Changeset bf12d1 for src

Timestamp:

Dec 19, 2012, 3:25:30 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:

dda3e8

Parents:

f06d52

git-author:

Frederik Heber <heber@…> (11/19/12 14:21:33)

git-committer:

Frederik Heber <heber@…> (12/19/12 15:25:30)

Message:

FIX: WriteTable might fail because of size_t difference.

• MaxLevel-StartLevel might wrap and hence cause ASSERT in writeTable to wrongly fail.
• added checks in printReceivedFullResults() whether we actually have MaxLevel larger than 2.
• also enhanced documentation a bit.

Location:

src

Files:

• Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) (7 diffs)
• Fragmentation/Summation/writeTable.hpp (modified) (1 diff)

src/Actions/FragmentationAction/FragmentationAutomationAction.cpp

@@ -324 +324 @@
   }
 
+  if (results.Result_LongRange_fused.size() >= (results.getMaxLevel()-2))
   {
     const std::string gridresult =
@@ -334 +335 @@
   }
 
+  if (results.Result_LongRangeIntegrated_fused.size() >= (results.getMaxLevel()-2))
   {
     const std::string gridresult =
@@ -383 +385 @@
     const std::string &KeySetFilename)
 {
-  // read homology container (if present)
+  /// read homology container (if present)
   HomologyContainer homology_container;
   if (boost::filesystem::exists(homology_file)) {
@@ -399 +401 @@
   }
 
-  // append all fragments to a HomologyContainer
+  /// append all fragments to a HomologyContainer
   HomologyContainer::container_t values;
   const size_t FragmentCounter = results.Result_perIndexSet_Energy.size();
@@ -409 +411 @@
   IndexSetContainer::Container_t::const_iterator iter = Indices.begin();
   IndexSetContainer::Container_t::const_iterator forceiter = ForceIndices.begin();
+  /// go through all fragments
   for (;iter != Indices.end(); ++iter, ++forceiter) // go through each IndexSet
   {
-    // create graph from the force indices (i.e. with hydrogens)
+    /// create new graph entry in HomologyContainer which is (key,value) type
     LOG(1, "INFO: Creating new graph with " << **forceiter << ".");
     HomologyGraph graph(**forceiter);
-    LOG(1, "INFO: Created graph " << graph << ".");
-    // obtain information for value of HomologyContainer entry with normal indices
+    LOG(2, "DEBUG: Created graph " << graph << ".");
     const IndexSet::ptr &index = *iter;
     HomologyContainer::value_t value;
+
+    // obtain fragment as key
     std::map<IndexSet::ptr, std::pair< MPQCDataFragmentMap_t, MPQCDataFragmentMap_t> >::const_iterator fragmentiter
         = results.Result_perIndexSet_Fragment.find(index);
@@ -424 +428 @@
         +" in FragmentResults.");
     value.first = boost::fusion::at_key<MPQCDataFused::fragment>(fragmentiter->second.first);
+
+    // obtain energy as value
     std::map<IndexSet::ptr, std::pair< MPQCDataEnergyMap_t, MPQCDataEnergyMap_t> >::const_iterator energyiter
         = results.Result_perIndexSet_Energy.find(index);
@@ -450 +456 @@
   }
 
-  // store homology container again
+  /// store homology container again
   std::ofstream outputstream(homology_file.string().c_str());
   if (outputstream.good()) { // check if opened

src/Fragmentation/Summation/writeTable.hpp

@@ -36 +36 @@
   {
     std::stringstream resultstream;
-    // create header line for energy
+
+    /// create header line for energy
     HeaderPrinter header("level");
     boost::mpl::for_each<VectorType>(boost::ref(header));
     resultstream << header.get() << std::endl;
 
-    // print values per line
-    ASSERT( results.size() >= (MaxLevel-StartLevel),
-        "writeTable<M,V>() - results has insufficient size.");
-    for (size_t level = StartLevel; level <= MaxLevel; ++level) {
-      ValuePrinter<MapType, numprecision> values(results[level-1], level);
-      boost::mpl::for_each<VectorType>(boost::ref(values));
-      resultstream << values.get() << std::endl;
+    /// print values per line
+    if (MaxLevel >= StartLevel) {
+      ASSERT( results.size() >= (MaxLevel-StartLevel),
+          "writeTable<M,V>() - results has insufficient size.");
+      for (size_t level = StartLevel; level <= MaxLevel; ++level) {
+        ValuePrinter<MapType, numprecision> values(results[level-1], level);
+        boost::mpl::for_each<VectorType>(boost::ref(values));
+        resultstream << values.get() << std::endl;
+      }
+    } else {
+      ELOG(2, "writeTable does not output as MaxLevel(" << MaxLevel
+          << ") < StartLevel(" << StartLevel << ".");
     }
     return resultstream.str();