Changeset 5f0c60 for src

Timestamp:

Jul 8, 2013, 2:22:01 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:

a953c4

Parents:

bbc422

git-author:

Frederik Heber <heber@…> (06/26/13 18:37:57)

git-committer:

Frederik Heber <heber@…> (07/08/13 14:22:01)

Message:

FIX: SerializablePotential::stream_from(), several fixes.

• equalitysep with tokenizer would have required copying string. Hence, we simply copy and split via string functions as there is only one equality sign.
• particle types index was off by one.
• SetParticleType() did not check whether we actually needed to resize and was off by one.

Location:

src/Potentials

Files:

• SerializablePotential.cpp (modified) (2 diffs)
• SerializablePotential.hpp (modified) (1 diff)

src/Potentials/SerializablePotential.cpp

@@ -113 +113 @@
   typedef boost::tokenizer<boost::char_separator<char> > tokenizer;
   boost::char_separator<char> pairsep(",\t ;");
-  boost::char_separator<char> keyvaluesep("=");
   std::string remainderstring(linestring.substr(colonpos+1));
-//  {
-//    std::stringstream remainderstream
-//    remainderstream >> std::ws >> remainderstring;
-//  }
   tokenizer tokens(remainderstring, pairsep); //skip colon
 
@@ -128 +123 @@
     tok_iter != tokens.end(); ++tok_iter) {
     const std::string &keyvalue = *tok_iter;
-    tokenizer keyvaluetoken(keyvalue, keyvaluesep);
-    tokenizer::iterator keyvalue_iter = keyvaluetoken.begin();
-    const std::string &key = *keyvalue_iter;
+    const size_t equalitypos = keyvalue.find("=");
+    const std::string key = keyvalue.substr(0,equalitypos);
+    const std::string value = keyvalue.substr(equalitypos+1);
 
     /// parse the particle_types
-    const size_t pos = key.find("particle_type");
+    const std::string typetoken("particle_type");
+    const size_t pos = key.find(typetoken);
     if (pos != std::string::npos) {
       // split of type and convert rest to index
-      const size_t index = ConvertToIndex(key.substr(pos, std::string::npos));
+      const size_t indexpos = pos+typetoken.length();
+      const std::string &indexstring = key.substr(indexpos);
+      const size_t index = ConvertToIndex(indexstring);
+      if(index == 0)
+          throw SerializablePotentialMissingValueException() << SerializablePotentialKey(key);
       // and set the type
-      if (++keyvalue_iter == keyvaluetoken.end())
+      if (equalitypos == std::string::npos)
         throw SerializablePotentialMissingValueException() << SerializablePotentialKey(key);
-      const std::string &value = *keyvalue_iter;
-      setParticleType(index, ConvertToParticleType(value));
+      setParticleType(index-1, ConvertToParticleType(value));
     } else {
       const size_t index = getParameterIndex(key);
       // parse the coefficients
       if (index != (size_t)-1) {
-        if (++keyvalue_iter == keyvaluetoken.end())
+        if (equalitypos == std::string::npos)
           throw SerializablePotentialMissingValueException() << SerializablePotentialKey(key);
-        const std::string &value = *keyvalue_iter;
         params[index] = ConvertToValue(value);
       } else {

src/Potentials/SerializablePotential.hpp

@@ -141 +141 @@
   void setParticleType(const size_t index, const ParticleType_t& _designation)
   {
-    const_cast<ParticleTypes_t &>(ParticleTypes).resize(index);
+    if (ParticleTypes.size() <= index)
+      const_cast<ParticleTypes_t &>(ParticleTypes).resize(index+1);
     const_cast<ParticleTypes_t &>(ParticleTypes)[index] = _designation;
   }