Changes in / [311da7b:b6b3b2]


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Files:
6 added
16 edited

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Removed

  • src/Actions/Makefile.am

    r311da7b rb6b3b2  
    128128
    129129PARSERACTIONSOURCE = \
     130  ParserAction/ParseTremoloPotentialsAction.cpp \
    130131  ParserAction/SetMpqcParametersAction.cpp \
    131132  ParserAction/SetOutputFormatsAction.cpp
    132133PARSERACTIONHEADER = \
     134  ParserAction/ParseTremoloPotentialsAction.hpp \
    133135  ParserAction/SetMpqcParametersAction.hpp \
    134136  ParserAction/SetOutputFormatsAction.hpp               

  • src/Actions/RandomNumbersAction/SetRandomNumbersDistributionAction.cpp

    r311da7b rb6b3b2  
    5959  // set each parameter (that is not -1);
    6060  if (!params.parameters.isDefault()) {
    61     RandomNumberDistribution_Parameters *oldparameters =
     61    RandomNumberDistribution_Parameters *currentparameters =
    6262        RandomNumberDistributionFactory::getInstance().getPrototype().getParameterSet();
    63     oldparameters->update(params.parameters);
     63    currentparameters->update(params.parameters);
    6464    DoLog(1) && (Log() << Verbose(1) << "Changing prototype's parameters to "
    6565        << params.parameters << "." << std::endl);
    66     RandomNumberDistributionFactory::getInstance().manipulatePrototype(*oldparameters);
     66    RandomNumberDistributionFactory::getInstance().manipulatePrototype(*currentparameters);
     67    delete currentparameters;
    6768  }
    6869

  • src/Parser/TremoloAtomInfoContainer.cpp

    r311da7b rb6b3b2  
    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

    r311da7b rb6b3b2  
    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

    r311da7b rb6b3b2  
    2222#include "CodePatterns/Assert.hpp"
    2323#include "CodePatterns/Log.hpp"
     24#include "CodePatterns/toString.hpp"
    2425#include "CodePatterns/Verbose.hpp"
    2526#include "TremoloParser.hpp"
    … …  
    6667  knownKeys["torsion"] = TremoloKey::torsion;
    6768
     69  createKnownTypesByIdentity();
     70
    6871  // default behavior: use all possible keys on output
    6972  for (std::map<std::string, TremoloKey::atomDataKey>::iterator iter = knownKeys.begin(); iter != knownKeys.end(); ++iter)
    … …  
    7275  // and noKey afterwards(!) such that it is not used in usedFields
    7376  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();
    7483}
    7584
    … …  
    131140  vector<string>::iterator it;
    132141
     142  DoLog(3) && (Log() << Verbose(3) << "additionalAtomData contains: " << additionalAtomData << std::endl);
     143
    133144  *file << "# ATOMDATA";
    134145  for (it=usedFields.begin(); it < usedFields.end(); it++) {
    … …  
    162173  vector<string>::iterator it;
    163174  TremoloKey::atomDataKey currentField;
     175
     176  DoLog(4) && (Log() << Verbose(4) << "INFO: Saving atom " << *currentAtom << ", its father id is " << currentAtom->GetTrueFather()->getId() << std::endl);
    164177
    165178  for (it = usedFields.begin(); it != usedFields.end(); it++) {
    … …  
    168181      case TremoloKey::x :
    169182        // for the moment, assume there are always three dimensions
     183        DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << currentAtom->getPosition() << std::endl);
    170184        *file << currentAtom->at(0) << "\t";
    171185        *file << currentAtom->at(1) << "\t";
    … …  
    174188      case TremoloKey::u :
    175189        // for the moment, assume there are always three dimensions
     190        DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << currentAtom->AtomicVelocity << std::endl);
    176191        *file << currentAtom->AtomicVelocity[0] << "\t";
    177192        *file << currentAtom->AtomicVelocity[1] << "\t";
    … …  
    179194        break;
    180195      case TremoloKey::Type :
    181         *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        }
    182216        break;
    183217      case TremoloKey::Id :
     218        DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << currentAtom->getId()+1 << std::endl);
    184219        *file << currentAtom->getId()+1 << "\t";
    185220        break;
    186221      case TremoloKey::neighbors :
     222        DoLog(3) && (Log() << Verbose(3) << "Writing type " << knownKeyNames[currentField] << std::endl);
    187223        writeNeighbors(file, atoi(it->substr(it->find("=") + 1, 1).c_str()), currentAtom);
    188224        break;
    189225      case TremoloKey::resSeq :
    190         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);
    191228          *file << additionalAtomData[currentAtom->getId()].get(currentField);
    192229        } 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);
    193231          *file << setw(4) << currentAtom->getMolecule()->getId()+1;
    194232        } else {
     233          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " default value: " << defaultAdditionalData.get(currentField) << std::endl);
    195234          *file << defaultAdditionalData.get(currentField);
    196235        }
    197236        *file << "\t";
    198       break;
     237        break;
    199238      default :
    200         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);
    201241          *file << additionalAtomData[currentAtom->getId()].get(currentField);
    202         } 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);
    203244          *file << additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField);
    204245        } else {
     246          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " the default: " << defaultAdditionalData.get(currentField) << std::endl);
    205247          *file << defaultAdditionalData.get(currentField);
    206248        }
    … …  
    306348        break;
    307349      case TremoloKey::Type :
    308         char type[3];
     350      {
    309351        ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for "+keyName+"!");
    310         //DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
    311         strncpy(type, (*tok_iter).c_str(), 3);
     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);
    312357        tok_iter++;
    313         //type[1]='\0'; // cutoff after first char, correct for ATOM entries
    314         newAtom->setType(World::getInstance().getPeriode()->FindElement(type));
     358        newAtom->setType(World::getInstance().getPeriode()->FindElement(element));
    315359        ASSERT(newAtom->getType(), "Type was not set for this atom");
    316360        break;
     361      }
    317362      case TremoloKey::Id :
    318363        ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for "+keyName+"!");
    … …  
    476521}
    477522
     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

    r311da7b rb6b3b2  
    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/ParserTremoloUnitTest.cpp

    r311da7b rb6b3b2  
    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/RandomNumberDistributionFactory.hpp

    r311da7b rb6b3b2  
    1616#include "CodePatterns/Singleton.hpp"
    1717
     18#include "RandomNumberDistribution.hpp"
     19#include "RandomNumberDistribution_Parameters.hpp"
     20
    1821// this defines stuff necessary PREVIOUS of PrototypeFactory.hpp inclusion
    1922#include "RandomNumberDistributionFactory.def"
    … …  
    2528#include <map>
    2629
    27 class RandomNumberDistribution;
    28 class RandomNumberDistribution_Parameters;
    2930class RandomNumberDistributionFactoryUnitTest;
    3031class CommandSetRandomNumbersDistributionAction;

  • src/RandomNumbers/RandomNumberDistribution_Parameters.cpp

    r311da7b rb6b3b2  
    180180      tokenizer::iterator tok_valueiter = tok_paramiter;
    181181      tokenizer::iterator tok_checkiter = ++tok_valueiter;
    182       ASSERT(tok_valueiter == params.end(),
    183           "operator<< on RandomNumberDistribution_Parameters - missing value before ';'!");
     182      ASSERT(tok_paramiter != paramtokens.end(),
     183          "operator<< on RandomNumberDistribution_Parameters - missing value before '='!");
     184      ASSERT(tok_valueiter != paramtokens.end(),
     185          "operator<< on RandomNumberDistribution_Parameters - missing value after '='!");
    184186      ++tok_checkiter;
    185       ASSERT(tok_checkiter == params.end(),
     187      ASSERT(tok_checkiter == paramtokens.end(),
    186188          "operator<< on RandomNumberDistribution_Parameters - still tokens before ';'!");
    187189      DoLog(0) && (Log() << Verbose(0) << "INFO: Token pair is " << *tok_paramiter << "," << *tok_valueiter << std::endl);

  • src/RandomNumbers/RandomNumberEngineFactory.hpp

    r311da7b rb6b3b2  
    1616#include "CodePatterns/Singleton.hpp"
    1717
     18#include "RandomNumberEngine.hpp"
     19#include "RandomNumberEngine_Parameters.hpp"
     20
    1821// this defines stuff necessary PREVIOUS of PrototypeFactory.hpp inclusion
    1922#include "RandomNumberEngineFactory.def"
    … …  
    2528#include <map>
    2629
    27 class RandomNumberEngine;
    28 class RandomNumberEngine_Parameters;
    2930class RandomNumberEngineFactoryUnitTest;
    3031class CommandSetRandomNumbersEngineAction;

  • src/RandomNumbers/RandomNumberEngine_Parameters.cpp

    r311da7b rb6b3b2  
    103103      tokenizer::iterator tok_valueiter = tok_paramiter;
    104104      tokenizer::iterator tok_checkiter = ++tok_valueiter;
    105       ASSERT(tok_valueiter == params.end(),
    106           "operator<< on RandomNumberEngine_Parameters - missing value before ';'!");
     105      ASSERT(tok_paramiter != paramtokens.end(),
     106          "operator<< on RandomNumberEngine_Parameters - missing value before '=' in token"
     107          +*tok_iter+"!");
     108      ASSERT(tok_valueiter != paramtokens.end(),
     109          "operator<< on RandomNumberEngine_Parameters - missing value after '=' in token"
     110          +*tok_iter+"!");
    107111      ++tok_checkiter;
    108       ASSERT(tok_checkiter == params.end(),
    109           "operator<< on RandomNumberEngine_Parameters - still tokens before ';'!");
     112      ASSERT(tok_checkiter == paramtokens.end(),
     113          "operator<< on RandomNumberEngine_Parameters - still tokens before ';' in token"
     114          +*tok_iter+": "+*tok_checkiter+"!");
    110115      DoLog(0) && (Log() << Verbose(0) << "INFO: Token pair is " << *tok_paramiter << "," << *tok_valueiter << std::endl);
    111116      std::stringstream value(*tok_valueiter);

  • src/RandomNumbers/RandomNumberGeneratorFactory.hpp

    r311da7b rb6b3b2  
    2323#include <map>
    2424
    25 #include "unittests/RandomNumberGeneratorFactoryUnitTest.hpp"
    26 
    2725class RandomNumberGenerator;
     26class RandomNumberGeneratorFactoryTest;
    2827
    2928/** This is the abstract factory class for random number generators.

  • src/RandomNumbers/unittests/RandomNumberEngineFactoryUnitTest.cpp

    r311da7b rb6b3b2  
    130130
    131131  // change the prototype directly
    132   CPPUNIT_ASSERT ( 0 != prototype.getseed() );
    133   prototype.seed(0);
     132  CPPUNIT_ASSERT ( 2 != prototype.getseed() );
     133  prototype.seed(2);  // note for this prototype seed of 0 is not allowd by boost::random
    134134
    135135  // check that prototype has indeed been manipulated
    136136  rndA_2 = RandomNumberEngineFactory::getInstance().
    137137      getProduct(RandomNumberEngineFactory::minstd_rand0);
    138   CPPUNIT_ASSERT_EQUAL( (unsigned int)0, rndA_2->getseed() );
     138  CPPUNIT_ASSERT_EQUAL( (unsigned int)2, rndA_2->getseed() );
    139139  CPPUNIT_ASSERT( rndA_2->getseed() != rndA_1->getseed());
    140140

  • src/config.cpp

    r311da7b rb6b3b2  
    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

    r311da7b rb6b3b2  
    5050    bool FastParsing;
    5151    double Deltat;
    52     string basis;
    5352
    5453    char *databasepath;

  • tests/regression/Molecules/Copy/testsuite-molecules-copy-molecule.at

    r311da7b rb6b3b2  
    1212AT_CHECK([../../molecuilder -i test-copy.xyz  --copy-molecule 0 --position "0,0,10" --undo --redo], 0, [stdout], [stderr])
    1313AT_CHECK([diff -I '.*Created by molecuilder.*' test-copy.xyz ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/post/test-copy.xyz], 0, [ignore], [ignore])
     14AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/pre/tensid.* .], 0)
     15AT_CHECK([../../molecuilder --parse-tremolo-potentials tensid.potentials -i tensid.data  --copy-molecule 0 --position "0,0,10"], 0, [stdout], [stderr])
     16AT_CHECK([diff -I '.*Created by molecuilder.*' tensid.data ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/Copy/post/tensid.data], 0, [ignore], [ignore])
    1417AT_CLEANUP
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