- Timestamp:
- Jun 1, 2010, 7:59:25 PM (15 years ago)
- 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:
- 15b670
- Parents:
- acf800
- Location:
- src
- Files:
-
- 3 edited
Legend:
- Unmodified
- Added
- Removed
-
src/helpers.hpp
racf800 r0de7e8 97 97 98 98 if (LookupTable != NULL) { 99 Do Log(0) && (Log() << Verbose(0) << "Pointer for Lookup table is not NULL! Aborting ..." <<endl);99 DoeLog(0) && (eLog() << Verbose(0) << "Pointer for Lookup table is not NULL! Aborting ..." <<endl); 100 100 return false; 101 101 } … … 110 110 } 111 111 if (count <= 0) { 112 Do Log(0) && (Log() << Verbose(0) << "Count of lookup list is 0 or less." << endl);112 DoeLog(1) && (eLog() << Verbose(1) << "Count of lookup list is 0 or less." << endl); 113 113 return false; 114 114 } … … 129 129 LookupTable[AtomNo] = Walker; 130 130 } else { 131 Do Log(0) && (Log() << Verbose(0) << "Walker " << *Walker << " exceeded range of nuclear ids [0, " << count << ")." << endl);131 DoeLog(2) && (eLog() << Verbose(2) << "Walker " << *Walker << " exceeded range of nuclear ids [0, " << count << ")." << endl); 132 132 status = false; 133 133 break; -
src/molecule_fragmentation.cpp
racf800 r0de7e8 120 120 InputFile.close(); 121 121 InputFile.clear(); 122 DoLog(1) && (Log() << Verbose(1) << " done." << endl);122 DoLog(1) && (Log() << Verbose(1) << "\t ... done." << endl); 123 123 } else { 124 DoLog(1) && (Log() << Verbose(1) << " File " << filename << " not found." << endl);124 DoLog(1) && (Log() << Verbose(1) << "\t ... File " << filename << " not found." << endl); 125 125 status = false; 126 126 } … … 845 845 SetAtomValueToIndexedArray( MaxArray, &atom::nr, &atom::MaxOrder ); 846 846 847 DoLog(1) && (Log() << Verbose(1) << " done." << endl);847 DoLog(1) && (Log() << Verbose(1) << "\t ... done." << endl); 848 848 status = true; 849 849 } else { 850 DoLog(1) && (Log() << Verbose(1) << " failed to open file " << line.str() << "." << endl);850 DoLog(1) && (Log() << Verbose(1) << "\t ... failed to open file " << line.str() << "." << endl); 851 851 status = false; 852 852 } -
src/molecule_graph.cpp
racf800 r0de7e8 1089 1089 filename << path << "/" << FRAGMENTPREFIX << ADJACENCYFILE; 1090 1090 File.open(filename.str().c_str(), ios::out); 1091 DoLog(1) && (Log() << Verbose(1) << "Looking at bond structure stored in adjacency file and comparing to present one ... " );1091 DoLog(1) && (Log() << Verbose(1) << "Looking at bond structure stored in adjacency file and comparing to present one ... " << endl); 1092 1092 if (File == NULL) 1093 1093 return false; … … 1125 1125 NonMatchNumber++; 1126 1126 status = false; 1127 DoeLog(2) && (eLog() << Verbose(2) << id << " can not be found in list." << endl); 1128 } else { 1127 1129 //Log() << Verbose(0) << "[" << id << "]\t"; 1128 } else {1129 //Log() << Verbose(0) << id << "\t";1130 1130 } 1131 1131 } … … 1152 1152 int NonMatchNumber = 0; // will number of atoms with differing bond structure 1153 1153 size_t CurrentBondsOfAtom = -1; 1154 const int AtomCount = getAtomCount(); 1154 1155 1155 1156 if (!CheckAdjacencyFileAgainstMolecule_Init(path, File, CurrentBonds)) { … … 1168 1169 CurrentBondsOfAtom = -1; // we count one too far due to line end 1169 1170 // parse into structure 1170 if ((AtomNr >= 0) && (AtomNr < getAtomCount())) {1171 if ((AtomNr >= 0) && (AtomNr < AtomCount)) { 1171 1172 Walker = ListOfAtoms[AtomNr]; 1172 1173 while (!line.eof()) … … 1174 1175 // compare against present bonds 1175 1176 CheckAdjacencyFileAgainstMolecule_CompareBonds(status, NonMatchNumber, Walker, CurrentBondsOfAtom, AtomNr, CurrentBonds, ListOfAtoms); 1177 } else { 1178 if (AtomNr != -1) 1179 DoeLog(2) && (eLog() << Verbose(2) << AtomNr << " is not valid in the range of ids [" << 0 << "," << AtomCount << ")." << endl); 1176 1180 } 1177 1181 }
Note:
See TracChangeset
for help on using the changeset viewer.