Changeset 7ace68

Timestamp:

Dec 14, 2012, 2:29:34 PM (12 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:

0cfc27

Parents:

14de8e1

git-author:

Frederik Heber <heber@…> (02/06/12 15:04:48)

git-committer:

Frederik Heber <heber@…> (12/14/12 14:29:34)

Message:

Added multiplicity guesser for Psi3Parser's UHF.

• TESTFIX: changed multp in testuhf.psi and testtwocon.psi of regression tests Parser/Psi3 due to multiplicity guesser.
• TESTFIX: changed multp in the same way in ParserPsi3UnitTest.

Files:

• src/Parser/Psi3Parser.cpp (modified) (3 diffs)
• src/Parser/Psi3Parser.hpp (modified) (1 diff)
• src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) (2 diffs)
• tests/regression/Parser/Psi3/pre/testtwocon.psi (modified) (1 diff)
• tests/regression/Parser/Psi3/pre/testuhf.psi (modified) (1 diff)

src/Parser/Psi3Parser.cpp

@@ -44 +44 @@
 
 #include "Atom/atom.hpp"
+#include "Bond/bond.hpp"
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/toString.hpp"
@@ -216 +217 @@
     if ((reference == getParams().getReferenceName(Psi3Parser_Parameters::UHF))
         || (reference == getParams().getReferenceName(Psi3Parser_Parameters::TWOCON))) {
+      const unsigned int multiplicity = calculateMultiplicity(atoms);
       *file << "\t" << getParams().getParameterName(Psi3Parser_Parameters::multiplicityParam)
-                    << " = " << getParams().getParameter(Psi3Parser_Parameters::multiplicityParam) << std::endl;
+                    << " = " << multiplicity << std::endl;
+//                    << " = " << getParams().getParameter(Psi3Parser_Parameters::multiplicityParam) << std::endl;
       *file << "\t" << getParams().getParameterName(Psi3Parser_Parameters::chargeParam)
                     << " = " << getParams().getParameter(Psi3Parser_Parameters::chargeParam) << std::endl;
@@ -254 +257 @@
 }
 
-
+unsigned int FormatParser< psi3 >::calculateMultiplicity(const std::vector<atom *> &atoms) const
+{
+  // add up the number of electrons
+  double valencies = 0.;
+  BOOST_FOREACH(atom *_atom, atoms) {
+    valencies += _atom->getType()->getAtomicNumber();
+  }
+
+  // add doubly up all bond degrees (two electrons per bond)
+  unsigned int degrees = 0;
+  BOOST_FOREACH(atom *_atom, atoms) {
+    BOOST_FOREACH(bond *_bond, _atom->getListOfBonds()) {
+      degrees += 2*_bond->BondDegree;
+    }
+  }
+
+  // return difference+1 as multiplicity
+  return (int)fabs(valencies-degrees)+1;
+}

src/Parser/Psi3Parser.hpp

@@ -61 +61 @@
 
 private:
+  /** Prints the config line for the given \a _atom in PSI3 style.
+   *
+   * \param out output stream
+   * \param _atom atom to print
+   * \param center correct atom position by this vector
+   */
   void OutputPsi3Line(ostream * const out, const atom &_atom, const Vector *center) const;
+
+  /** Calculates multiplicites for a given set of \a atoms.
+   *
+   * \param atoms set of atoms
+   * \return mulitplicity
+   */
+  unsigned int calculateMultiplicity(const std::vector<atom *> &atoms) const;
 
   static ConvertTo<bool> Converter;

src/Parser/unittests/ParserPsi3UnitTest.cpp

@@ -102 +102 @@
 \treference = uhf\n\
 \tbasis = \"cc-pVTZ\"\n\
-\tmultp = 2\n\
+\tmultp = 3\n\
 \tcharge = 2\n\
 \tfreeze_core = no\n\
@@ -121 +121 @@
 \treference = twocon\n\
 \tbasis = \"cc-pVTZ\"\n\
-\tmultp = 1\n\
+\tmultp = 3\n\
 \tcharge = 2\n\
 \tsocc = ( 1 1 0 0 0 0 0 0 )\n\

tests/regression/Parser/Psi3/pre/testtwocon.psi

@@ -6 +6 @@
 reference = twocon
 basis = "cc-pVTZ"
-multp = 1
+multp = 3
 charge = 2
 socc = ( 1 0 1 0 0 0 0 0)

tests/regression/Parser/Psi3/pre/testuhf.psi

@@ -6 +6 @@
 reference = uhf
 basis = "cc-pVTZ"
-multp = 1
+multp = 3
 charge = 2
 freeze_core = no