Changeset 03a589 for src/Parser

Timestamp:

Apr 4, 2012, 11:30:11 AM (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:

47ed3d

Parents:

ce7bfd

git-author:

Frederik Heber <heber@…> (03/26/12 07:44:19)

git-committer:

Frederik Heber <heber@…> (04/04/12 11:30:11)

Message:

Removed lots of remnant output functions in atom and molecule that are not used anymore.

• Removed functions in atom: OutputMPQCLine(), OutputPsi3Line(), OutputXYZLine(), OutputTrajectories(), OutputTrajectoryXYZ()
• functionality of outputters has been shifted to Psi3Parser and MPQCParser.
• Removed functions in molecule: OutputTrajectories(), OutputTrajectoriesXYZ(), OutputXYZ()
• Removed in CounBondsUnitTest: OutputTestMolecule().

Location:

src/Parser

Files:

• MpqcParser.cpp (modified) (3 diffs)
• MpqcParser.hpp (modified) (2 diffs)
• Psi3Parser.cpp (modified) (3 diffs)
• Psi3Parser.hpp (modified) (2 diffs)

src/Parser/MpqcParser.cpp

@@ -19 +19 @@
 
 #include <iostream>
+#include <boost/foreach.hpp>
 #include <boost/tokenizer.hpp>
 #include <string>
@@ -216 +217 @@
 }
 
+void FormatParser< mpqc >::OutputMPQCLine(ostream * const out, const atom &_atom, const Vector *center) const
+{
+  Vector recentered(_atom.getPosition());
+  recentered -= *center;
+  *out << "\t\t" << _atom.getType()->getSymbol() << " [ " << recentered[0] << "\t" << recentered[1] << "\t" << recentered[2] << " ]" << std::endl;
+};
+
+
 /** Saves all atoms and data into a MPQC config file.
  * \param *file output stream
@@ -306 +315 @@
     *file << "\t{ atoms geometry } = {" << endl;
     // output of atoms
-    for (std::vector<atom *>::const_iterator AtomRunner = atoms.begin(); AtomRunner != atoms.end(); ++AtomRunner) {
-      (*AtomRunner)->OutputMPQCLine(file, &center);
+    BOOST_FOREACH(const atom *_atom, atoms) {
+      OutputMPQCLine(file, *_atom, &center);
     }
     *file << "\t}" << endl;

src/Parser/MpqcParser.hpp

@@ -25 +25 @@
 
 #include <iosfwd>
+
+class Vector;
 
 // declaration of specialized FormatParserTrait
@@ -59 +61 @@
 
 private:
+  void OutputMPQCLine(ostream * const out, const atom &_atom, const Vector *center) const;
+
   static ConvertTo<bool> Converter;
 };

src/Parser/Psi3Parser.cpp

@@ -19 +19 @@
 
 #include <iostream>
+#include <boost/foreach.hpp>
 #include <boost/tokenizer.hpp>
 #include <string>
@@ -153 +154 @@
 }
 
+void FormatParser< psi3 >::OutputPsi3Line(ostream * const out, const atom &_atom, const Vector *center) const
+{
+  Vector recentered(_atom.getPosition());
+  recentered -= *center;
+  *out << "\t( " << _atom.getType()->getSymbol() << "\t" << recentered[0] << "\t" << recentered[1] << "\t" << recentered[2] << " )" << endl;
+};
+
+
 /** Saves all atoms and data into a PSI3 config file.
  * \param *file output stream
@@ -220 +229 @@
     *file << "\tgeometry = (" << std::endl;
     // output of atoms
-    for (std::vector<atom *>::const_iterator AtomRunner = atoms.begin(); AtomRunner != atoms.end(); ++AtomRunner) {
-      (*AtomRunner)->OutputPsi3Line(file, &center);
+    BOOST_FOREACH(const atom *_atom, atoms) {
+      OutputPsi3Line(file, *_atom, &center);
     }
     *file << "\t)" << std::endl;

src/Parser/Psi3Parser.hpp

@@ -25 +25 @@
 
 #include <iosfwd>
+
+class Vector;
 
 // declaration of specialized FormatParserTrait
@@ -59 +61 @@
 
 private:
+  void OutputPsi3Line(ostream * const out, const atom &_atom, const Vector *center) const;
+
   static ConvertTo<bool> Converter;
 };