Changeset 4d4d33


Ignore:
Timestamp:
Feb 9, 2011, 5:25:13 PM (14 years ago)
Author:
Frederik Heber <heber@…>
Branches:
Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable
Children:
acd638
Parents:
1a6bda
git-author:
Frederik Heber <heber@…> (02/09/11 16:18:50)
git-committer:
Frederik Heber <heber@…> (02/09/11 17:25:13)
Message:

Added tremolo's potential file parsing, reported by Daniel Dueck.

TremoloParser cannot interpret Type with HLA2 because it lacks mapping of the
value to an element. Hence, ...

  • new Action ParseTremoloPotentialsAction.
  • TremoloParser::knownTypes new map to contain: HLA2 -> H, ... map.
  • TremoloParser::createKnownTypesByIdentity() creates identity mapping.
  • TremoloParser::parseKnownTypes() parses potentials file.
Location:
src
Files:
3 added
6 edited

Legend:

Unmodified
Added
Removed
  • src/Actions/Makefile.am

    r1a6bda r4d4d33  
    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/Parser/TremoloAtomInfoContainer.cpp

    r1a6bda r4d4d33  
    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

    r1a6bda r4d4d33  
    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

    r1a6bda r4d4d33  
    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
     
    163172  TremoloKey::atomDataKey currentField;
    164173
     174  DoLog(3) && (Log() << Verbose(3) << "additionalAtomData contains: " << additionalAtomData << std::endl);
     175
    165176  for (it = usedFields.begin(); it != usedFields.end(); it++) {
    166177    currentField = knownKeys[it->substr(0, it->find("="))];
     
    168179      case TremoloKey::x :
    169180        // for the moment, assume there are always three dimensions
     181        DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << currentAtom->getPosition() << std::endl);
    170182        *file << currentAtom->at(0) << "\t";
    171183        *file << currentAtom->at(1) << "\t";
     
    174186      case TremoloKey::u :
    175187        // for the moment, assume there are always three dimensions
     188        DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << currentAtom->AtomicVelocity << std::endl);
    176189        *file << currentAtom->AtomicVelocity[0] << "\t";
    177190        *file << currentAtom->AtomicVelocity[1] << "\t";
     
    179192        break;
    180193      case TremoloKey::Type :
    181         *file << currentAtom->getType()->getSymbol() << "\t";
     194        if ((!additionalAtomData.count(currentAtom->getId())) || (additionalAtomData[currentAtom->getId()].get(currentField) == "-")) {
     195          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " default value: " << currentAtom->getType()->getSymbol() << std::endl);
     196          *file << currentAtom->getType()->getSymbol() << "\t";
     197        } else {
     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        }
    182201        break;
    183202      case TremoloKey::Id :
     203        DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << currentAtom->getId()+1 << std::endl);
    184204        *file << currentAtom->getId()+1 << "\t";
    185205        break;
    186206      case TremoloKey::neighbors :
     207        DoLog(3) && (Log() << Verbose(3) << "Writing type " << knownKeyNames[currentField] << std::endl);
    187208        writeNeighbors(file, atoi(it->substr(it->find("=") + 1, 1).c_str()), currentAtom);
    188209        break;
    189210      case TremoloKey::resSeq :
    190         if (additionalAtomData.find(currentAtom->getId()) != additionalAtomData.end()) {
     211        if (additionalAtomData.count(currentAtom->getId())) {
     212          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << additionalAtomData[currentAtom->getId()].get(currentField) << std::endl);
    191213          *file << additionalAtomData[currentAtom->getId()].get(currentField);
    192214        } else if (currentAtom->getMolecule() != NULL) {
     215          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " its own id: " << currentAtom->getMolecule()->getId()+1 << std::endl);
    193216          *file << setw(4) << currentAtom->getMolecule()->getId()+1;
    194217        } else {
     218          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " default value: " << defaultAdditionalData.get(currentField) << std::endl);
    195219          *file << defaultAdditionalData.get(currentField);
    196220        }
    197221        *file << "\t";
    198       break;
     222        break;
    199223      default :
    200         if (additionalAtomData.find(currentAtom->getId()) != additionalAtomData.end()) {
     224        if (additionalAtomData.count(currentAtom->getId())) {
     225          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << additionalAtomData[currentAtom->getId()].get(currentField) << std::endl);
    201226          *file << additionalAtomData[currentAtom->getId()].get(currentField);
    202         } else if (additionalAtomData.find(currentAtom->GetTrueFather()->getId()) != additionalAtomData.end()) {
     227        } else if (additionalAtomData.count(currentAtom->GetTrueFather()->getId())) {
     228          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " stuff from father: " << additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField) << std::endl);
    203229          *file << additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField);
    204230        } else {
     231          DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " the default: " << defaultAdditionalData.get(currentField) << std::endl);
    205232          *file << defaultAdditionalData.get(currentField);
    206233        }
     
    306333        break;
    307334      case TremoloKey::Type :
    308         char type[3];
     335      {
    309336        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);
     337        DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
     338        std::string element(knownTypes[(*tok_iter)]);
     339        // put type name into container for later use
     340        atomInfo->set(currentField, *tok_iter);
     341        DoLog(1) && (Log() << Verbose(1) << "INFO: Parsing element " << (*tok_iter) << " as " << element << " according to KnownTypes." << std::endl);
    312342        tok_iter++;
    313         //type[1]='\0'; // cutoff after first char, correct for ATOM entries
    314         newAtom->setType(World::getInstance().getPeriode()->FindElement(type));
     343        newAtom->setType(World::getInstance().getPeriode()->FindElement(element));
    315344        ASSERT(newAtom->getType(), "Type was not set for this atom");
    316345        break;
     346      }
    317347      case TremoloKey::Id :
    318348        ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for "+keyName+"!");
     
    476506}
    477507
     508/** Creates knownTypes as the identity, e.g. H -> H, He -> He, ... .
     509 *
     510 */
     511void TremoloParser::createKnownTypesByIdentity()
     512{
     513  // remove old mapping
     514  knownTypes.clear();
     515  // make knownTypes the identity mapping
     516  const periodentafel *periode = World::getInstance().getPeriode();
     517  for (periodentafel::const_iterator iter = periode->begin();
     518      iter != periode->end();
     519      ++iter) {
     520    knownTypes.insert( make_pair(iter->second->getSymbol(), iter->second->getSymbol()) );
     521  }
     522}
     523
     524/** Parses a .potentials file and creates from it the knownTypes file.
     525 *
     526 * @param file input stream of .potentials file
     527 */
     528void TremoloParser::parseKnownTypes(std::istream &file)
     529{
     530  const periodentafel *periode = World::getInstance().getPeriode();
     531  // remove old mapping
     532  knownTypes.clear();
     533
     534  DoLog(3) && (Log() << Verbose(3) << "additionalAtomData contains: " << additionalAtomData << std::endl);
     535
     536  // parse in file
     537  typedef boost::tokenizer<boost::char_separator<char> >
     538      tokenizer;
     539  boost::char_separator<char> tokensep(":\t ,;");
     540  boost::char_separator<char> equalitysep("\t =");
     541  std::string line;
     542  while (file.good()) {
     543    std::getline( file, line );
     544    DoLog(4) && (Log() << Verbose(4) << "INFO: full line of parameters is '" << line << "'" << std::endl);
     545    if (line.find("particle:") != string::npos) {
     546      DoLog(3) && (Log() << Verbose(3) << "INFO: found line '" << line << "' containing keyword 'particle:'." << std::endl);
     547      tokenizer tokens(line, tokensep);
     548      ASSERT(tokens.begin() != tokens.end(),
     549          "TremoloParser::parseKnownTypes() - line with 'particle:' but no particles separated by comma.");
     550      // look for particle_type
     551      std::string particle_type("NULL");
     552      std::string element_type("NULL");
     553      for (tokenizer::iterator tok_iter = tokens.begin();
     554          tok_iter != tokens.end();
     555          ++tok_iter) {
     556        if ((*tok_iter).find("particle_type") != string::npos) {
     557          DoLog(3) && (Log() << Verbose(3) << "INFO: found line '" << line << "' containing keyword 'particle_type'." << std::endl);
     558          tokenizer token((*tok_iter), equalitysep);
     559          ASSERT(token.begin() != token.end(),
     560                    "TremoloParser::parseKnownTypes() - could not split particle_type by equality sign");
     561          tokenizer::iterator particle_iter = token.begin();
     562          particle_iter++;
     563          particle_type = *particle_iter;
     564        }
     565        if ((*tok_iter).find("element_name") != string::npos) {
     566          DoLog(3) && (Log() << Verbose(3) << "INFO: found line '" << line << "' containing keyword 'element_name'." << std::endl);
     567          tokenizer token((*tok_iter), equalitysep);
     568          ASSERT(token.begin() != token.end(),
     569                    "TremoloParser::parseKnownTypes() - could not split particle_type by equality sign");
     570          tokenizer::iterator element_iter = token.begin();
     571          element_iter++;
     572          element_type = *element_iter;
     573        }
     574      }
     575      if ((particle_type != "NULL") && (element_type != "NULL")) {
     576        if (periode->FindElement(element_type) != NULL) {
     577          DoLog(1) && (Log() << Verbose(1) << "INFO: Added Type " << particle_type << " as reference to element " << element_type << "." << std::endl);
     578          knownTypes.insert( make_pair (particle_type, element_type) );
     579        } else {
     580          DoeLog(1) && (Log() << Verbose(1) << "INFO: Either Type " << particle_type << " or " << element_type << " could not be recognized." << std::endl);
     581        }
     582      } else {
     583        DoeLog(1) && (Log() << Verbose(1) << "INFO: Desired element " << element_type << " is not known." << std::endl);
     584      }
     585    }
     586  }
     587
     588}
  • src/Parser/TremoloParser.hpp

    r1a6bda r4d4d33  
    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

    r1a6bda r4d4d33  
    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();
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