)/Molecules/RotateToPrincipalAxisSystem/testsuite-molecules-rotate-to-principal-axis-system.at \
     64        $(srcdir)/Molecules/RotateAroundOrigin/testsuite-molecules-rotate-around-origin.at \
     65        $(srcdir)/Molecules/RotateAroundSelf/testsuite-molecules-rotate-around-self.at \
     66        $(srcdir)/Molecules/Copy/testsuite-molecules-copy-molecule.at \
     67        $(srcdir)/Options/testsuite-options.at \
     68        $(srcdir)/Options/Verbosity/testsuite-options-verbosity.at \
     69        $(srcdir)/Options/Warranty/testsuite-options-warranty.at \
     70        $(srcdir)/Options/Help/testsuite-options-help.at \
     71        $(srcdir)/Options/ElementsDb/testsuite-options-no-elements-db.at \
     72        $(srcdir)/Options/ElementsDb/testsuite-options-elements-db.at \
     73        $(srcdir)/Options/BondLengthTable/testsuite-options-bond-length-table.at \
     74        $(srcdir)/Options/FastParsing/testsuite-options-fast-parsing.at \
     75        $(srcdir)/Options/SetDefaultName/testsuite-options-set-default-name.at \
     76        $(srcdir)/Options/Empty/testsuite-options-empty-configs.at \
     77        $(srcdir)/Options/InvalidCommands/testsuite-options-invalid-commands.at \
     78        $(srcdir)/Parser/testsuite-parser.at \
     79        $(srcdir)/Parser/Mpqc/testsuite-parser-mpqc.at \
     80        $(srcdir)/Parser/Mpqc-SetParameters/testsuite-parser-mpqc-set-parameters.at \
     81        $(srcdir)/Parser/Pcp/testsuite-parser-pcp.at \
     82        $(srcdir)/Parser/Pdb/testsuite-parser-pdb.at \
     83        $(srcdir)/Parser/Tremolo/testsuite-parser-tremolo.at \
     84        $(srcdir)/Parser/Xyz/testsuite-parser-xyz.at \
    3785        $(srcdir)/RandomNumbers/testsuite-randomnumbers.at \
    3886        $(srcdir)/RandomNumbers/Distribution/testsuite-set-random-number-distribution.at \
    3987        $(srcdir)/RandomNumbers/Engine/testsuite-set-random-number-engine.at \
    4088        $(srcdir)/Selection/testsuite-selection.at \
    41         $(srcdir)/Selection/Atoms/testsuite-selection-all-atoms.at \
    42         $(srcdir)/Selection/Atoms/testsuite-selection-atoms-by-element.at \
    43         $(srcdir)/Selection/Atoms/testsuite-selection-atom-by-id.at \
    44         $(srcdir)/Selection/Atoms/testsuite-selection-atoms-inside-cuboid.at \
    45         $(srcdir)/Selection/Atoms/testsuite-selection-atoms-inside-sphere.at \
    46         $(srcdir)/Selection/Atoms/testsuite-selection-atoms-of-molecule.at \
    47         $(srcdir)/Selection/Atoms/testsuite-selection-clear-atoms.at \
    48         $(srcdir)/Selection/Molecules/testsuite-selection-all-molecules.at \
    49         $(srcdir)/Selection/Molecules/testsuite-selection-clear-molecules.at \
    50         $(srcdir)/Selection/Molecules/testsuite-selection-molecules-by-formula.at \
    51         $(srcdir)/Selection/Molecules/testsuite-selection-molecule-by-id.at \
    52         $(srcdir)/Selection/Molecules/testsuite-selection-molecules-by-name.at \
    53         $(srcdir)/Selection/Molecules/testsuite-selection-molecules-of-atoms.at \
    54         $(srcdir)/testsuite-specifics.at \
    55         $(srcdir)/testsuite-standard_options.at \
    56         $(srcdir)/testsuite-tesselation.at
     89        $(srcdir)/Selection/Atoms/AllAtoms/testsuite-selection-all-atoms.at \
     90        $(srcdir)/Selection/Atoms/AllAtomsOfMolecule/testsuite-selection-all-atoms-of-molecule.at \
     91        $(srcdir)/Selection/Atoms/AtomByElement/testsuite-selection-atoms-by-element.at \
     92        $(srcdir)/Selection/Atoms/AtomById/testsuite-selection-atom-by-id.at \
     93        $(srcdir)/Selection/Atoms/AtomsInsideCuboid/testsuite-selection-atoms-inside-cuboid.at \
     94        $(srcdir)/Selection/Atoms/AtomsInsideSphere/testsuite-selection-atoms-inside-sphere.at \
     95        $(srcdir)/Selection/Atoms/ClearAtoms/testsuite-selection-clear-atoms.at \
     96        $(srcdir)/Selection/Molecules/AllMolecules/testsuite-selection-all-molecules.at \
     97        $(srcdir)/Selection/Molecules/ClearMolecules/testsuite-selection-clear-molecules.at \
     98        $(srcdir)/Selection/Molecules/MoleculeByFormula/testsuite-selection-molecules-by-formula.at \
     99        $(srcdir)/Selection/Molecules/MoleculeById/testsuite-selection-molecule-by-id.at \
     100        $(srcdir)/Selection/Molecules/MoleculeByName/testsuite-selection-molecules-by-name.at \
     101        $(srcdir)/Selection/Molecules/MoleculeOfAtom/testsuite-selection-atoms-molecules.at \
     102        $(srcdir)/Tesselation/testsuite-tesselation.at \
     103        $(srcdir)/Tesselation/NonConvex/testsuite-tesselation-non-convex-envelope.at \
     104        $(srcdir)/Tesselation/Convex/testsuite-tesselation-convex-envelope.at \
     105        $(srcdir)/Tesselation/BigNonConvex/testsuite-tesselation-big-non-convex-envelope.at \
     106        $(srcdir)/Tesselation/BigConvex/testsuite-tesselation-big-convex-envelope.at
    57107
    58108

  • tests/regression/Selection/testsuite-selection.at

    rc14c78 r0bfe73  
    33### ATOMS ####
    44
    5 # 5. (un)select atoms by element
    6 m4_include(Selection/Atoms/testsuite-selection-atoms-by-element.at)
     5# (un)select all atoms
     6m4_include(Selection/Atoms/AllAtoms/testsuite-selection-all-atoms.at)
    77
    8 # 6. (un)select atom by id
    9 m4_include(Selection/Atoms/testsuite-selection-atom-by-id.at)
     8# (un)select all atoms of molecule
     9m4_include(Selection/Atoms/AllAtomsOfMolecule/testsuite-selection-all-atoms-of-molecule.at)
    1010
    11 # 1. (un)select all atoms
    12 m4_include(Selection/Atoms/testsuite-selection-all-atoms.at)
     11# (un)select atoms by element
     12m4_include(Selection/Atoms/AtomByElement/testsuite-selection-atoms-by-element.at)
    1313
    14 # 2. (un)select all atoms inside cuboid
    15 m4_include(Selection/Atoms/testsuite-selection-atoms-inside-cuboid.at)
     14# (un)select atom by id
     15m4_include(Selection/Atoms/AtomById/testsuite-selection-atom-by-id.at)
    1616
    17 # 3. (un)select all atoms inside sphere
    18 m4_include(Selection/Atoms/testsuite-selection-atoms-inside-sphere.at)
     17# (un)select atoms inside cuboid
     18m4_include(Selection/Atoms/AtomsInsideCuboid/testsuite-selection-atoms-inside-cuboid.at)
    1919
    20 # 4. (un)select all atoms of molecule
    21 m4_include(Selection/Atoms/testsuite-selection-atoms-of-molecule.at)
     20# (un)select atoms inside sphere
     21m4_include(Selection/Atoms/AtomsInsideSphere/testsuite-selection-atoms-inside-sphere.at)
    2222
    23 # 7. clear atom selection
    24 m4_include(Selection/Atoms/testsuite-selection-clear-atoms.at)
     23# clear atom selection
     24m4_include(Selection/Atoms/ClearAtoms/testsuite-selection-clear-atoms.at)
    2525
    2626### Molecules ###
    2727
    28 # 1. (un)select all molecules
    29 m4_include(Selection/Molecules/testsuite-selection-all-molecules.at)
     28# (un)select all molecules
     29m4_include(Selection/Molecules/AllMolecules/testsuite-selection-all-molecules.at)
    3030
    31 # 2. clear molecule selection
    32 m4_include(Selection/Molecules/testsuite-selection-clear-molecules.at)
     31# clear molecule selection
     32m4_include(Selection/Molecules/ClearMolecules/testsuite-selection-clear-molecules.at)
    3333
    34 # 3. (un)select molecules by formula
    35 m4_include(Selection/Molecules/testsuite-selection-molecules-by-formula.at)
     34# (un)select molecules by formula
     35m4_include(Selection/Molecules/MoleculeByFormula/testsuite-selection-molecules-by-formula.at)
    3636
    37 # 4. (un)select molecule by id
    38 m4_include(Selection/Molecules/testsuite-selection-molecule-by-id.at)
     37# (un)select molecule by id
     38m4_include(Selection/Molecules/MoleculeById/testsuite-selection-molecule-by-id.at)
    3939
    40 # 5. (un)select molecule by name
    41 m4_include(Selection/Molecules/testsuite-selection-molecules-by-name.at)
     40# (un)select molecule by name
     41m4_include(Selection/Molecules/MoleculeByName/testsuite-selection-molecules-by-name.at)
    4242
    43 # 6. (un)select molecule from atom selection
    44 m4_include(Selection/Molecules/testsuite-selection-molecules-of-atoms.at)
     43# (un)select molecule from atom selection
     44m4_include(Selection/Molecules/MoleculeOfAtom/testsuite-selection-atoms-molecules.at)

  • tests/regression/testsuite.at

    rc14c78 r0bfe73  
    77AT_TESTED(diff grep egrep fgrep)
    88
     9# makes functions in CheckCommand.sh available within the tests
     10# This is not yet working due to a bug in autotest (AC_CHECK cannot be used inside diversion)
     11#m4_divert_push([PREPARE_TESTS])
     12#m4_include([CheckCommand.sh])
     13#m4_divert_pop([PREPARE_TESTS])
     14
    915# Use colored output with new-enough Autotest.
    1016m4_ifdef([AT_COLOR_TESTS], [AT_COLOR_TESTS])
    1117
    12 m4_include(testsuite-standard_options.at)
     18m4_include(Options/testsuite-options.at)
    1319
    14 m4_include(testsuite-specifics.at)
     20m4_include(Parser/testsuite-parser.at)
    1521
    16 m4_include(testsuite-simple_configuration.at)
     22m4_include(Atoms/testsuite-atoms.at)
    1723
    1824m4_include(Selection/testsuite-selection.at)
    … …  
    2026m4_include(RandomNumbers/testsuite-randomnumbers.at)
    2127
    22 m4_include(testsuite-domain.at)
     28m4_include(Domain/testsuite-domain.at)
    2329
    24 m4_include(testsuite-graph.at)
     30m4_include(Graph/testsuite-graph.at)
    2531
    26 m4_include(testsuite-molecules.at)
     32m4_include(Molecules/testsuite-molecules.at)
    2733
    28 m4_include(testsuite-fragmentation.at)
     34m4_include(Fragmentation/testsuite-fragmentation.at)
    2935
    30 m4_include(testsuite-tesselation.at)
     36m4_include(Tesselation/testsuite-tesselation.at)
    3137
    3238m4_include(Filling/testsuite-filling.at)
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