Changeset 4fdc65 for src

Timestamp:

Apr 18, 2011, 2:59:46 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:

7a1dd0

Parents:

305e7e

git-author:

Frederik Heber <heber@…> (04/18/11 14:57:15)

git-committer:

Frederik Heber <heber@…> (04/18/11 14:59:46)

Message:

FIX: XyzParser and PcpParser fail on empty but present config files.

• XyzParser::load() do..while -> while
• ConfigFileBuffer::InitFileBuffer() do..while -> while
• ParseForParameter() - check whether initially CurrentLine < NoLines.
• NOTE: ConfigFileBuffer is not written in a stable manner, checks and encapsulation are missing. It should be refactored.

Location:

src

Files:

• ConfigFileBuffer.cpp (modified) (1 diff)
• Parser/XyzParser.cpp (modified) (2 diffs)
• config.cpp (modified) (1 diff)

src/ConfigFileBuffer.cpp

@@ -135 +135 @@
   NoLines = 0; // we're overcounting by one
   long file_position = file->tellg(); // mark current position
-  do {
+  while (file->good()) {
     file->getline(line, MAXSTRINGSIZE-1);
     NoLines++;
-  } while (!file->eof());
+  }
   file->clear();
   file->seekg(file_position, ios::beg);

src/Parser/XyzParser.cpp

@@ -70 +70 @@
   *file >> number >> ws;
   unsigned int step = 0;
-  do {
+  while (file->good()) {
     std::stringstream numberstream(number);
     numberstream >> numberOfAtoms;
@@ -115 +115 @@
     LOG(3, "INFO: I skipped "+toString(counter)+" empty lines.");
     ++step;
-  } while (file->good());
+  }
   BOOST_FOREACH(atom *_atom, World::getInstance().getAllAtoms())
     LOG(3, "INFO: Atom " << _atom->getName() << " " << *dynamic_cast<AtomInfo *>(_atom) << ".");

src/config.cpp

@@ -1440 +1440 @@
     dummy1 = dummy = NULL;
     do {
-      free_dummy = dummy1 = FileBuffer->buffer[ FileBuffer->LineMapping[FileBuffer->CurrentLine++] ];
+      if (FileBuffer->CurrentLine < FileBuffer->NoLines)
+        free_dummy = dummy1 = FileBuffer->buffer[ FileBuffer->LineMapping[FileBuffer->CurrentLine++] ];
       if (FileBuffer->CurrentLine >= FileBuffer->NoLines) {
         if ((critical) && (found == 0)) {