Changeset 637358

Timestamp:

Mar 1, 2011, 10:16:38 AM (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:

4afa46

Parents:

0180d6

git-author:

Frederik Heber <heber@…> (02/18/11 23:38:44)

git-committer:

Frederik Heber <heber@…> (03/01/11 10:16:38)

Message:

Changed slightly XyzParser::load().

• AddedAtoms is now a vector.

File:

• src/Parser/XyzParser.cpp (modified) (4 diffs)

src/Parser/XyzParser.cpp

@@ -19 +19 @@
 
 #include "CodePatterns/MemDebug.hpp"
+
+#include <vector>
 
 #include "CodePatterns/Log.hpp"
@@ -56 +58 @@
   char commentBuffer[512], type[3];
   string number;
-  std::list<atom *> AddedAtoms;
+  std::vector<atom *> AddedAtoms;
 
   // create the molecule
@@ -68 +70 @@
   *file >> number >> ws;
   unsigned int step = 0;
-  std::list<atom *>::iterator CurrentAtom;
   do {
-    CurrentAtom = AddedAtoms.begin();
     std::stringstream numberstream(number);
     numberstream >> numberOfAtoms;
+    if (step == 0)
+      AddedAtoms.resize(numberOfAtoms);
     // the second line is always a comment
     file->getline(commentBuffer, 512);
@@ -91 +93 @@
         newAtom->setType(World::getInstance().getPeriode()->FindElement(type));
         newmol->AddAtom(newAtom);
-        AddedAtoms.push_back(newAtom);
-        LOG(5, "INFO: Created new atom.");
+        AddedAtoms[i] = newAtom;
+        LOG(5, "INFO: Created new atom, setting " << i << " th component of AddedAtoms.");
       } else {
-        ASSERT(CurrentAtom != AddedAtoms.end(),
-            "XyzParser::load() - not enough added atoms.");
-        newAtom = *CurrentAtom++;
+        newAtom = AddedAtoms[i];
+        LOG(5, "INFO: Using present atom " << *newAtom << " from " << i << " th component of AddedAtoms.");
         ASSERT(newAtom->getType() == World::getInstance().getPeriode()->FindElement(type),
-            "XyzParser::load() - atom has different type, mixed up order?");
-        LOG(5, "INFO: Using present atom " << *newAtom << ".");
+            "XyzParser::load() - atom has different type "+newAtom->getType()->getSymbol()+" than parsed now "+type+", mixed up order?");
       }
       newAtom->setPositionAtStep(step, tempVector);