Changeset 1b2d30 for src/Parser/MpqcParser.cpp

Timestamp:

Jun 12, 2010, 10:19:48 PM (16 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, Candidate_v1.7.0, 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)

File:

• src/Parser/MpqcParser.cpp (modified) (1 diff)

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;
+}