Changeset 78bb14 for src/Actions

Timestamp:

Dec 22, 2010, 5:27:31 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:

f28a26

Parents:

ff3c40

git-author:

Frederik Heber <heber@…> (12/17/10 15:57:59)

git-committer:

Frederik Heber <heber@…> (12/22/10 17:27:31)

Message:

BUGFIX: SetOutputFormatsAction seemed to add last format twice. Thanks Daniel!

• this was a bug in ValueStorage: while-loop checked for stream.fail(), but the stream might also fail within and nonetheless we pushed the (then unaltered from last iteration) temp value. Hence, doubly occuring last item.
• to prevent this, we test within for stream.fail() and for all others we placed ASSERT's everywhere (as internally strings are used for conversion and for a vector, we have to parse (at least) three strings).
• if std::vector<>'s are parsed, we ASSERT only that at least one value was parsed.
• FormatParserStorage now just gives a warning, when an already presen Parser is added again, but gives a not that input type is not needed to be specified as output type as well.

thanks Daniel for pointing this out!

Location:

src/Actions

Files:

• ValueStorage.cpp (modified) (10 diffs)
• ValueStorage.hpp (modified) (1 diff)
• WorldAction/SetOutputFormatsAction.cpp (modified) (1 diff)

src/Actions/ValueStorage.cpp

@@ -28 +28 @@
 #include "Descriptors/AtomIdDescriptor.hpp"
 #include "Descriptors/MoleculeIdDescriptor.hpp"
+#include "Helpers/Assert.hpp"
 #include "Helpers/Log.hpp"
 #include "Helpers/Verbose.hpp"
@@ -126 +127 @@
     std::istringstream stream(CurrentValueMap[name]);
     CurrentValueMap.erase(name);
-    stream >> _T[0];
-    stream >> _T[1];
-    stream >> _T[2];
+    for (size_t i = 0; i < NDIM; ++i) {
+      stream >> _T[i];
+      ASSERT(!stream.fail(),
+          "ValueStorage::queryCurrentValue() - Vector in value map has only "+toString(i)+" components!");
+    }
   } else
     throw IllegalTypeException(__FILE__,__LINE__);
@@ -137 +140 @@
     std::istringstream stream(CurrentValueMap[name]);
     CurrentValueMap.erase(name);
-    stream >> _T[0];
-    stream >> _T[1];
-    stream >> _T[2];
+    for (size_t i = 0; i < NDIM; ++i) {
+      stream >> _T[i];
+      ASSERT(!stream.fail(),
+          "ValueStorage::queryCurrentValue() - BoxVector in value map has only "+toString(i)+" components!");
+    }
   } else
     throw IllegalTypeException(__FILE__,__LINE__);
@@ -147 +152 @@
 {
   int atomID = -1;
+  size_t count = 0;
   atom *Walker = NULL;
   if (typeid( std::vector<const atom *> ) == *(OptionRegistry_instance.getOptionByName(name)->getType())) {
@@ -155 +161 @@
     while (!stream.fail()) {
       stream >> atomID >> ws;
-      Walker = World::getInstance().getAtom(AtomById(atomID));
-      if (Walker != NULL)
-        _T.push_back(Walker);
-      atomID = -1;
-      Walker = NULL;
+      ASSERT((!stream.fail()) || (count != 0),
+          "ValueStorage::queryCurrentValue() - Atom is missing id!");
+      if (!stream.fail()) {
+        Walker = World::getInstance().getAtom(AtomById(atomID));
+        if (Walker != NULL)
+          _T.push_back(Walker);
+        atomID = -1;
+        Walker = NULL;
+        ++count;
+      }
     }
   } else
@@ -168 +179 @@
 {
   int Z = -1;
+  size_t count = 0;
   const element *elemental = NULL;
   if (typeid( std::vector<const element *> ) == *(OptionRegistry_instance.getOptionByName(name)->getType())) {
@@ -176 +188 @@
     while (!stream.fail()) {
       stream >> Z >> ws;
-      elemental = World::getInstance().getPeriode()->FindElement(Z);
-      if (elemental != NULL)
-        _T.push_back(elemental);
-      Z = -1;
+      ASSERT((!stream.fail()) || (count != 0),
+          "ValueStorage::queryCurrentValue() - atomic number is missing!");
+      if (!stream.fail()) {
+        elemental = World::getInstance().getPeriode()->FindElement(Z);
+        if (elemental != NULL)
+          _T.push_back(elemental);
+        Z = -1;
+        ++count;
+      }
     }
   } else
@@ -188 +205 @@
 {
   int molID = -1;
+  size_t count = 0;
   molecule *mol = NULL;
   if (typeid( std::vector<const molecule *> ) == *(OptionRegistry_instance.getOptionByName(name)->getType())) {
@@ -196 +214 @@
     while (!stream.fail()) {
       stream >> molID >> ws;
-      mol = World::getInstance().getMolecule(MoleculeById(molID));
-      if (mol != NULL)
-        _T.push_back(mol);
-      molID = -1;
-      mol = NULL;
+      ASSERT((!stream.fail()) || (count != 0),
+          "ValueStorage::queryCurrentValue() - molecule is missing id!");
+      if (!stream.fail()) {
+        mol = World::getInstance().getMolecule(MoleculeById(molID));
+        if (mol != NULL)
+          _T.push_back(mol);
+        molID = -1;
+        mol = NULL;
+        ++count;
+      }
     }
   } else
@@ -214 +237 @@
     std::istringstream stream(CurrentValueMap[name]);
     CurrentValueMap.erase(name);
-    if (!stream.fail()) {
-      stream >> tmp >> ws;
-      _T = tmp;
-    }
+    stream >> tmp >> ws;
+    ASSERT(!stream.fail(),
+        "ValueStorage::queryCurrentValue() - boost::filesystem::path is missing!");
+    _T = tmp;
   } else
     throw IllegalTypeException(__FILE__,__LINE__);

src/Actions/ValueStorage.hpp

@@ -87 +87 @@
       while (!stream.fail()) {
         stream >> temp >> std::ws;
-        _T.push_back(temp);
+        if (!stream.fail()) {
+          _T.push_back(temp);
+        }
       }
     } else

src/Actions/WorldAction/SetOutputFormatsAction.cpp

@@ -41 +41 @@
   getParametersfromValueStorage();
 
+  DoLog(1) && (Log() << Verbose(1) << "Format list is: " << params.FormatList << std::endl);
   for (vector<std::string>::iterator iter = params.FormatList.begin(); iter != params.FormatList.end(); ++iter) {
     if (!FormatParserStorage::getInstance().add(*iter)) {
-      DoeLog(1) && (eLog() << Verbose(1) << "Unknown parser format in WorldSetOutputFormatsAction:" << *iter << endl);
+      DoeLog(1) && (eLog() << Verbose(1) << "Unknown parser format in WorldSetOutputFormatsAction: '" << *iter << "'" << endl);
     }
   }
-  ChangeTracker::getInstance().saveStatus();
   return Action::success;
 }