Changeset 1b2d30 for src

Timestamp:

Jun 12, 2010, 10:19:48 PM (15 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:

55240c4

Parents:

43dad6

git-author:

Frederik Heber <heber@…> (06/12/10 21:59:36)

git-committer:

Frederik Heber <heber@…> (06/12/10 22:19:48)

Message:

Extended PcpParser, completed MpqcParser.

• BUGFIX: ConfigFileBuffer::InitFileBuffer() did not clear istream before re-use.
• class PcpParser
  • operator== - compares every variable by ASSERTs.
  • constructor initializes variables all to sensible values.
• class MpqcParser
  • new function save() - calls either SaveHessian() or Save() according to flag HessianPresent.
  • new functions SaveHessian() and Save() which contain both parts of config::SaveMPQC().
  • no function load() - this functionality has not been present and is not needed right away.
• Extended ParserUnitTest
  • new test case readwritePcpTest() - load from static string, store, load again and compare both.
  • new test case writeMpqcTest() - write a state of the world and compare to one from static string.
  • all static strings have been made static and set before all functions.
  • new string containing an example pcp config file.
  • we check whether hydrogen and oxygen are known to the world as we test with these two elements.
• atom::OutputMPQCLine() - now takes ostream instead of ofstream.
• config::SaveMPQC() - adapted accordingly (cast is necessary)

Location:

src

Files:

• ConfigFileBuffer.cpp (modified) (2 diffs)
• Parser/MpqcParser.cpp (modified) (1 diff)
• Parser/MpqcParser.hpp (modified) (1 diff)
• Parser/PcpParser.cpp (modified) (4 diffs)
• Parser/PcpParser.hpp (modified) (1 diff)
• atom.cpp (modified) (1 diff)
• atom.hpp (modified) (1 diff)
• config.cpp (modified) (2 diffs)
• unittests/ParserUnitTest.cpp (modified) (11 diffs)
• unittests/ParserUnitTest.hpp (modified) (2 diffs)

src/ConfigFileBuffer.cpp

@@ -82 +82 @@
   long file_position = file->tellg(); // mark current position
   do {
-    file->getline(line, 256);
+    file->getline(line, MAXSTRINGSIZE-1);
     NoLines++;
   } while (!file->eof());
@@ -108 +108 @@
   } while((!file->eof()) && (lines < NoLines));
   DoLog(1) && (Log() << Verbose(1) << lines-1 << " lines were read into the buffer." << endl);
+  file->clear();
+  file->seekg(file_position, ios::beg);
 
   InitMapping();

src/Parser/MpqcParser.cpp

@@ -6 +6 @@
  */
 
+#include <iostream>
+
+#include "MpqcParser.hpp"
+
+#include "atom.hpp"
+#include "config.hpp"
+#include "element.hpp"
+#include "log.hpp"
+#include "periodentafel.hpp"
+#include "vector.hpp"
+#include "verbose.hpp"
+#include "World.hpp"
+
+
+/** Constructor of MpqcParser.
+ *
+ */
+MpqcParser::MpqcParser()
+{
+
+}
+
+/** Destructor of MpqcParser.
+ *
+ */
+MpqcParser::~MpqcParser() {
+
+}
+
+/** Load an MPQC config file into the World.
+ * \param *file input stream
+ */
+void MpqcParser::load(istream *file)
+{
+  DoeLog(0) && (Log() << Verbose(0) << "Not yet implemented" << endl) ;
+}
+
+void MpqcParser::save(ostream *file)
+{
+  if (HessianPresent)
+    saveHessian(file);
+  else
+    saveSimple(file);
+}
+
+/** Saves all atoms and data into a MPQC config file without hessian.
+ * \param *file output stream
+ */
+void MpqcParser::saveSimple(ostream *file)
+{
+  int AtomNo = 0;
+  Vector center;
+  vector<atom *> allatoms = World::getInstance().getAllAtoms();
+
+  // first without hessian
+  if (file->fail()) {
+    DoeLog(1) && (eLog()<< Verbose(1) << "Cannot open mpqc output file." << endl);
+  } else {
+    *file << "% Created by MoleCuilder" << endl;
+    *file << "mpqc: (" << endl;
+    *file << "\tsavestate = no" << endl;
+    *file << "\tdo_gradient = yes" << endl;
+    *file << "\tmole<MBPT2>: (" << endl;
+    *file << "\t\tmaxiter = 200" << endl;
+    *file << "\t\tbasis = $:basis" << endl;
+    *file << "\t\tmolecule = $:molecule" << endl;
+    *file << "\t\treference<CLHF>: (" << endl;
+    *file << "\t\t\tbasis = $:basis" << endl;
+    *file << "\t\t\tmolecule = $:molecule" << endl;
+    *file << "\t\t)" << endl;
+    *file << "\t)" << endl;
+    *file << ")" << endl;
+    *file << "molecule<Molecule>: (" << endl;
+    *file << "\tunit = " << (World::getInstance().getConfig()->GetIsAngstroem() ? "angstrom" : "bohr" ) << endl;
+    *file << "\t{ atoms geometry } = {" << endl;
+    // output of atoms
+    for (vector<atom *>::iterator AtomRunner = allatoms.begin(); AtomRunner != allatoms.end(); ++AtomRunner) {
+      (*AtomRunner)->OutputMPQCLine(file, &center, &AtomNo);
+    }
+    *file << "\t}" << endl;
+    *file << ")" << endl;
+    *file << "basis<GaussianBasisSet>: (" << endl;
+    *file << "\tname = \"" << World::getInstance().getConfig()->basis << "\"" << endl;
+    *file << "\tmolecule = $:molecule" << endl;
+    *file << ")" << endl;
+  }
+}
+
+/** Saves all atoms and data into a MPQC config file with hessian.
+ * \param *file output stream
+ */
+void MpqcParser::saveHessian(ostream *file)
+{
+  int AtomNo = 0;
+  Vector center;
+  vector<atom *> allatoms = World::getInstance().getAllAtoms();
+
+  // with hessian
+  if (file->fail()) {
+    DoeLog(1) && (eLog()<< Verbose(1) << "Cannot open mpqc output file." << endl);
+  } else {
+    *file << "% Created by MoleCuilder" << endl;
+    *file << "mpqc: (" << endl;
+    *file << "\tsavestate = no" << endl;
+    *file << "\tdo_gradient = yes" << endl;
+    *file << "\tmole<CLHF>: (" << endl;
+    *file << "\t\tmaxiter = 200" << endl;
+    *file << "\t\tbasis = $:basis" << endl;
+    *file << "\t\tmolecule = $:molecule" << endl;
+    *file << "\t)" << endl;
+    *file << "\tfreq<MolecularFrequencies>: (" << endl;
+    *file << "\t\tmolecule=$:molecule" << endl;
+    *file << "\t)" << endl;
+    *file << ")" << endl;
+    *file << "molecule<Molecule>: (" << endl;
+    *file << "\tunit = " << (World::getInstance().getConfig()->GetIsAngstroem() ? "angstrom" : "bohr" ) << endl;
+    *file << "\t{ atoms geometry } = {" << endl;
+    // output of atoms
+    for (vector<atom *>::iterator AtomRunner = allatoms.begin(); AtomRunner != allatoms.end(); ++AtomRunner) {
+      (*AtomRunner)->OutputMPQCLine(file, &center, &AtomNo);
+    }
+    *file << "\t}" << endl;
+    *file << ")" << endl;
+    *file << "basis<GaussianBasisSet>: (" << endl;
+    *file << "\tname = \"" << World::getInstance().getConfig()->basis << "\"" << endl;
+    *file << "\tmolecule = $:molecule" << endl;
+    *file << ")" << endl;
+  }
+}
+
+/** Sets whether hessian is desired or not
+ * \param hessian statement
+ */
+void MpqcParser::setHessian(bool hessian)
+{
+  HessianPresent = hessian;
+}

src/Parser/MpqcParser.hpp

@@ -23 +23 @@
   void save(std::ostream* file);
 
+  void setHessian(bool hessian);
 
 private:
-}
+  // whether output with computing hessian is desired.
+  bool HessianPresent;
+
+  void saveSimple(std::ostream *file);
+  void saveHessian(std::ostream *file);
+};
 
 #endif /* MPQCPARSER_HPP_ */

src/Parser/PcpParser.cpp

@@ -12 +12 @@
 #include "ConfigFileBuffer.hpp"
 #include "element.hpp"
+#include "Helpers/Assert.hpp"
 #include "log.hpp"
 #include "molecule.hpp"
@@ -24 +25 @@
  */
 PcpParser::PcpParser()
-{}
+{
+  Parallelization.ProcPEGamma = 1;
+  Parallelization.ProcPEPsi = 1;
+
+  Paths.databasepath = NULL;
+  Paths.configpath = NULL;
+  Paths.configname = NULL;
+  Paths.mainname = NULL;
+  Paths.defaultpath = NULL;
+  Paths.pseudopotpath = NULL;
+
+  Switches.DoConstrainedMD = 0;
+  Switches.DoOutVis = 0;
+  Switches.DoOutMes = 1;
+  Switches.DoOutNICS = 0;
+  Switches.DoOutOrbitals = 0;
+  Switches.DoOutCurrent = 0;
+  Switches.DoFullCurrent = 0;
+  Switches.DoPerturbation = 0;
+  Switches.DoWannier = 0;
+
+  LocalizedOrbitals.CommonWannier = 0;
+  LocalizedOrbitals.SawtoothStart = 0.01;
+  LocalizedOrbitals.VectorPlane = 0;
+  LocalizedOrbitals.VectorCut = 0;
+  LocalizedOrbitals.UseAddGramSch = 1;
+  LocalizedOrbitals.Seed = 1;
+  LocalizedOrbitals.EpsWannier = 1e-7;
+
+  StepCounts.MaxMinStopStep = 0;
+  StepCounts.InitMaxMinStopStep = 0;
+  StepCounts.OutVisStep = 10;
+  StepCounts.OutSrcStep = 5;
+  StepCounts.MaxPsiStep = 3;
+  StepCounts.MaxOuterStep = 0;
+  StepCounts.MaxMinStep = 100;
+  StepCounts.RelEpsTotalEnergy = 1e-07;
+  StepCounts.RelEpsKineticEnergy = 1e-05;
+  StepCounts.MaxMinGapStopStep = 0;
+  StepCounts.MaxInitMinStep = 100;
+  StepCounts.InitRelEpsTotalEnergy = 1e-05;
+  StepCounts.InitRelEpsKineticEnergy = 0.0001;
+  StepCounts.InitMaxMinGapStopStep = 1;
+
+  PlaneWaveSpecifics.PsiType = 0;
+  PlaneWaveSpecifics.MaxPsiDouble = 0;
+  PlaneWaveSpecifics.PsiMaxNoUp = 0;
+  PlaneWaveSpecifics.PsiMaxNoDown = 0;
+  PlaneWaveSpecifics.ECut = 128;
+  PlaneWaveSpecifics.MaxLevel = 5;
+  PlaneWaveSpecifics.RiemannTensor = 0;
+  PlaneWaveSpecifics.LevRFactor = 0;
+  PlaneWaveSpecifics.RiemannLevel = 0;
+  PlaneWaveSpecifics.Lev0Factor = 2;
+  PlaneWaveSpecifics.RTActualUse = 0;
+  PlaneWaveSpecifics.AddPsis = 0;
+  PlaneWaveSpecifics.RCut = 20;
+  PlaneWaveSpecifics.PsiType = 0;
+
+  FastParsing = false;
+
+  Deltat = 0.01;
+  IsAngstroem = 1;
+  RelativeCoord = 0;
+  MaxTypes = 0;
+}
 
 /** Destructor of PcpParser.
@@ -415 +481 @@
   map<int, int> ZtoCountMap;
   pair <   map<int, int>::iterator, bool > Inserter;
+  int nr = 0;
   for (vector<atom *>::iterator AtomRunner = allatoms.begin();AtomRunner != allatoms.end();++AtomRunner) {
     Inserter = ZtoCountMap.insert( pair<int, int>((*AtomRunner)->type->Z, 1) );
     if (!Inserter.second)
       Inserter.first->second += 1;
-    (*AtomRunner)->OutputArrayIndexed(file, &ZtoIndexMap[(*AtomRunner)->type->Z], &ZtoCountMap[Inserter.first->second], NULL);
+    *file << "Ion_Type" << ZtoIndexMap[(*AtomRunner)->type->Z] << "_" << ZtoCountMap[Inserter.first->second] << "\t"  << fixed << setprecision(9) << showpoint;
+    *file << (*AtomRunner)->x[0] << "\t" << (*AtomRunner)->x[1] << "\t" << (*AtomRunner)->x[2];
+    *file << "\t" << (*AtomRunner)->FixedIon;
+    if ((*AtomRunner)->v.Norm() > MYEPSILON)
+      *file << "\t" << scientific << setprecision(6) << (*AtomRunner)->v[0] << "\t" << (*AtomRunner)->v[1] << "\t" << (*AtomRunner)->v[2] << "\t";
+    *file << " # molecule nr " << nr++ << endl;
   }
 }
@@ -499 +571 @@
 };
 
+bool PcpParser::operator==(const PcpParser& b) const
+{
+  ASSERT(Parallelization.ProcPEGamma == b.Parallelization.ProcPEGamma, "PcpParser ==: ProcPEGamma not");
+  ASSERT(Parallelization.ProcPEPsi == b.Parallelization.ProcPEPsi, "PcpParser ==: ProcPEPsi not");
+
+  if ((Paths.databasepath != NULL) && (b.Paths.databasepath != NULL))
+    ASSERT(strcmp(Paths.databasepath, b.Paths.databasepath), "PcpParser ==: databasepath not");
+  if ((Paths.configpath != NULL) && (b.Paths.configpath != NULL))
+    ASSERT(strcmp(Paths.configpath, b.Paths.configpath), "PcpParser ==: configpath not");
+  if ((Paths.configname != NULL) && (b.Paths.configname != NULL))
+    ASSERT(strcmp(Paths.configname, b.Paths.configname), "PcpParser ==: configname not");
+  if ((Paths.mainname != NULL) && (b.Paths.mainname != NULL))
+    ASSERT(strcmp(Paths.mainname, b.Paths.mainname), "PcpParser ==: mainname not");
+  if ((Paths.defaultpath != NULL) && (b.Paths.defaultpath != NULL))
+    ASSERT(strcmp(Paths.defaultpath, b.Paths.defaultpath), "PcpParser ==: defaultpath not");
+  if ((Paths.pseudopotpath != NULL) && (b.Paths.pseudopotpath != NULL))
+    ASSERT(strcmp(Paths.pseudopotpath, b.Paths.pseudopotpath), "PcpParser ==: pseudopotpath not");
+
+  ASSERT(Switches.DoConstrainedMD == b.Switches.DoConstrainedMD, "PcpParser ==: DoConstrainedMD not");
+  ASSERT(Switches.DoOutVis == b.Switches.DoOutVis, "PcpParser ==: DoOutVis not");
+  ASSERT(Switches.DoOutMes == b.Switches.DoOutMes, "PcpParser ==: DoOutMes not");
+  ASSERT(Switches.DoOutNICS == b.Switches.DoOutNICS, "PcpParser ==: DoOutNICS not");
+  ASSERT(Switches.DoOutOrbitals == b.Switches.DoOutOrbitals, "PcpParser ==: DoOutOrbitals not");
+  ASSERT(Switches.DoOutCurrent == b.Switches.DoOutCurrent, "PcpParser ==: DoOutCurrent not");
+  ASSERT(Switches.DoFullCurrent == b.Switches.DoFullCurrent, "PcpParser ==: DoFullCurrent not");
+  ASSERT(Switches.DoPerturbation == b.Switches.DoPerturbation, "PcpParser ==: DoPerturbation not");
+  ASSERT(Switches.DoWannier == b.Switches.DoWannier, "PcpParser ==: DoWannier not");
+
+  ASSERT(LocalizedOrbitals.CommonWannier == b.LocalizedOrbitals.CommonWannier, "PcpParser ==: CommonWannier not");
+  ASSERT(LocalizedOrbitals.SawtoothStart == b.LocalizedOrbitals.SawtoothStart, "PcpParser ==: SawtoothStart not");
+  ASSERT(LocalizedOrbitals.VectorPlane == b.LocalizedOrbitals.VectorPlane, "PcpParser ==: VectorPlane not");
+  ASSERT(LocalizedOrbitals.VectorCut == b.LocalizedOrbitals.VectorCut, "PcpParser ==: VectorCut not");
+  ASSERT(LocalizedOrbitals.UseAddGramSch == b.LocalizedOrbitals.UseAddGramSch, "PcpParser ==: UseAddGramSch not");
+  ASSERT(LocalizedOrbitals.Seed == b.LocalizedOrbitals.Seed, "PcpParser ==: Seed not");
+  ASSERT(LocalizedOrbitals.EpsWannier == b.LocalizedOrbitals.EpsWannier, "PcpParser ==: EpsWannier not");
+
+  ASSERT(StepCounts.MaxMinStopStep == b.StepCounts.MaxMinStopStep, "PcpParser ==: MaxMinStopStep not");
+  ASSERT(StepCounts.InitMaxMinStopStep == b.StepCounts.InitMaxMinStopStep, "PcpParser ==: InitMaxMinStopStep not");
+  ASSERT(StepCounts.OutVisStep == b.StepCounts.OutVisStep, "PcpParser ==: OutVisStep not");
+  ASSERT(StepCounts.OutSrcStep == b.StepCounts.OutSrcStep, "PcpParser ==: OutSrcStep not");
+  ASSERT(StepCounts.MaxPsiStep == b.StepCounts.MaxPsiStep, "PcpParser ==: MaxPsiStep not");
+  ASSERT(StepCounts.MaxOuterStep == b.StepCounts.MaxOuterStep, "PcpParser ==: MaxOuterStep not");
+  ASSERT(StepCounts.MaxMinStep == b.StepCounts.MaxMinStep, "PcpParser ==: MaxMinStep not");
+  ASSERT(StepCounts.RelEpsTotalEnergy == b.StepCounts.RelEpsTotalEnergy, "PcpParser ==: RelEpsTotalEnergy not");
+  ASSERT(StepCounts.MaxMinGapStopStep == b.StepCounts.MaxMinGapStopStep, "PcpParser ==: MaxMinGapStopStep not");
+  ASSERT(StepCounts.MaxInitMinStep == b.StepCounts.MaxInitMinStep, "PcpParser ==: MaxInitMinStep not");
+  ASSERT(StepCounts.InitRelEpsTotalEnergy == b.StepCounts.InitRelEpsTotalEnergy, "PcpParser ==: InitRelEpsTotalEnergy not");
+  ASSERT(StepCounts.InitRelEpsKineticEnergy == b.StepCounts.InitRelEpsKineticEnergy, "PcpParser ==: InitRelEpsKineticEnergy not");
+  ASSERT(StepCounts.InitMaxMinGapStopStep == b.StepCounts.InitMaxMinGapStopStep, "PcpParser ==: InitMaxMinGapStopStep not");
+
+  ASSERT(PlaneWaveSpecifics.PsiType == b.PlaneWaveSpecifics.PsiType, "PcpParser ==: PsiType not");
+  ASSERT(PlaneWaveSpecifics.MaxPsiDouble == b.PlaneWaveSpecifics.MaxPsiDouble, "PcpParser ==: MaxPsiDouble not");
+  ASSERT(PlaneWaveSpecifics.PsiMaxNoUp == b.PlaneWaveSpecifics.PsiMaxNoUp, "PcpParser ==: PsiMaxNoUp not");
+  ASSERT(PlaneWaveSpecifics.PsiMaxNoDown == b.PlaneWaveSpecifics.PsiMaxNoDown, "PcpParser ==: PsiMaxNoDown not");
+  ASSERT(PlaneWaveSpecifics.ECut == b.PlaneWaveSpecifics.ECut, "PcpParser ==: ECut not");
+  ASSERT(PlaneWaveSpecifics.MaxLevel == b.PlaneWaveSpecifics.MaxLevel, "PcpParser ==: MaxLevel not");
+  ASSERT(PlaneWaveSpecifics.RiemannTensor == b.PlaneWaveSpecifics.RiemannTensor, "PcpParser ==: RiemannTensor not");
+  ASSERT(PlaneWaveSpecifics.LevRFactor == b.PlaneWaveSpecifics.LevRFactor, "PcpParser ==: LevRFactor not");
+  ASSERT(PlaneWaveSpecifics.RiemannLevel == b.PlaneWaveSpecifics.RiemannLevel, "PcpParser ==: RiemannLevel not");
+  ASSERT(PlaneWaveSpecifics.Lev0Factor == b.PlaneWaveSpecifics.Lev0Factor, "PcpParser ==: Lev0Factor not");
+  ASSERT(PlaneWaveSpecifics.RTActualUse == b.PlaneWaveSpecifics.RTActualUse, "PcpParser ==: RTActualUse not");
+  ASSERT(PlaneWaveSpecifics.AddPsis == b.PlaneWaveSpecifics.AddPsis, "PcpParser ==: AddPsis not");
+  ASSERT(PlaneWaveSpecifics.AddPsis == b.PlaneWaveSpecifics.AddPsis, "PcpParser ==: AddPsis not");
+  ASSERT(PlaneWaveSpecifics.RCut == b.PlaneWaveSpecifics.RCut, "PcpParser ==: RCut not");
+
+  ASSERT(FastParsing == b.FastParsing, "PcpParser ==: FastParsing not");
+
+  ASSERT(Deltat == b.Deltat, "PcpParser ==: Deltat not");
+  ASSERT(IsAngstroem == b.IsAngstroem, "PcpParser ==: IsAngstroem not");
+  ASSERT(RelativeCoord == b.RelativeCoord, "PcpParser ==: RelativeCoord not");
+  ASSERT(StructOpt == b.StructOpt, "PcpParser ==: StructOpt not");
+  ASSERT(MaxTypes == b.MaxTypes, "PcpParser ==: MaxTypes not");
+  ASSERT(basis == b.basis, "PcpParser ==: basis not");
+
+  return true;
+}

src/Parser/PcpParser.hpp

@@ -21 +21 @@
   void load(std::istream* file);
   void save(std::ostream* file);
+
+  bool operator==(const PcpParser& b) const;
 
 private:

src/atom.cpp

@@ -226 +226 @@
  * \param *AtomNo pointer to atom counter that is increased by one
  */
-void atom::OutputMPQCLine(ofstream * const out, const Vector *center, int *AtomNo = NULL) const
+void atom::OutputMPQCLine(ostream * const out, const Vector *center, int *AtomNo = NULL) const
 {
   *out << "\t\t" << type->symbol << " [ " << x[0]-center->at(0) << "\t" << x[1]-center->at(1) << "\t" << x[2]-center->at(2) << " ]" << endl;

src/atom.hpp

@@ -56 +56 @@
   bool OutputTrajectory(ofstream * const out, const int *ElementNo, int *AtomNo, const int step) const;
   bool OutputTrajectoryXYZ(ofstream * const out, const int step) const;
-  void OutputMPQCLine(ofstream * const out, const Vector *center, int *AtomNo) const;
+  void OutputMPQCLine(ostream * const out, const Vector *center, int *AtomNo) const;
 
   void InitComponentNr();

src/config.cpp

@@ -1220 +1220 @@
     // output of atoms
     AtomNo = 0;
-    mol->ActOnAllAtoms( &atom::OutputMPQCLine, output, (const Vector *)center, &AtomNo );
+    mol->ActOnAllAtoms( &atom::OutputMPQCLine, (ostream * const) output, (const Vector *)center, &AtomNo );
     delete(center);
     *output << "\t}" << endl;
@@ -1262 +1262 @@
     // output of atoms
     AtomNo = 0;
-    mol->ActOnAllAtoms( &atom::OutputMPQCLine, output, (const Vector *)center, &AtomNo );
+    mol->ActOnAllAtoms( &atom::OutputMPQCLine, (ostream * const) output, (const Vector *)center, &AtomNo );
     delete(center);
     *output << "\t}" << endl;

src/unittests/ParserUnitTest.cpp

@@ -12 +12 @@
 #include <cppunit/ui/text/TestRunner.h>
 
+#include "Parser/MpqcParser.hpp"
+#include "Parser/PcpParser.hpp"
+#include "Parser/TremoloParser.hpp"
 #include "Parser/XyzParser.hpp"
-#include "Parser/TremoloParser.hpp"
 #include "World.hpp"
 #include "atom.hpp"
@@ -29 +31 @@
 CPPUNIT_TEST_SUITE_REGISTRATION( ParserUnitTest );
 
+static string waterPcp = "# ParallelCarParinello - main configuration file - created with molecuilder\n\
+\n\
+mainname\tpcp\t# programm name (for runtime files)\n\
+defaultpath\not specified\t# where to put files during runtime\n\
+pseudopotpath\not specified\t# where to find pseudopotentials\n\
+\n\
+ProcPEGamma\t8\t# for parallel computing: share constants\n\
+ProcPEPsi\t1\t# for parallel computing: share wave functions\n\
+DoOutVis\t0\t# Output data for OpenDX\n\
+DoOutMes\t1\t# Output data for measurements\n\
+DoOutOrbitals\t0\t# Output all Orbitals\n\
+DoOutCurr\t0\t# Ouput current density for OpenDx\n\
+DoOutNICS\t0\t# Output Nucleus independent current shieldings\n\
+DoPerturbation\t0\t# Do perturbation calculate and determine susceptibility and shielding\n\
+DoFullCurrent\t0\t# Do full perturbation\n\
+DoConstrainedMD\t0\t# Do perform a constrained (>0, relating to current MD step) instead of unconstrained (0) MD\n\
+Thermostat\tBerendsen\t2.5\t# Which Thermostat and its parameters to use in MD case.\n\
+CommonWannier\t0\t# Put virtual centers at indivual orbits, all common, merged by variance, to grid point, to cell center\n\
+SawtoothStart\t0.01\t# Absolute value for smooth transition at cell border \n\
+VectorPlane\t0\t# Cut plane axis (x, y or z: 0,1,2) for two-dim current vector plot\n\
+VectorCut\t0\t# Cut plane axis value\n\
+AddGramSch\t1\t# Additional GramSchmidtOrtogonalization to be safe\n\
+Seed\t1\t# initial value for random seed for Psi coefficients\n\
+\n\
+MaxOuterStep\t0\t# number of MolecularDynamics/Structure optimization steps\n\
+Deltat\t0.01\t# time per MD step\n\
+OutVisStep\t10\t# Output visual data every ...th step\n\
+OutSrcStep\t5\t# Output \"restart\" data every ..th step\n\
+TargetTemp\t0.000950045\t# Target temperature\n\
+MaxPsiStep\t3\t# number of Minimisation steps per state (0 - default)\n\
+EpsWannier\t1e-07\t# tolerance value for spread minimisation of orbitals\n\
+# Values specifying when to stop\n\
+MaxMinStep\t100\t# Maximum number of steps\n\
+RelEpsTotalE\t1e-07\t# relative change in total energy\n\
+RelEpsKineticE\t1e-05\t# relative change in kinetic energy\n\
+MaxMinStopStep\t0\t# check every ..th steps\n\
+MaxMinGapStopStep\t1\t# check every ..th steps\n\
+\n\
+# Values specifying when to stop for INIT, otherwise same as above\n\
+MaxInitMinStep\t100\t# Maximum number of steps\n\
+InitRelEpsTotalE\t1e-05\t# relative change in total energy\n\
+InitRelEpsKineticE\t0.0001\t# relative change in kinetic energy\n\
+InitMaxMinStopStep\t0\t# check every ..th steps\n\
+InitMaxMinGapStopStep\t1\t# check every ..th steps\n\
+\n\
+BoxLength\t# (Length of a unit cell)\n\
+20\n\
+0\t20\n\
+0\t0\t20\n\
+\n\
+ECut\t128\t# energy cutoff for discretization in Hartrees\n\
+MaxLevel\t5\t# number of different levels in the code, >=2\n\
+Level0Factor\t2\t# factor by which node number increases from S to 0 level\n\
+RiemannTensor\t0\t# (Use metric)\n\
+PsiType\t0\t# 0 - doubly occupied, 1 - SpinUp,SpinDown\n\
+MaxPsiDouble\t0\t# here: specifying both maximum number of SpinUp- and -Down-states\n\
+PsiMaxNoUp\t0\t# here: specifying maximum number of SpinUp-states\n\
+PsiMaxNoDown\t0\t# here: specifying maximum number of SpinDown-states\n\
+AddPsis\t0\t# Additional unoccupied Psis for bandgap determination\n\
+\n\
+RCut\t20\t# R-cut for the ewald summation\n\
+StructOpt\t0\t# Do structure optimization beforehand\n\
+IsAngstroem\t1\t# 0 - Bohr, 1 - Angstroem\n\
+RelativeCoord\t0\t# whether ion coordinates are relative (1) or absolute (0)\n\
+MaxTypes\t2\t# maximum number of different ion types\n\
+\n\
+# Ion type data (PP = PseudoPotential, Z = atomic number)\n\
+#Ion_TypeNr.\tAmount\tZ\tRGauss\tL_Max(PP)L_Loc(PP)IonMass\t# chemical name, symbol\n\
+Ion_Type1\t2\t1\t1.0\t3\t3\t1.008\tHydrogen\tH\n\
+Ion_Type2\t1\t8\t1.0\t3\t3\t15.999\tOxygen\tO\n\
+#Ion_TypeNr._Nr.R[0]\tR[1]\tR[2]\tMoveType (0 MoveIon, 1 FixedIon)\n\
+Ion_Type2_1\t0.000000000\t0.000000000\t0.000000000\t0 # molecule nr 0\n\
+Ion_Type1_1\t0.758602\t0.000000000\t0.504284\t0 # molecule nr 1\n\
+Ion_Type1_2\t0.758602\t0.000000000\t-0.504284\t0 # molecule nr 2\n";
+static string waterMpqc ="% Created by MoleCuilder\n\
+mpqc: (\n\
+\tsavestate = no\n\
+\tdo_gradient = yes\n\
+\tmole<MBPT2>: (\n\
+\t\tmaxiter = 200\n\
+\t\tbasis = $:basis\n\
+\t\tmolecule = $:molecule\n\
+\t\treference<CLHF>: (\n\
+\t\t\tbasis = $:basis\n\
+\t\t\tmolecule = $:molecule\n\
+\t\t)\n\
+\t)\n\
+)\n\
+molecule<Molecule>: (\n\
+\tunit = angstrom\n\
+\t{ atoms geometry } = {\n\
+\t\tO [ 0\t0\t0 ]\n\
+\t\tH [ 0.758602\t0\t0.504284 ]\n\
+\t\tH [ 0.758602\t0\t-0.504284 ]\n\
+\t}\n\
+)\n\
+basis<GaussianBasisSet>: (\n\
+\tname = \"3-21G\"\n\
+\tmolecule = $:molecule\n\
+)\n";
+static string waterXyz = "3\nH2O: water molecule\nO\t0.000000\t0.000000\t0.000000\nH\t0.758602\t0.000000\t0.504284\nH\t0.758602\t0.000000\t-0.504284\n";
+static string Tremolo_Atomdata1 = "# ATOMDATA\tId\tname\tType\tx=3\n";
+static string Tremolo_Atomdata2 = "#\n#ATOMDATA Id name Type x=3\n1 hydrogen H 3.0 4.5 0.1\n\n";
+static string Tremolo_invalidkey = "#\n#ATOMDATA Id name foo Type x=3\n\n\n";
+static string Tremolo_velocity = "#\n#ATOMDATA Id name Type u=3\n1 hydrogen H 3.0 4.5 0.1\n\n";
+static string Tremolo_neighbours = "#\n#ATOMDATA Id Type neighbors=2\n1 H 3 0\n2 H 3 0\n3 O 1 2\n";
+static string Tremolo_improper = "#\n#ATOMDATA Id Type imprData\n8 H 9-10\n9 H 10-8,8-10\n10 O -\n";
+static string Tremolo_torsion = "#\n#ATOMDATA Id Type torsion\n8 H 9-10\n9 H 10-8,8-10\n10 O -\n";
+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\t0\t0\t0\t0\t0\t0\t-\t0\tH\t-\t-\t-\t0\t0\t0\t0\t0\t0\t0\t0\t-\t\n";
 
 void ParserUnitTest::setUp() {
   World::getInstance();
+
+  // we need hydrogens and oxygens in the following tests
+  CPPUNIT_ASSERT(World::getInstance().getPeriode()->FindElement(1) != NULL);
+  CPPUNIT_ASSERT(World::getInstance().getPeriode()->FindElement(8) != NULL);
 }
 
@@ -43 +158 @@
   cout << "Testing the XYZ parser." << endl;
   XyzParser* testParser = new XyzParser();
-  string waterXyz = "3\nH2O: water molecule\nO\t0.000000\t0.000000\t0.000000\nH\t0.758602\t0.000000\t0.504284\nH\t0.758602\t0.000000\t-0.504284\n";
   stringstream input;
   input << waterXyz;
@@ -62 +176 @@
   TremoloParser* testParser = new TremoloParser();
   stringstream input, output;
-  string waterTremolo;
 
   // Atomdata beginning with "# ATOMDATA"
-  waterTremolo = "# ATOMDATA\tId\tname\tType\tx=3\n";
-  input << waterTremolo;
-  testParser->load(&input);
-  testParser->save(&output);
-  CPPUNIT_ASSERT(waterTremolo == output.str());
+  input << Tremolo_Atomdata1;
+  testParser->load(&input);
+  testParser->save(&output);
+  CPPUNIT_ASSERT(Tremolo_Atomdata1 == output.str());
   input.clear();
   output.clear();
 
   // Atomdata beginning with "#ATOMDATA"
-  waterTremolo = "#\n#ATOMDATA Id name Type x=3\n1 hydrogen H 3.0 4.5 0.1\n\n";
-  input << waterTremolo;
+  input << Tremolo_Atomdata2;
   testParser->load(&input);
   testParser->save(&output);
@@ -83 +194 @@
 
   // Invalid key in Atomdata line
-  waterTremolo = "#\n#ATOMDATA Id name foo Type x=3\n\n\n";
-  input << waterTremolo;
+  input << Tremolo_invalidkey;
   testParser->load(&input);
   //TODO: proove invalidity
@@ -93 +203 @@
   TremoloParser* testParser = new TremoloParser();
   stringstream input;
-  string waterTremolo;
 
   // One simple data line
-  waterTremolo = "#\n#ATOMDATA Id name Type x=3\n1 hydrogen H 3.0 4.5 0.1\n\n";
-  input << waterTremolo;
+  input << Tremolo_Atomdata2;
   testParser->load(&input);
   CPPUNIT_ASSERT(World::getInstance().getAtom(AtomByType(1))->x[0] == 3.0);
@@ -106 +214 @@
   TremoloParser* testParser = new TremoloParser();
   stringstream input;
-  string waterTremolo;
 
   // One simple data line
-  waterTremolo = "#\n#ATOMDATA Id name Type u=3\n1 hydrogen H 3.0 4.5 0.1\n\n";
-  input << waterTremolo;
+  input << Tremolo_velocity;
   testParser->load(&input);
   CPPUNIT_ASSERT(World::getInstance().getAtom(AtomByType(1))->v[0] == 3.0);
@@ -119 +225 @@
   TremoloParser* testParser = new TremoloParser();
   stringstream input;
-  string waterTremolo;
 
   // Neighbor data
-  waterTremolo = "#\n#ATOMDATA Id Type neighbors=2\n1 H 3 0\n2 H 3 0\n3 O 1 2\n";
-  input << waterTremolo;
+  input << Tremolo_neighbours;
   testParser->load(&input);
 
@@ -135 +239 @@
   TremoloParser* testParser = new TremoloParser();
   stringstream input, output;
-  string waterTremolo;
 
   // Neighbor data
-  waterTremolo = "#\n#ATOMDATA Id Type imprData\n8 H 9-10\n9 H 10-8,8-10\n10 O -\n";
-  input << waterTremolo;
+  input << Tremolo_improper;
   testParser->load(&input);
   testParser->save(&output);
@@ -151 +253 @@
   TremoloParser* testParser = new TremoloParser();
   stringstream input, output;
-  string waterTremolo;
 
   // Neighbor data
-  waterTremolo = "#\n#ATOMDATA Id Type torsion\n8 H 9-10\n9 H 10-8,8-10\n10 O -\n";
-  input << waterTremolo;
+  input << Tremolo_torsion;
   testParser->load(&input);
   testParser->save(&output);
@@ -173 +273 @@
   testParser->setFieldsForSave("x=3 u=3 F stress Id neighbors=5 imprData GroupMeasureTypeNo Type extType name resName chainID resSeq occupancy tempFactor segID Charge charge GrpTypeNo torsion");
   testParser->save(&output);
-  CPPUNIT_ASSERT(output.str() == "# 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\t0\t0\t0\t0\t0\t0\t-\t0\tH\t-\t-\t-\t0\t0\t0\t0\t0\t0\t0\t0\t-\t\n");
+  CPPUNIT_ASSERT(output.str() == Tremolo_full);
 
   cout << "testing the tremolo parser is done" << endl;
 }
+
+void ParserUnitTest::readwritePcpTest() {
+  stringstream input(waterPcp);
+  PcpParser* testParser = new PcpParser();
+  testParser->load(&input);
+  input.clear();
+
+  CPPUNIT_ASSERT_EQUAL(3, World::getInstance().numAtoms());
+
+  string newWaterPcp = "";
+  stringstream output;
+  testParser->save(&output);
+
+  input << output;
+  PcpParser* testParser2 = new PcpParser();
+  testParser2->load(&input);
+
+  CPPUNIT_ASSERT_EQUAL(6, World::getInstance().numAtoms());
+
+  CPPUNIT_ASSERT(*testParser == *testParser2);
+}
+
+void ParserUnitTest::writeMpqcTest() {
+  // build up water molecule
+  atom *Walker = NULL;
+  Walker = World::getInstance().createAtom();
+  Walker->type = World::getInstance().getPeriode()->FindElement(8);
+  Walker->x = Vector(0,0,0);
+  Walker = World::getInstance().createAtom();
+  Walker->type = World::getInstance().getPeriode()->FindElement(1);
+  Walker->x = Vector(0.758602,0,0.504284);
+  Walker = World::getInstance().createAtom();
+  Walker->type = World::getInstance().getPeriode()->FindElement(1);
+  Walker->x = Vector(0.758602,0,-0.504284);
+  CPPUNIT_ASSERT_EQUAL(3, World::getInstance().numAtoms());
+
+  // create two stringstreams, one stored, one created
+  stringstream input(waterMpqc);
+  MpqcParser* testParser = new MpqcParser();
+  stringstream output;
+  testParser->save(&output);
+
+  // compare both configs
+  CPPUNIT_ASSERT(input.str() == output.str());
+}

src/unittests/ParserUnitTest.hpp

@@ -22 +22 @@
   CPPUNIT_TEST ( readAndWriteTremoloTorsionInformationTest );
   CPPUNIT_TEST ( writeTremoloTest );
+  CPPUNIT_TEST ( readwritePcpTest );
+  CPPUNIT_TEST ( writeMpqcTest );
   CPPUNIT_TEST_SUITE_END();
 
@@ -36 +38 @@
   void readAndWriteTremoloTorsionInformationTest();
   void writeTremoloTest();
+  void readwritePcpTest();
+  void writeMpqcTest();
 };