Changeset 73916f for src/Parser/PcpParser.cpp

Timestamp:

Dec 16, 2010, 5:32:22 PM (15 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:

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/PcpParser.cpp (modified) (7 diffs)

src/Parser/PcpParser.cpp

@@ -368 +368 @@
 }
 
-/** Saves the World into a PCP config file.
- * \param *file output stream to save to
- */
-void PcpParser::save(std::ostream* file)
+/**
+ * Saves the \a atoms into as a PCP file.
+ *
+ * \param file where to save the state
+ * \param atoms atoms to store
+ */
+void PcpParser::save(std::ostream* file, const std::vector<atom *> &atoms)
 {
   DoLog(0) && (Log() << Verbose(0) << "Saving changes to pcp." << std::endl);
@@ -379 +382 @@
   if (!file->fail()) {
     // calculate number of Psis
-    vector<atom *> allatoms = World::getInstance().getAllAtoms();
-    CalculateOrbitals(allatoms);
+    CalculateOrbitals(atoms);
     *file << "# ParallelCarParinello - main configuration file - created with molecuilder" << endl;
     *file << endl;
@@ -468 +470 @@
     *file << "RelativeCoord\t" << RelativeCoord << "\t# whether ion coordinates are relative (1) or absolute (0)" << endl;
     map<int, int> ZtoIndexMap;
-    OutputElements(file, allatoms, ZtoIndexMap);
-    OutputAtoms(file, allatoms, ZtoIndexMap);
+    OutputElements(file, atoms, ZtoIndexMap);
+    OutputAtoms(file, atoms, ZtoIndexMap);
   } else {
     DoeLog(1) && (eLog()<< Verbose(1) << "Cannot open output file." << endl);
@@ -479 +481 @@
  * \param &allatoms all atoms to store away
  */
-void PcpParser::CalculateOrbitals(vector<atom *> &allatoms)
+void PcpParser::CalculateOrbitals(const std::vector<atom *> &allatoms)
 {
   PlaneWaveSpecifics.MaxPsiDouble = PlaneWaveSpecifics.PsiMaxNoDown = PlaneWaveSpecifics.PsiMaxNoUp = PlaneWaveSpecifics.PsiType = 0;
-  for (vector<atom *>::iterator runner = allatoms.begin(); runner != allatoms.end(); ++runner) {
+  for (vector<atom *>::const_iterator runner = allatoms.begin(); runner != allatoms.end(); ++runner) {
     PlaneWaveSpecifics.MaxPsiDouble += (*runner)->getType()->getNoValenceOrbitals();
   }
@@ -512 +514 @@
  * \param &ZtoIndexMap map of which atoms belong to which ion number
  */
-void PcpParser::OutputElements(ostream *file, vector<atom *> &allatoms, map<int, int> &ZtoIndexMap)
+void PcpParser::OutputElements(ostream *file, const std::vector<atom *> &allatoms, map<int, int> &ZtoIndexMap)
 {
   map<int, int> PresentElements;
   pair <   map<int, int>::iterator, bool > Inserter;
   // insert all found elements into the map
-  for (vector<atom *>::iterator AtomRunner = allatoms.begin();AtomRunner != allatoms.end();++AtomRunner) {
+  for (vector<atom *>::const_iterator AtomRunner = allatoms.begin();AtomRunner != allatoms.end();++AtomRunner) {
     Inserter = PresentElements.insert(pair<int, int>((*AtomRunner)->getType()->getAtomicNumber(), 1));
     if (!Inserter.second) // increase if present
@@ -542 +544 @@
  * \param &ZtoIndexMap map of which atoms belong to which ion number
  */
-void PcpParser::OutputAtoms(ostream *file, vector<atom *> &allatoms, map<int, int> &ZtoIndexMap)
+void PcpParser::OutputAtoms(ostream *file, const std::vector<atom *> &allatoms, map<int, int> &ZtoIndexMap)
 {
   *file << "#Ion_TypeNr._Nr.R[0]    R[1]    R[2]    MoveType (0 MoveIon, 1 FixedIon)" << endl;
@@ -548 +550 @@
   pair <   map<int, int>::iterator, bool > Inserter;
   int nr = 0;
-  for (vector<atom *>::iterator AtomRunner = allatoms.begin();AtomRunner != allatoms.end();++AtomRunner) {
+  for (vector<atom *>::const_iterator AtomRunner = allatoms.begin();AtomRunner != allatoms.end();++AtomRunner) {
     Inserter = ZtoCountMap.insert( pair<int, int>((*AtomRunner)->getType()->getAtomicNumber(), 1) );
     if (!Inserter.second)