Changeset 58fccca

Timestamp:

Feb 13, 2013, 3:47:45 PM (12 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:

42f2f0

Parents:

b4b364

git-author:

Frederik Heber <heber@…> (01/08/13 14:40:11)

git-committer:

Frederik Heber <heber@…> (02/13/13 15:47:45)

Message:

FIX: XyzParser::load() stumbled if no empty line between timesteps.

• also replaced char* by string and using getline().

File:

• src/Parser/XyzParser.cpp (modified) (3 diffs)

src/Parser/XyzParser.cpp

@@ -81 +81 @@
   molecule* newmol = NULL;
   int numberOfAtoms;
-  char commentBuffer[512], type[3];
-  string number;
+  string elementtype;
+  string streambuffer;
   std::vector<atom *> AddedAtoms;
 
@@ -93 +93 @@
   // the first line tells number of atoms,
   // where we need this construct due to skipping of empty lines below
-  file->getline(commentBuffer, 512);
+  getline(*file, streambuffer);
   unsigned int step = 0;
   while (file->good()) {
-    std::stringstream numberstream(commentBuffer);
+    std::stringstream numberstream(streambuffer);
     numberstream >> numberOfAtoms;
     if (step == 0)
       AddedAtoms.resize(numberOfAtoms);
     // the second line is always a comment
-    file->getline(commentBuffer, 512);
-    comment = commentBuffer;
+    getline(*file, streambuffer);
+    comment = streambuffer;
     LOG(3, "DEBUG: comment is '" << comment << "'.");
 
     for (int i = 0; i < numberOfAtoms; i++) {
       // parse type and position
-      *file >> type;
+      *file >> elementtype;
       Vector tempVector;
       for (int j=0;j<NDIM;j++) {
         *file >> tempVector[j];
       }
-      LOG(4, "INFO: Parsed type as " << type << " and position at "
+      LOG(4, "INFO: Parsed type as " << elementtype << " and position at "
           << tempVector << " for time step " << step);
 
       if (step == 0) {
         newAtom = World::getInstance().createAtom();
-        newAtom->setType(World::getInstance().getPeriode()->FindElement(type));
+        newAtom->setType(World::getInstance().getPeriode()->FindElement(elementtype.c_str()));
         newmol->AddAtom(newAtom);
         AddedAtoms[i] = newAtom;
@@ -124 +124 @@
         newAtom = AddedAtoms[i];
         LOG(5, "INFO: Using present atom " << *newAtom << " from " << i << " th component of AddedAtoms.");
-        ASSERT(newAtom->getType() == World::getInstance().getPeriode()->FindElement(type),
-            "FormatParser< xyz >::load() - atom has different type "+newAtom->getType()->getSymbol()+" than parsed now "+type+", mixed up order?");
+        ASSERT(newAtom->getType() == World::getInstance().getPeriode()->FindElement(elementtype.c_str()),
+            "FormatParser< xyz >::load() - atom has different type "+newAtom->getType()->getSymbol()+" than parsed now "+elementtype+", mixed up order?");
       }
       newAtom->setPositionAtStep(step, tempVector);
     }
-    getline (*file, number);  // eat away rest of last line
+    getline (*file, streambuffer);  // eat away rest of last line
     // skip empty lines
     unsigned int counter = 0;
     while (file->good()) {
-      getline (*file, number);
-      LOG(4, "INFO: Skipped line is '" << number << "'");
+      getline (*file, streambuffer);
+      LOG(4, "INFO: Skipped line is '" << streambuffer << "'");
       counter++;
-      if (!number.empty())
+      if (!streambuffer.empty())
         break;
     }