Changeset 4b10fd for src/Parser/XmlParser.cpp

Timestamp:

Apr 29, 2014, 12:42:43 PM (11 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:

ec7511

Parents:

57388c9

git-author:

Frederik Heber <heber@…> (10/23/13 21:57:07)

git-committer:

Frederik Heber <heber@…> (04/29/14 12:42:43)

Message:

XmlParser::load() now gives each different charge a different element.

• this allows search&replace to the correct element afterwards.

File:

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

src/Parser/XmlParser.cpp

@@ -166 +166 @@
   data.config.epsilon = toString(configuration.attribute("epsilon").value());
 
+  // use a map to at least give each charge a different element
+  typedef std::map<double, atomicNumber_t> charge_map_t;
+  charge_map_t charge_map;
+  size_t last_atomicnumber = 1;
   // particles
   for(pugi::xml_node::iterator iter = configuration.begin();
@@ -177 +181 @@
     LOG(2, "DEBUG: Parsing particle at " << p.position << ".");
     atom * const newAtom = World::getInstance().createAtom();
-    // for the moment each becomes a hydrogen
-    newAtom->setType(World::getInstance().getPeriode()->FindElement((atomicNumber_t)1));
+    charge_map_t::const_iterator chargeiter = charge_map.find(p.q);
+    if (chargeiter == charge_map.end()) {
+      // create new entry and set iter pointing to it
+      std::pair<charge_map_t::const_iterator, bool> inserter =
+          charge_map.insert( std::make_pair( p.q, last_atomicnumber++) );
+      chargeiter = inserter.first;
+    }
+    newAtom->setType(World::getInstance().getPeriode()->FindElement(chargeiter->second));
     newAtom->setPosition(p.position);
     newAtom->setCharge(p.q);