Changeset 032f31


Ignore:
Timestamp:
Oct 17, 2011, 4:56:37 PM (13 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:
a67cf0
Parents:
7f570c
git-author:
Frederik Heber <heber@…> (10/06/11 11:15:56)
git-committer:
Frederik Heber <heber@…> (10/17/11 16:56:37)
Message:

Implemented Psi3Parser::load().

  • also we now have working unit test on this functionality.
Location:
src/Parser
Files:
2 edited

Legend:

Unmodified
Added
Removed

  • src/Parser/Psi3Parser.cpp

    r7f570c r032f31  
    6464void FormatParser< psi3 >::load(istream *file)
    6565{
    66 //  bool Psi3Section = false;
    67 //  bool MoleculeSection = false;
    68 //  bool GeometrySection = false;
    69 //  bool BasisSection = false;
    70 //  bool AuxBasisSection = false;
    71 //  char line[MAXSTRINGSIZE];
    72 //  typedef boost::tokenizer<boost::char_separator<char> > tokenizer;
    73 //  boost::char_separator<char> sep("[]");
    74 //  boost::char_separator<char> angularsep("<>");
    75 //  boost::char_separator<char> equalitysep(" =");
    76 //  boost::char_separator<char> whitesep(" \t");
    77 //  ConvertTo<double> toDouble;
    78 //
    79 //  molecule *newmol = World::getInstance().createMolecule();
    80 //  newmol->ActiveFlag = true;
    81 //  // TODO: Remove the insertion into molecule when saving does not depend on them anymore. Also, remove molecule.hpp include
    82 //  World::getInstance().getMolecules()->insert(newmol);
    83 //  while (file->good()) {
    84 //    file->getline(line, MAXSTRINGSIZE-1);
    85 //    std::string linestring(line);
    86 //    if ((linestring.find("atoms geometry") == string::npos) && (linestring.find("}") != string::npos)) {
    87 //      GeometrySection = false;
    88 //    }
    89 //    if ((linestring.find(")") != string::npos)) { // ends a section which do not overlap
    90 //      Psi3Section = false;
    91 //      MoleculeSection = false;
    92 //      BasisSection = false;
    93 //      AuxBasisSection = false;
    94 //    }
    95 //    if (MoleculeSection) {
    96 //      if (GeometrySection) { // we have an atom
    97 //        tokenizer tokens(linestring, sep);
    98 //  //      if (tokens.size() != 2)
    99 //  //        throw Psi3ParseException;
    100 //        tokenizer::iterator tok_iter = tokens.begin();
    101 //        ASSERT(tok_iter != tokens.end(),
    102 //            "FormatParser< psi3 >::load() - missing token for MoleculeSection in line "+linestring+"!");
    103 //        std::stringstream whitespacefilter(*tok_iter++);
    104 //        std::string element;
    105 //        whitespacefilter >> ws >> element;
    106 //        ASSERT(tok_iter != tokens.end(),
    107 //            "FormatParser< psi3 >::load() - missing token for MoleculeSection in line "+linestring+"!");
    108 //        std::string vector = *tok_iter;
    109 //        tokenizer vectorcomponents(vector, whitesep);
    110 //        Vector X;
    111 //  //      if (vectorcomponents.size() != NDIM)
    112 //  //        throw Psi3ParseException;
    113 //        tok_iter = vectorcomponents.begin();
    114 //        for (int i=0; i<NDIM; ++i) {
    115 //          X[i] = toDouble(*tok_iter++);
    116 //        }
    117 //        // create atom
    118 //        atom *newAtom = World::getInstance().createAtom();
    119 //        newAtom->setType(World::getInstance().getPeriode()->FindElement(element));
    120 //        newAtom->setPosition(X);
    121 //        newmol->AddAtom(newAtom);
    122 //        DoLog(1) && (Log() << Verbose(1) << "Adding atom " << *newAtom << std::endl);
    123 //      }
    124 //    }
    125 //    if (Psi3Section) {
    126 //      if (linestring.find("mole<") != string::npos) { // get theory
    127 //        tokenizer tokens(linestring, angularsep);
    128 //        tokenizer::iterator tok_iter = tokens.begin();
    129 //        ++tok_iter;
    130 //        ASSERT(tok_iter != tokens.end(),
    131 //            "FormatParser< psi3 >::load() - missing token in brackets<> for mole< in line "+linestring+"!");
    132 //        std::string value(*tok_iter);
    133 //        std::stringstream linestream("theory = "+value);
    134 //        linestream >> getParams();
    135 //      } else if (linestring.find("integrals<") != string::npos) { // get theory
    136 //        tokenizer tokens(linestring, angularsep);
    137 //        tokenizer::iterator tok_iter = tokens.begin();
    138 //        ++tok_iter;
    139 //        ASSERT(tok_iter != tokens.end(),
    140 //            "FormatParser< psi3 >::load() - missing token in brackets<> for integrals< in line "+linestring+"!");
    141 //        std::string value(*tok_iter);
    142 //        std::stringstream linestream("integration = "+value);
    143 //        linestream >> getParams();
    144 //      } else if ((linestring.find("molecule") == string::npos) && (linestring.find("basis") == string::npos)){
    145 //        // molecule and basis must not be parsed in this section
    146 //        tokenizer tokens(linestring, equalitysep);
    147 //        tokenizer::iterator tok_iter = tokens.begin();
    148 //        ASSERT(tok_iter != tokens.end(),
    149 //            "FormatParser< psi3 >::load() - missing token before '=' for Psi3Section in line "+linestring+"!");
    150 //        std::stringstream whitespacefilter(*tok_iter);
    151 //        std::string key;
    152 //        whitespacefilter >> ws >> key;
    153 //        if (getParams().haveParameter(key)) {
    154 //          std::stringstream linestream(linestring);
    155 //          linestream >> getParams();
    156 //        } else { // unknown keys are simply ignored as long as parser is incomplete
    157 //          DoLog(2) && (Log() << Verbose(2) << "INFO: '"+key+"' is unknown and ignored." << std::endl);
    158 //        }
    159 //      }
    160 //    }
    161 //    if (BasisSection) {
    162 //      tokenizer tokens(linestring, equalitysep);
    163 //      tokenizer::iterator tok_iter = tokens.begin();
    164 //      ASSERT(tok_iter != tokens.end(),
    165 //          "FormatParser< psi3 >::load() - missing token for BasisSection in line "+linestring+"!");
    166 //      std::string key(*tok_iter++);
    167 //      ASSERT(tok_iter != tokens.end(),
    168 //          "FormatParser< psi3 >::load() - missing value for BasisSection after key "+key+" in line "+linestring+"!");
    169 //      std::string value(*tok_iter);
    170 //      tok_iter++;
    171 //      // TODO: use exception instead of ASSERT
    172 //      ASSERT(tok_iter == tokens.end(),
    173 //          "FormatParser< psi3 >::load() - more than (key = value) on line "+linestring+".");
    174 //      if (key == "name") {
    175 //        std::stringstream linestream("basis = "+value);
    176 //        linestream >> getParams();
    177 //      }
    178 //    }
    179 //    if (AuxBasisSection) {
    180 //      tokenizer tokens(linestring, equalitysep);
    181 //      tokenizer::iterator tok_iter = tokens.begin();
    182 //      ASSERT(tok_iter != tokens.end(),
    183 //          "FormatParser< psi3 >::load() - missing token for AuxBasisSection in line "+linestring+"!");
    184 //      std::string key(*tok_iter++);
    185 //      ASSERT(tok_iter != tokens.end(),
    186 //          "FormatParser< psi3 >::load() - missing value for BasisSection after key "+key+" in line "+linestring+"!");
    187 //      std::string value(*tok_iter);
    188 //      tok_iter++;
    189 //      // TODO: use exception instead of ASSERT
    190 //      ASSERT(tok_iter == tokens.end(),
    191 //          "FormatParser< psi3 >::load() - more than (key = value) on line "+linestring+".");
    192 //      if (key == "name") {
    193 //        std::stringstream linestream("aux_basis = "+value);
    194 //        linestream >> getParams();
    195 //      }
    196 //    }
    197 //    // set some scan flags
    198 //    if (linestring.find("psi3:") != string::npos) {
    199 //      Psi3Section = true;
    200 //    }
    201 //    if (linestring.find("molecule<Molecule>:") != string::npos) {
    202 //      MoleculeSection = true;
    203 //    }
    204 //    if (linestring.find("atoms geometry") != string::npos) {
    205 //      GeometrySection = true;
    206 //    }
    207 //    if ((linestring.find("basis<GaussianBasisSet>:") != string::npos) && ((linestring.find("abasis<") == string::npos))) {
    208 //      BasisSection = true;
    209 //    }
    210 //    if (linestring.find("abasis<") != string::npos) {
    211 //      AuxBasisSection = true;
    212 //    }
    213 //  }
    214 //  // refresh atom::nr and atom::name
    215 //  newmol->getAtomCount();
     66  bool Psi3Section = false;
     67  bool GeometrySection = false;
     68  char line[MAXSTRINGSIZE];
     69  typedef boost::tokenizer<boost::char_separator<char> > tokenizer;
     70  boost::char_separator<char> sep("()");
     71  boost::char_separator<char> angularsep("<>");
     72  boost::char_separator<char> equalitysep(" =");
     73  boost::char_separator<char> whitesep(" \t");
     74  ConvertTo<double> toDouble;
     75
     76  molecule *newmol = World::getInstance().createMolecule();
     77  newmol->ActiveFlag = true;
     78  // TODO: Remove the insertion into molecule when saving does not depend on them anymore. Also, remove molecule.hpp include
     79  World::getInstance().getMolecules()->insert(newmol);
     80  while (file->good()) {
     81    file->getline(line, MAXSTRINGSIZE-1);
     82    std::string linestring(line);
     83    LOG(3, "INFO: Current line is: " << line);
     84    if ((linestring.find(")") != string::npos) && (linestring.find("(") == string::npos)) {
     85      LOG(3, "INFO: Line contains ')' and no '(' (end of section): " << line);
     86      // ends a section which do not overlap
     87      if (GeometrySection)
     88        GeometrySection = false;
     89      else
     90        Psi3Section = false;
     91    }
     92    if (GeometrySection) { // we have an atom
     93      tokenizer tokens(linestring, sep);
     94//      if (tokens.size() != 2)
     95//        throw Psi3ParseException;
     96      tokenizer::iterator tok_iter = tokens.begin();
     97      ASSERT(tok_iter != tokens.end(),
     98          "FormatParser< psi3 >::load() - missing token for MoleculeSection in line "+linestring+"!");
     99      std::stringstream whitespacefilter(*++tok_iter);
     100      std::string element;
     101      whitespacefilter >> ws >> element;
     102      LOG(2, "INFO: element of atom is " << element);
     103      ASSERT(tok_iter != tokens.end(),
     104          "FormatParser< psi3 >::load() - missing token for MoleculeSection in line "+linestring+"!");
     105      std::string vector = *tok_iter;
     106      tokenizer vectorcomponents(vector, whitesep);
     107      Vector X;
     108//      if (vectorcomponents.size() != NDIM)
     109//        throw Psi3ParseException;
     110      tok_iter = vectorcomponents.begin();
     111      ++tok_iter;
     112      for (int i=0; i<NDIM; ++i) {
     113        LOG(4, "INFO: Current value is " << *tok_iter << ".");
     114        X[i] = toDouble(*tok_iter++);
     115      }
     116      LOG(2, "INFO: position of atom is " << X);
     117      // create atom
     118      atom *newAtom = World::getInstance().createAtom();
     119      newAtom->setType(World::getInstance().getPeriode()->FindElement(element));
     120      newAtom->setPosition(X);
     121      newmol->AddAtom(newAtom);
     122      DoLog(1) && (Log() << Verbose(1) << "Adding atom " << *newAtom << std::endl);
     123    }
     124    if ((Psi3Section) && (!GeometrySection)) {
     125      if (linestring.find("=") != string::npos) { // get param value
     126        tokenizer tokens(linestring, equalitysep);
     127        tokenizer::iterator tok_iter = tokens.begin();
     128        ASSERT(tok_iter != tokens.end(),
     129            "FormatParser< psi3 >::load() - missing token before '=' for Psi3Section in line "+linestring+"!");
     130        std::stringstream whitespacefilter(*tok_iter);
     131        std::string key;
     132        whitespacefilter >> ws >> key;
     133        //LOG(2, "INFO: key to check is: " << key);
     134        if (getParams().haveParameter(key)) {
     135          //LOG(2, "INFO: Line submitted to parameter is: " << linestring);
     136          std::stringstream linestream(linestring);
     137          linestream >> getParams();
     138        } else { // unknown keys are simply ignored as long as parser is incomplete
     139          LOG(3, "INFO: '"+key+"' is unknown and ignored.");
     140        }
     141      }
     142    }
     143    if ((linestring.find("geometry") != string::npos) && (linestring.find("(") != string::npos)) {
     144      LOG(3, "INFO: Line contains geometry and '(': " << line);
     145      GeometrySection = true;
     146    }
     147    if ((linestring.find("psi:") != string::npos) && (linestring.find("(") != string::npos)) {
     148      LOG(3, "INFO: Line contains psi: and '(': " << line);
     149      Psi3Section = true;
     150    }
     151  }
     152  // refresh atom::nr and atom::name
     153  newmol->getAtomCount();
    216154}
    217155

  • src/Parser/unittests/ParserPsi3UnitTest.cpp

    r7f570c r032f31  
    267267
    268268void ParserPsi3UnitTest::readPsi3Test() {
    269 //  stringstream input(waterPsi3_CLHF);
    270 //  params->setParameter(
    271 //      Psi3Parser_Parameters::theoryParam,
    272 //      params->getTheoryName(Psi3Parser_Parameters::CLHF)
    273 //          );
    274 //  parser->load(&input);
    275 //
    276 //  CPPUNIT_ASSERT_EQUAL(3, World::getInstance().numAtoms());
     269  stringstream input(hydrogenPsi3_RHF);
     270  // set some other parameter for jobtype
     271  params->setParameter(
     272      Psi3Parser_Parameters::jobtypeParam,
     273      params->ValidJobtypes[Psi3Parser_Parameters::OPT]
     274          );
     275  parser->load(&input);
     276
     277  // check for jobtype from file
     278  CPPUNIT_ASSERT(params->getParameter(Psi3Parser_Parameters::jobtypeParam) == params->ValidJobtypes[Psi3Parser_Parameters::SP]);
     279  // check for 2 hydrogens
     280  CPPUNIT_ASSERT_EQUAL(2, World::getInstance().numAtoms());
     281  // check that positions are right
     282  Vector PositionSum;
     283  std::vector<atom *> atoms = World::getInstance().getAllAtoms();
     284  for (std::vector<atom *>::const_iterator iter = atoms.begin();
     285      iter != atoms.end();
     286      ++iter)
     287    PositionSum += (*iter)->getPosition();
     288  CPPUNIT_ASSERT_EQUAL( PositionSum, Vector(0,0,0.74) );
    277289}
    278290
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