Changeset 73916f for src/Parser/XyzParser.cpp

Timestamp:

Dec 16, 2010, 5:32:22 PM (14 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:

fc5c3a

Parents:

512f85

git-author:

Frederik Heber <heber@…> (12/11/10 15:57:00)

git-committer:

Frederik Heber <heber@…> (12/16/10 17:32:22)

Message:

Extended FormatParser::save() to use vector<atom *> to save.

• This is needed to make the save functions also work on selected atoms or molecules only.
• Within ParserCommonUnitTest, ParserTremoloUnitTest we create the vector by calling World's getAllAtoms() (which would have been done before in the specialized save() functions).
• new functions in FormatParserStorage:
  • saveSelectedAtoms().
  • saveSelectedMolecules().
  • saveWorld().
• renamed ::get() and ::put() to ::load() and ::save() to have it more consistent with underlying FormatParser functions and also to avoid misinterpretation with all ::get...() functions.

File:

• src/Parser/XyzParser.cpp (modified) (2 diffs)

src/Parser/XyzParser.cpp

@@ -78 +78 @@
 
 /**
- * Saves the current state of the World into the given XYZ file.
+ * Saves the \a atoms into as a XYZ file.
  *
- * \param XYZ file
+ * \param file where to save the state
+ * \param atoms atoms to store
  */
-void XyzParser::save(ostream* file) {
+void XyzParser::save(ostream* file, const std::vector<atom *> &atoms) {
   DoLog(0) && (Log() << Verbose(0) << "Saving changes to xyz." << std::endl);
   //if (comment == "") {
@@ -95 +96 @@
       comment += time;
   //}
-  *file << World::getInstance().numAtoms() << endl << "\t" << comment << endl;
+  *file << atoms.size() << endl << "\t" << comment << endl;
 
-  vector<atom*> atoms = World::getInstance().getAllAtoms();
-  for(vector<atom*>::iterator it = atoms.begin(); it != atoms.end(); it++) {
+  for(vector<atom*>::const_iterator it = atoms.begin(); it != atoms.end(); it++) {
     *file << noshowpoint << (*it)->getType()->getSymbol() << "\t" << (*it)->at(0) << "\t" << (*it)->at(1) << "\t" << (*it)->at(2) << endl;
   }