Changeset 03a589 for src/Atom

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/Atom

Files:

• atom.cpp (modified) (1 diff)
• atom.hpp (modified) (1 diff)

src/Atom/atom.cpp

@@ -159 +159 @@
 };
 
-bool atom::OutputXYZLine(ofstream *out) const
-{
-  if (out != NULL) {
-    *out << getType()->getSymbol() << "\t" << at(0) << "\t" << at(1) << "\t" << at(2) << "\t" << endl;
-    return true;
-  } else
-    return false;
-};
-
-bool atom::OutputTrajectory(ofstream * const out, const enumeration<const element*> &elementLookup, int *AtomNo, const int step) const
-{
-  AtomNo[getType()->getAtomicNumber()]++;
-  if (out != NULL) {
-    const element *elemental = getType();
-    ASSERT(elementLookup.there.find(elemental)!=elementLookup.there.end(),"Type of this atom was not in the formula upon enumeration");
-    *out << "Ion_Type" << elementLookup.there.find(elemental)->second << "_" << AtomNo[getType()->getAtomicNumber()] << "\t"  << fixed << setprecision(9) << showpoint;
-    *out << getPositionAtStep(step)[0] << "\t" << getPositionAtStep(step)[1] << "\t" << getPositionAtStep(step)[2];
-    *out << "\t" << (int)(getFixedIon());
-    if (getAtomicVelocityAtStep(step).Norm() > MYEPSILON)
-      *out << "\t" << scientific << setprecision(6) << getAtomicVelocityAtStep(step)[0] << "\t" << getAtomicVelocityAtStep(step)[1] << "\t" << getAtomicVelocityAtStep(step)[2] << "\t";
-    if (getAtomicForceAtStep(step).Norm() > MYEPSILON)
-      *out << "\t" << scientific << setprecision(6) << getAtomicForceAtStep(step)[0] << "\t" << getAtomicForceAtStep(step)[1] << "\t" << getAtomicForceAtStep(step)[2] << "\t";
-    *out << "\t# Number in molecule " << getNr() << endl;
-    return true;
-  } else
-    return false;
-};
-
-bool atom::OutputTrajectoryXYZ(ofstream * const out, const int step) const
-{
-  if (out != NULL) {
-    *out << getType()->getSymbol() << "\t";
-    *out << getPositionAtStep(step)[0] << "\t";
-    *out << getPositionAtStep(step)[1] << "\t";
-    *out << getPositionAtStep(step)[2] << endl;
-    return true;
-  } else
-    return false;
-};
-
-void atom::OutputMPQCLine(ostream * const out, const Vector *center) const
-{
-  Vector recentered(getPosition());
-  recentered -= *center;
-  *out << "\t\t" << getType()->getSymbol() << " [ " << recentered[0] << "\t" << recentered[1] << "\t" << recentered[2] << " ]" << endl;
-};
-
-void atom::OutputPsi3Line(ostream * const out, const Vector *center) const
-{
-  Vector recentered(getPosition());
-  recentered -= *center;
-  *out << "\t( " << getType()->getSymbol() << "\t" << recentered[0] << "\t" << recentered[1] << "\t" << recentered[2] << " )" << endl;
-};
-
 bool atom::Compare(const atom &ptr) const
 {

src/Atom/atom.hpp

@@ -84 +84 @@
    */
   bool OutputArrayIndexed(ostream * const out,const enumeration<const element*>&, int *AtomNo, const char *comment = NULL) const;
-
-  /** Output of a single atom as one line in xyz file.
-   * \param *out stream to output to
-   * \return true - \a *out present, false - \a *out is NULL
-   */
-  bool OutputXYZLine(ofstream *out) const;
-
-  /** Output of a single atom as one line in xyz file.
-   * \param *out stream to output to
-   * \param *ElementNo array with ion type number in the config file this atom's element shall have
-   * \param *AtomNo array with atom number in the config file this atom shall have, is increase by one automatically
-   * \param step Trajectory time step to output
-   * \return true - \a *out present, false - \a *out is NULL
-   */
-  bool OutputTrajectory(ofstream * const out, const enumeration<const element*>&, int *AtomNo, const int step) const;
-
-  /** Output of a single atom as one lin in xyz file.
-   * \param *out stream to output to
-   * \param step Trajectory time step to output
-   * \return true - \a *out present, false - \a *out is NULL
-   */
-  bool OutputTrajectoryXYZ(ofstream * const out, const int step) const;
-
-  /** Outputs the MPQC configuration line for this atom.
-   * \param *out output stream
-   * \param *center center of molecule subtracted from position
-   * \param *AtomNo pointer to atom counter that is increased by one
-   */
-  void OutputMPQCLine(ostream * const out, const Vector *center) const;
-
-  /** Outputs the Psi3 configuration line for this atom.
-   * \param *out output stream
-   * \param *center center of molecule subtracted from position
-   * \param *AtomNo pointer to atom counter that is increased by one
-   */
-  void OutputPsi3Line(ostream * const out, const Vector *center) const;
 
   /** Initialises the component number array.