Changeset 1d5afa5 for src

Timestamp:

Feb 4, 2011, 6:56:38 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:

00b59d5

Parents:

17f3cd

git-author:

Frederik Heber <heber@…> (01/17/11 11:21:17)

git-committer:

Frederik Heber <heber@…> (02/04/11 18:56:38)

Message:

BUGFIX: CheckAdjacencyFileAgainstMolecule() hiccup'ed on parsed files.

• we checked for iostream::eof() which seemed not to work in all cases. Now we use while (line << tmp) directly and this works.
• maximum number of bonds is now (at least) a define MAXBONDS.
• ASSERT that we parse not more than MAXBONDS bonds.

File:

• src/molecule_graph.cpp (modified) (4 diffs)

src/molecule_graph.cpp

@@ -26 +26 @@
 #include "bondgraph.hpp"
 #include "config.hpp"
+#include "element.hpp"
 #include "Helpers/defs.hpp"
-#include "element.hpp"
+#include "Helpers/fast_functions.hpp"
 #include "Helpers/helpers.hpp"
-#include "CodePatterns/Info.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "linkedcell.hpp"
 #include "lists.hpp"
-#include "CodePatterns/Verbose.hpp"
-#include "CodePatterns/Log.hpp"
 #include "molecule.hpp"
 #include "World.hpp"
-#include "Helpers/fast_functions.hpp"
+#include "Box.hpp"
+
 #include "CodePatterns/Assert.hpp"
-#include "LinearAlgebra/RealSpaceMatrix.hpp"
-#include "Box.hpp"
+#include "CodePatterns/Info.hpp"
+#include "CodePatterns/Log.hpp"
+#include "CodePatterns/Verbose.hpp"
+
+#define MAXBONDS 8
 
 struct BFSAccounting
@@ -1144 +1147 @@
 
   // allocate storage structure
-  CurrentBonds = new int[8]; // contains parsed bonds of current atom
-  for(int i=0;i<8;i++)
+  CurrentBonds = new int[MAXBONDS]; // contains parsed bonds of current atom
+  for(int i=0;i<MAXBONDS;i++)
     CurrentBonds[i] = 0;
   return true;
@@ -1210 +1213 @@
 
   char buffer[MAXSTRINGSIZE];
+  int tmp;
   // Parse the file line by line and count the bonds
   while (!File.eof()) {
@@ -1221 +1225 @@
     if ((AtomNr >= 0) && (AtomNr < AtomCount)) {
       Walker = ListOfAtoms[AtomNr];
-      while (!line.eof())
-        line >> CurrentBonds[++CurrentBondsOfAtom];
+      while (line >> ws >> tmp) {
+        std::cout << "Recognized bond partner " << tmp << std::endl;
+        CurrentBonds[++CurrentBondsOfAtom] = tmp;
+        ASSERT(CurrentBondsOfAtom < MAXBONDS,
+            "molecule::CheckAdjacencyFileAgainstMolecule() - encountered more bonds than allowed: "
+            +toString(CurrentBondsOfAtom)+" >= "+toString(MAXBONDS)+"!");
+      }
       // compare against present bonds
       CheckAdjacencyFileAgainstMolecule_CompareBonds(status, NonMatchNumber, Walker, CurrentBondsOfAtom, AtomNr, CurrentBonds, ListOfAtoms);