2024-03-28 07:24 ftp://ftp.de.debian.org/debian/pool/main/m/molmodel/molmodel_3.1.0.orig.tar.gz cppcheck-options: --library=posix --library=gnu --library=bsd --inconclusive --enable=style,information --inline-suppr --template=daca2 --disable=missingInclude --suppress=unmatchedSuppression --check-library --debug-warnings --suppress=autoNoType --suppress=valueFlowBailout --suppress=bailoutUninitVar --suppress=symbolDatabaseWarning -D__GNUC__ --platform=unix64 -j4 platform: Linux-6.1.0-18-amd64-x86_64-with-glibc2.36 python: 3.11.2 client-version: 1.3.55 compiler: g++ (Debian 12.2.0-14) 12.2.0 cppcheck: head 2.13.0 head-info: 98951f5 (2024-03-27 21:50:05 +0100) count: 735 418 elapsed-time: 3.1 4.9 head-timing-info: old-timing-info: head results: molmodel-3.1.0/CoarseDNA/TestCoarseDNA.cpp:1419:30: error: syntax error: ) . } [syntaxError] molmodel-3.1.0/examples/ExampleAdenylateMobilitiesVMD.cpp:27:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Free [valueFlowBailoutIncompleteVar] molmodel-3.1.0/examples/ExampleAdenylateMobilitiesViz.cpp:26:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Free [valueFlowBailoutIncompleteVar] molmodel-3.1.0/examples/ExampleCreatePropane.cpp:119:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable YAxis [valueFlowBailoutIncompleteVar] molmodel-3.1.0/OpenMMPlugin/OpenMMPlugin.cpp:146:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LorentzBerthelot [valueFlowBailoutIncompleteVar] molmodel-3.1.0/examples/ExampleLoadPdb.cpp:48:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] molmodel-3.1.0/examples/ExampleFoldPolyalanine.cpp:61:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Dynamics [valueFlowBailoutIncompleteVar] molmodel-3.1.0/examples/ExampleFoldPolyalanine.cpp:101:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/examples/ExampleFoldPolyalanine.cpp:149:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/examples/ExampleLoadPdb2.cpp:53:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] molmodel-3.1.0/examples/ExampleRigidProtein.cpp:27:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Rigid [valueFlowBailoutIncompleteVar] molmodel-3.1.0/OpenMMPlugin/OpenMMPlugin.cpp:65:5: style: Class 'OpenMMInterface' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/OpenMMPlugin/OpenMMPlugin.cpp:290:29: style:inconclusive: Function 'calcOpenMMNonbondedAndGBSAForces' argument 5 names different: declaration 'includedBodyForce_G' definition 'includedBodyForces_G'. [funcArgNamesDifferent] molmodel-3.1.0/OpenMMPlugin/OpenMMPlugin.cpp:91:33: note: Function 'calcOpenMMNonbondedAndGBSAForces' argument 5 names different: declaration 'includedBodyForce_G' definition 'includedBodyForces_G'. molmodel-3.1.0/OpenMMPlugin/OpenMMPlugin.cpp:290:29: note: Function 'calcOpenMMNonbondedAndGBSAForces' argument 5 names different: declaration 'includedBodyForce_G' definition 'includedBodyForces_G'. molmodel-3.1.0/examples/ExampleSimpleProtein.cpp:61:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] molmodel-3.1.0/examples/ExampleSimpleRNA.cpp:68:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/examples/ExampleTwoArgonAtoms.cpp:70:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] molmodel-3.1.0/examples/ExampleTwoEthanes.cpp:46:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/examples/MolmodelInstallTest.cpp:18:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/examplesNotReadyYet/ExampleLoadRNA.cpp:45:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] molmodel-3.1.0/examples/MolmodelInstallTestNoViz.cpp:19:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clog [valueFlowBailoutIncompleteVar] molmodel-3.1.0/examplesNotReadyYet/ExamplePuckerRibose.cpp:34:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] molmodel-3.1.0/examplesNotReadyYet/ExampleSodiumChloride.cpp:61:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] molmodel-3.1.0/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:30:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] molmodel-3.1.0/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:49:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:216:100: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Rigid [valueFlowBailoutIncompleteVar] molmodel-3.1.0/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:40:14: style:inconclusive: Member variable 'WritePdbReporter::currentModelNumber' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:22:5: note: Member variable 'WritePdbReporter::currentModelNumber' is in the wrong place in the initializer list. molmodel-3.1.0/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:40:14: note: Member variable 'WritePdbReporter::currentModelNumber' is in the wrong place in the initializer list. molmodel-3.1.0/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:222:23: warning: Opposite inner 'if' condition leads to a dead code block. [oppositeInnerCondition] molmodel-3.1.0/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:219:51: note: outer condition: integratorIndex<=1 molmodel-3.1.0/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:222:23: note: opposite inner condition: integratorIndex==2 molmodel-3.1.0/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:216:25: style: Variable 'mobilityList' can be declared as const array [constVariable] molmodel-3.1.0/src/AtomSubsystem.cpp:86:83: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/AtomSubsystem.cpp:120:83: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/AtomSubsystem.cpp:158:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomsByBody [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/AtomSubsystem.cpp:162:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/AtomSubsystem.cpp:185:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable systemBodyIxToLocalBodyIx [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/AtomSubsystem.cpp:199:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atoms [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/AtomSubsystem.cpp:203:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atoms [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/AtomSubsystem.cpp:225:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bonds [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/AtomSubsystem.cpp:231:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bonds [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/AtomSubsystem.cpp:241:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomPositionCacheIndex [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/AtomSubsystem.cpp:252:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomBodyStationCacheIndex [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/AtomSubsystem.cpp:263:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomVelocityCacheIndex [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/AtomSubsystem.cpp:298:81: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/AtomSubsystem.cpp:339:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable N_SQUARED [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/AtomSubsystem.cpp:408:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable body1 [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/AtomSubsystem.cpp:421:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomsByBody [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/AtomSubsystem.cpp:440:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable square_nanometers [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/AtomSubsystem.cpp:490:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bUseVoxelHash [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/AtomSubsystem.cpp:557:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bUseVoxelHash [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/AtomSubsystem.cpp:613:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable state [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/AtomSubsystem.cpp:619:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable currentPair [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/AtomSubsystem.cpp:624:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable currentPair [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/AtomSubsystem.cpp:37:5: style: Class 'Impl' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/src/CompoundAtom.h:221:64: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable XAxis [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundAtom.h:350:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundAtom.h:487:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Pi [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundAtom.h:497:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Pi [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundAtom.h:579:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundAtom.h:605:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundAtom.h:632:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundAtom.h:659:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundAtom.h:706:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NaN [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundAtom.h:721:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ZAxis [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundAtom.h:759:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable XAxis [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:187:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:462:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:484:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:644:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Pi [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:684:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Pi [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:709:76: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:727:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:773:76: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:953:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Position [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:961:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Velocity [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:969:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Acceleration [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:1130:83: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:1348:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:1372:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:1415:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:1443:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:1806:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:1812:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:1894:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:2151:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:2323:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:2373:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Position [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundSystem.cpp:79:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundSystem.cpp:139:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/BiotypeRep.h:107:89: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:270:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable KJ2Kcal [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Biotype.cpp:173:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Any [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:415:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Biotype.cpp:291:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:458:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Biotype.cpp:303:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Any [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:489:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Rad2Deg [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Biotype.cpp:318:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:542:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Pi [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Biotype.cpp:324:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:555:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Pi [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Biotype.cpp:330:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:567:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Rad2Deg [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Biotype.cpp:341:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Any [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:612:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable periodicity [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Biotype.cpp:484:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Any [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:619:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable periodicity [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:675:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:811:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NaN [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1056:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable InvalidAtomIndex [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1116:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1125:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1401:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WaldmanHagler [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1508:79: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1516:79: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1532:94: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1539:94: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1582:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clusterIndex [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1627:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomIndex [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:94:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atoms [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:98:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomClasses [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:101:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomClasses [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:107:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:255:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:321:91: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NaN [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:478:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1066:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gbsaSolventDielectric [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1069:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gbsaSoluteDielectric [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1100:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inclList [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1109:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inclList [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1120:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inclList [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1127:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inclList [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1134:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inclList [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1142:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inclList [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1150:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inclList [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1160:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inclList [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1176:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inclList [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1186:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inclList [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1203:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atoms [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1209:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chargedAtomTypes [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1214:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chargedAtomTypes [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1263:84: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable vdwGlobalScaleFactor [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1264:84: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable coulombGlobalScaleFactor [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1265:84: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gbsaGlobalScaleFactor [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1266:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bondStretchGlobalScaleFactor [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1267:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bondBendGlobalScaleFactor [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1268:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bondTorsionGlobalScaleFactor [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1269:97: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable amberImproperTorsionGlobalScaleFactor [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1270:94: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable customBondStretchGlobalScaleFactor [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1271:94: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable customBondBendGlobalScaleFactor [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1272:94: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable customBondTorsionGlobalScaleFactor [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1275:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tracing [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1279:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable useMultithreadedComputation [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1283:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable useMultithreadedComputation [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1286:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable usingMultithreaded [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1289:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable numThreadsRequested [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1293:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable numThreadsRequested [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1296:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable numThreadsInUse [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1300:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable wantOpenMMAcceleration [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1304:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable wantOpenMMAcceleration [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1307:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable allowOpenMMReference [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1311:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable allowOpenMMReference [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1314:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable usingOpenMM [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1317:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable openMMPlatformInUse [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1570:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atoms [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1603:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Green [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1853:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable forcefieldName [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Util.h:11:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:814:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:853:75: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:874:81: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:903:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:908:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:933:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:983:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:1028:97: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residueNumber [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:1324:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:2192:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Position [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:2352:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable synonyms [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:2399:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:2403:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:2433:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomIdsByName [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:2489:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Any [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:2503:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residueIdsByName [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:2579:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:2759:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AminoAcidResidue [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:2824:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:2833:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:2990:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Position [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:3069:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NaN [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:703:25: style:inconclusive: Member variable 'AtomPlacement::station' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:698:69: note: Member variable 'AtomPlacement::station' is in the wrong place in the initializer list. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:703:25: note: Member variable 'AtomPlacement::station' is in the wrong place in the initializer list. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:726:25: style:inconclusive: Member variable 'ClusterPlacement::placement' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:721:83: note: Member variable 'ClusterPlacement::placement' is in the wrong place in the initializer list. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:726:25: note: Member variable 'ClusterPlacement::placement' is in the wrong place in the initializer list. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1401:9: performance: Variable 'vdwMixingRule' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1402:9: performance: Variable 'vdwGlobalScaleFactor' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1402:30: performance: Variable 'coulombGlobalScaleFactor' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1402:55: performance: Variable 'gbsaGlobalScaleFactor' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1403:9: performance: Variable 'bondStretchGlobalScaleFactor' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1403:38: performance: Variable 'bondBendGlobalScaleFactor' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1404:13: performance: Variable 'bondTorsionGlobalScaleFactor' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1404:42: performance: Variable 'amberImproperTorsionGlobalScaleFactor' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1405:9: performance: Variable 'customBondStretchGlobalScaleFactor' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1405:44: performance: Variable 'customBondBendGlobalScaleFactor' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1406:13: performance: Variable 'customBondTorsionGlobalScaleFactor' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1408:9: performance: Variable 'vdwScale12' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1408:20: performance: Variable 'coulombScale12' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1408:35: performance: Variable 'vdwScale13' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1408:46: performance: Variable 'coulombScale13' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1409:9: performance: Variable 'vdwScale14' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1409:20: performance: Variable 'coulombScale14' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1409:35: performance: Variable 'vdwScale15' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1409:46: performance: Variable 'coulombScale15' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1419:9: performance: Variable 'gbsaSolventDielectric' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1420:9: performance: Variable 'gbsaSoluteDielectric' is assigned in constructor body. Consider performing initialization in initialization list. [useInitializationList] molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.h:124:9: warning:inconclusive: Class 'ImplicitSolventParameters' which has virtual members does not have a virtual destructor. [virtualDestructor] molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.h:158:9: warning:inconclusive: Class 'CpuImplicitSolvent' which has virtual members does not have a virtual destructor. [virtualDestructor] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1110:10: performance:inconclusive: Technically the member function 'Cluster::invalidateTopologicalCache' can be static (but you may consider moving to unnamed namespace). [functionStatic] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1112:10: performance:inconclusive: Technically the member function 'Cluster::realizeTopologicalCache' can be static (but you may consider moving to unnamed namespace). [functionStatic] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1115:10: performance:inconclusive: Technically the member function 'Cluster::dumpX' can be static (but you may consider moving to unnamed namespace). [functionStatic] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1250:10: performance:inconclusive: Technically the member function 'DuMMBody::invalidateTopologicalCache' can be static (but you may consider moving to unnamed namespace). [functionStatic] molmodel-3.1.0/src/gbsa/CpuObc.h:171:19: warning: The class 'CpuObc' defines member function with name 'getStateString' also defined in its parent class 'CpuImplicitSolvent'. [duplInheritedMember] molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.h:446:19: note: Parent function 'CpuImplicitSolvent::getStateString' molmodel-3.1.0/src/gbsa/CpuObc.h:171:19: note: Derived function 'CpuObc::getStateString' molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.h:116:8: style: Class 'ImplicitSolventParameters' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/src/gbsa/ObcParameters.h:81:8: style: Class 'ObcParameters' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.h:150:8: style: Class 'CpuImplicitSolvent' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/src/gbsa/CpuObc.h:65:8: style: Class 'CpuObc' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:585:5: style: Class 'BondTorsion' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1000:5: style: Class 'Cluster' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/src/gbsa/ObcParameters.h:217:25: style: The function 'getAtomicRadii' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.h:295:33: note: Virtual function in base class molmodel-3.1.0/src/gbsa/ObcParameters.h:217:25: note: Function in derived class molmodel-3.1.0/src/gbsa/ObcParameters.h:231:11: style: The function 'setAtomicRadii' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.h:336:19: note: Virtual function in base class molmodel-3.1.0/src/gbsa/ObcParameters.h:231:11: note: Function in derived class molmodel-3.1.0/src/gbsa/ObcParameters.h:245:11: style: The function 'setAtomicRadii' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.h:321:19: note: Virtual function in base class molmodel-3.1.0/src/gbsa/ObcParameters.h:245:11: note: Function in derived class molmodel-3.1.0/src/gbsa/ObcParameters.h:270:19: style: The function 'getStateString' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.h:350:27: note: Virtual function in base class molmodel-3.1.0/src/gbsa/ObcParameters.h:270:19: note: Function in derived class molmodel-3.1.0/src/gbsa/ObcParameters.h:280:11: style: The function 'isNotReady' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.h:370:19: note: Virtual function in base class molmodel-3.1.0/src/gbsa/ObcParameters.h:280:11: note: Function in derived class molmodel-3.1.0/src/gbsa/CpuObc.h:133:11: style: The function 'computeBornRadii' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.h:377:19: note: Virtual function in base class molmodel-3.1.0/src/gbsa/CpuObc.h:133:11: note: Function in derived class molmodel-3.1.0/src/gbsa/CpuObc.h:152:11: style: The function 'computeBornEnergyForces' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.h:395:19: note: Virtual function in base class molmodel-3.1.0/src/gbsa/CpuObc.h:152:11: note: Function in derived class molmodel-3.1.0/src/gbsa/CpuObc.h:186:11: style: The function 'writeBornEnergyForces' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.h:431:19: note: Virtual function in base class molmodel-3.1.0/src/gbsa/CpuObc.h:186:11: note: Function in derived class molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.h:503:43: performance: Function parameter 'infoFileName' should be passed by const reference. [passedByValue] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1112:62: style: Parameter 'mm' can be declared as reference to const [constParameterReference] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1709:42: style: Parameter 's' can be declared as reference to const [constParameterReference] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:793:24: style: Variable 'MethodName' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:803:24: style: Variable 'MethodName' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1074:24: style: Variable 'MethodName' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/src/CompoundAtom.h:540:1: style: The class 'CompoundAtom' does not declare a constructor although it has private member variables which likely require initialization. [noConstructor] molmodel-3.1.0/src/CompoundSystem.cpp:25:5: warning:inconclusive: Member variable 'RigidUnit::hasChild' is not initialized in the constructor. [uninitMemberVar] molmodel-3.1.0/src/CompoundAtom.h:238:11: style:inconclusive: Member variable 'Bond::defaultDihedral' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/src/CompoundAtom.h:128:31: note: Member variable 'Bond::defaultDihedral' is in the wrong place in the initializer list. molmodel-3.1.0/src/CompoundAtom.h:238:11: note: Member variable 'Bond::defaultDihedral' is in the wrong place in the initializer list. molmodel-3.1.0/src/CompoundRep.h:81:11: style:inconclusive: Member variable 'DihedralAngle::nomenclatureOffset' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/src/CompoundRep.h:68:47: note: Member variable 'DihedralAngle::nomenclatureOffset' is in the wrong place in the initializer list. molmodel-3.1.0/src/CompoundRep.h:81:11: note: Member variable 'DihedralAngle::nomenclatureOffset' is in the wrong place in the initializer list. molmodel-3.1.0/src/CompoundRep.h:2474:12: style:inconclusive: Member variable 'CompoundRep::pdbResidueName' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/src/CompoundRep.h:100:7: note: Member variable 'CompoundRep::pdbResidueName' is in the wrong place in the initializer list. molmodel-3.1.0/src/CompoundRep.h:2474:12: note: Member variable 'CompoundRep::pdbResidueName' is in the wrong place in the initializer list. molmodel-3.1.0/src/CompoundRep.h:2473:12: style:inconclusive: Member variable 'CompoundRep::pdbResidueNumber' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/src/CompoundRep.h:101:7: note: Member variable 'CompoundRep::pdbResidueNumber' is in the wrong place in the initializer list. molmodel-3.1.0/src/CompoundRep.h:2473:12: note: Member variable 'CompoundRep::pdbResidueNumber' is in the wrong place in the initializer list. molmodel-3.1.0/src/CompoundRep.h:2448:15: style:inconclusive: Member variable 'CompoundRep::topLevelTransform' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/src/CompoundRep.h:103:7: note: Member variable 'CompoundRep::topLevelTransform' is in the wrong place in the initializer list. molmodel-3.1.0/src/CompoundRep.h:2448:15: note: Member variable 'CompoundRep::topLevelTransform' is in the wrong place in the initializer list. molmodel-3.1.0/src/CompoundRep.h:2506:5: style: Class 'BiopolymerResidueRep' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/src/CompoundSystem.cpp:26:5: style: Class 'RigidUnit' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/src/CompoundSystem.cpp:48:5: style: Class 'AtomBonding' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/src/CompoundRep.h:2503:18: style: The destructor '~BiopolymerResidueRep' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride] molmodel-3.1.0/src/CompoundRep.h:120:14: note: Virtual destructor in base class molmodel-3.1.0/src/CompoundRep.h:2503:18: note: Destructor in derived class molmodel-3.1.0/src/CompoundRep.h:2504:39: style: The function 'clone' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] molmodel-3.1.0/src/CompoundRep.h:121:26: note: Virtual function in base class molmodel-3.1.0/src/CompoundRep.h:2504:39: note: Function in derived class molmodel-3.1.0/src/CompoundRep.h:2572:20: style: The function 'clone' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] molmodel-3.1.0/src/CompoundRep.h:121:26: note: Virtual function in base class molmodel-3.1.0/src/CompoundRep.h:2572:20: note: Function in derived class molmodel-3.1.0/src/CompoundRep.h:2634:32: style: The function 'populateDefaultPdbChain' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] molmodel-3.1.0/src/CompoundRep.h:1648:32: note: Virtual function in base class molmodel-3.1.0/src/CompoundRep.h:2634:32: note: Function in derived class molmodel-3.1.0/src/CompoundRep.h:2651:32: style: The function 'populatePdbChain' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] molmodel-3.1.0/src/CompoundRep.h:1691:32: note: Virtual function in base class molmodel-3.1.0/src/CompoundRep.h:2651:32: note: Function in derived class molmodel-3.1.0/src/CompoundAtom.h:162:40: warning: Logical disjunction always evaluates to true: defaultDihedral >= 0 || defaultDihedral <= 0. [incorrectLogicOperator] molmodel-3.1.0/src/CompoundAtom.h:176:40: warning: Logical disjunction always evaluates to true: defaultDihedral >= 0 || defaultDihedral <= 0. [incorrectLogicOperator] molmodel-3.1.0/src/CompoundSystem.cpp:139:9: style: Condition 'showDebugMessages' is always false [knownConditionTrueFalse] molmodel-3.1.0/src/CompoundSystem.cpp:138:30: note: Assignment 'showDebugMessages=false', assigned value is 0 molmodel-3.1.0/src/CompoundSystem.cpp:139:9: note: Condition 'showDebugMessages' is always false molmodel-3.1.0/src/CompoundSystem.cpp:160:9: style: Condition 'showDebugMessages' is always false [knownConditionTrueFalse] molmodel-3.1.0/src/CompoundSystem.cpp:138:30: note: Assignment 'showDebugMessages=false', assigned value is 0 molmodel-3.1.0/src/CompoundSystem.cpp:160:9: note: Condition 'showDebugMessages' is always false molmodel-3.1.0/src/CompoundSystem.cpp:185:9: style: Condition 'showDebugMessages' is always false [knownConditionTrueFalse] molmodel-3.1.0/src/CompoundSystem.cpp:138:30: note: Assignment 'showDebugMessages=false', assigned value is 0 molmodel-3.1.0/src/CompoundSystem.cpp:185:9: note: Condition 'showDebugMessages' is always false molmodel-3.1.0/src/CompoundSystem.cpp:556:17: style: Condition 'testRiboseMobilizer' is always false [knownConditionTrueFalse] molmodel-3.1.0/src/CompoundSystem.cpp:552:40: note: Assignment 'testRiboseMobilizer=false', assigned value is 0 molmodel-3.1.0/src/CompoundSystem.cpp:556:17: note: Condition 'testRiboseMobilizer' is always false molmodel-3.1.0/src/CompoundAtom.h:51:31: style: C-style reference casting [cstyleCast] molmodel-3.1.0/src/CompoundAtom.h:169:35: style: C-style reference casting [cstyleCast] molmodel-3.1.0/src/CompoundAtom.h:203:42: style: C-style reference casting [cstyleCast] molmodel-3.1.0/src/CompoundRep.h:778:40: style: C-style reference casting [cstyleCast] molmodel-3.1.0/src/CompoundRep.h:2356:47: style: C-style reference casting [cstyleCast] molmodel-3.1.0/src/CompoundRep.h:2389:47: style: C-style reference casting [cstyleCast] molmodel-3.1.0/src/CompoundSystem.cpp:154:37: style: C-style reference casting [cstyleCast] molmodel-3.1.0/src/CompoundRep.h:773:24: style: The scope of the variable 'dihedral' can be reduced. [variableScope] molmodel-3.1.0/src/CompoundRep.h:2384:25: style: Local variable 'bond' shadows outer variable [shadowVariable] molmodel-3.1.0/src/CompoundRep.h:2350:21: note: Shadowed declaration molmodel-3.1.0/src/CompoundRep.h:2384:25: note: Shadow variable molmodel-3.1.0/src/CompoundRep.h:2385:32: style: Local variable 'bodyId' shadows outer variable [shadowVariable] molmodel-3.1.0/src/CompoundRep.h:2351:28: note: Shadowed declaration molmodel-3.1.0/src/CompoundRep.h:2385:32: note: Shadow variable molmodel-3.1.0/src/CompoundRep.h:708:15: style: Variable 'bond' can be declared as reference to const [constVariableReference] molmodel-3.1.0/src/CompoundRep.h:709:24: style: Variable 'dihedral' can be declared as reference to const [constVariableReference] molmodel-3.1.0/src/CompoundRep.h:1010:95: performance: Searching before insertion is not necessary. Instead of 'bondMap[atomIndex1]=std::vector()' consider using 'bondMap.try_emplace(atomIndex1, std::vector());'. [stlFindInsert] molmodel-3.1.0/src/CompoundRep.h:1013:95: performance: Searching before insertion is not necessary. Instead of 'bondMap[atomIndex2]=std::vector()' consider using 'bondMap.try_emplace(atomIndex2, std::vector());'. [stlFindInsert] molmodel-3.1.0/src/Element.cpp:485:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable impl [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Element.cpp:490:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable impl [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/CompoundRep.h:1615:31: style: Variable 'residueNumber' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/src/CompoundRep.h:1616:32: style: Variable 'insertionCode' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/src/CompoundRep.h:2482:19: style: Variable 'x' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/src/Compound.cpp:1212:50: style:inconclusive: Boolean expression 'childAtomInfo.isBaseAtom()' is used in bitwise operation. Did you mean '&&'? [bitwiseOnBoolean] molmodel-3.1.0/src/ElementRep.h:75:19: style:inconclusive: Member variable 'Impl::name' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/src/ElementRep.h:51:29: note: Member variable 'Impl::name' is in the wrong place in the initializer list. molmodel-3.1.0/src/ElementRep.h:75:19: note: Member variable 'Impl::name' is in the wrong place in the initializer list. molmodel-3.1.0/src/ElementRep.h:74:21: style:inconclusive: Member variable 'Impl::symbol' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/src/ElementRep.h:51:39: note: Member variable 'Impl::symbol' is in the wrong place in the initializer list. molmodel-3.1.0/src/ElementRep.h:74:21: note: Member variable 'Impl::symbol' is in the wrong place in the initializer list. molmodel-3.1.0/src/MolecularMechanicsSystem.cpp:85:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable molecularMechanicsSub [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/MolecularMechanicsSystem.cpp:91:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable molecularMechanicsSub [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/MolecularMechanicsSystem.cpp:95:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable molecularMechanicsSub [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/MolecularMechanicsSystem.cpp:112:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Position [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/MolecularMechanicsSystem.cpp:170:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Position [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:180:13: warning: Member variable 'BondCenter::defaultDihedralReferenceCenter' is not initialized in the constructor. [uninitMemberVar] molmodel-3.1.0/src/CompoundAtom.h:302:31: style:inconclusive: Member variable 'BondInfo::childBondCenterIndex' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/src/Compound.cpp:136:9: note: Member variable 'BondInfo::childBondCenterIndex' is in the wrong place in the initializer list. molmodel-3.1.0/src/CompoundAtom.h:302:31: note: Member variable 'BondInfo::childBondCenterIndex' is in the wrong place in the initializer list. molmodel-3.1.0/src/CompoundAtom.h:525:10: style:inconclusive: Member variable 'BondCenter::inboard' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/src/Compound.cpp:183:5: note: Member variable 'BondCenter::inboard' is in the wrong place in the initializer list. molmodel-3.1.0/src/CompoundAtom.h:525:10: note: Member variable 'BondCenter::inboard' is in the wrong place in the initializer list. molmodel-3.1.0/src/CompoundAtom.h:526:10: style:inconclusive: Member variable 'BondCenter::bonded' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/src/Compound.cpp:198:5: note: Member variable 'BondCenter::bonded' is in the wrong place in the initializer list. molmodel-3.1.0/src/CompoundAtom.h:526:10: note: Member variable 'BondCenter::bonded' is in the wrong place in the initializer list. molmodel-3.1.0/src/CompoundAtom.h:525:10: style:inconclusive: Member variable 'BondCenter::inboard' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/src/Compound.cpp:199:5: note: Member variable 'BondCenter::inboard' is in the wrong place in the initializer list. molmodel-3.1.0/src/CompoundAtom.h:525:10: note: Member variable 'BondCenter::inboard' is in the wrong place in the initializer list. molmodel-3.1.0/src/CompoundAtom.h:986:10: style:inconclusive: Member variable 'AtomInfo::bIsBaseAtom' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/src/Compound.cpp:256:5: note: Member variable 'AtomInfo::bIsBaseAtom' is in the wrong place in the initializer list. molmodel-3.1.0/src/CompoundAtom.h:986:10: note: Member variable 'AtomInfo::bIsBaseAtom' is in the wrong place in the initializer list. molmodel-3.1.0/src/Compound.cpp:3016:6: style: Condition 'useObservedPointFitter' is always true [knownConditionTrueFalse] molmodel-3.1.0/src/Compound.cpp:3015:32: note: Assignment 'useObservedPointFitter=true', assigned value is 1 molmodel-3.1.0/src/Compound.cpp:3016:6: note: Condition 'useObservedPointFitter' is always true molmodel-3.1.0/src/Representation.h:205:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/PDBReader.cpp:64:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/PDBReader.cpp:79:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/PDBReader.cpp:89:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/PDBReader.cpp:108:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/PDBReader.cpp:217:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chains [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/PDBReader.cpp:329:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chains [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/PDBReader.cpp:371:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable impl [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/PDBReader.cpp:375:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable impl [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Compound.cpp:2674:93: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/Compound.cpp:130:17: style:inconclusive: Function 'BondInfo' argument 4 names different: declaration 'bond' definition 'b'. [funcArgNamesDifferent] molmodel-3.1.0/src/CompoundAtom.h:261:21: note: Function 'BondInfo' argument 4 names different: declaration 'bond' definition 'b'. molmodel-3.1.0/src/Compound.cpp:130:17: note: Function 'BondInfo' argument 4 names different: declaration 'bond' definition 'b'. molmodel-3.1.0/src/Compound.cpp:253:40: style:inconclusive: Function 'AtomInfo' argument 1 names different: declaration 'id' definition 'i'. [funcArgNamesDifferent] molmodel-3.1.0/src/CompoundAtom.h:933:34: note: Function 'AtomInfo' argument 1 names different: declaration 'id' definition 'i'. molmodel-3.1.0/src/Compound.cpp:253:40: note: Function 'AtomInfo' argument 1 names different: declaration 'id' definition 'i'. molmodel-3.1.0/src/Compound.cpp:385:37: style:inconclusive: Function 'bondCompound' argument 2 names different: declaration 'subcompound' definition 'subcompoundArg'. [funcArgNamesDifferent] molmodel-3.1.0/src/CompoundRep.h:201:25: note: Function 'bondCompound' argument 2 names different: declaration 'subcompound' definition 'subcompoundArg'. molmodel-3.1.0/src/Compound.cpp:385:37: note: Function 'bondCompound' argument 2 names different: declaration 'subcompound' definition 'subcompoundArg'. molmodel-3.1.0/src/Compound.cpp:781:123: style:inconclusive: Function 'nameAtom' argument 3 names different: declaration 'biotype' definition 'biotypeIx'. [funcArgNamesDifferent] molmodel-3.1.0/src/CompoundRep.h:320:22: note: Function 'nameAtom' argument 3 names different: declaration 'biotype' definition 'biotypeIx'. molmodel-3.1.0/src/Compound.cpp:781:123: note: Function 'nameAtom' argument 3 names different: declaration 'biotype' definition 'biotypeIx'. molmodel-3.1.0/src/Compound.cpp:998:102: style:inconclusive: Function 'writeDefaultPdb' argument 3 names different: declaration 'transform' definition 't'. [funcArgNamesDifferent] molmodel-3.1.0/src/CompoundRep.h:1728:93: note: Function 'writeDefaultPdb' argument 3 names different: declaration 'transform' definition 't'. molmodel-3.1.0/src/Compound.cpp:998:102: note: Function 'writeDefaultPdb' argument 3 names different: declaration 'transform' definition 't'. molmodel-3.1.0/src/Compound.cpp:1202:10: style:inconclusive: Function 'absorbSubcompound' argument 3 names different: declaration 'isBase' definition 'isBaseCompound'. [funcArgNamesDifferent] molmodel-3.1.0/src/CompoundRep.h:1795:106: note: Function 'absorbSubcompound' argument 3 names different: declaration 'isBase' definition 'isBaseCompound'. molmodel-3.1.0/src/Compound.cpp:1202:10: note: Function 'absorbSubcompound' argument 3 names different: declaration 'isBase' definition 'isBaseCompound'. molmodel-3.1.0/src/Compound.cpp:1316:53: style:inconclusive: Function 'hasAtom' argument 1 names different: declaration 'name' definition 'atomName'. [funcArgNamesDifferent] molmodel-3.1.0/src/CompoundRep.h:1916:44: note: Function 'hasAtom' argument 1 names different: declaration 'name' definition 'atomName'. molmodel-3.1.0/src/Compound.cpp:1316:53: note: Function 'hasAtom' argument 1 names different: declaration 'name' definition 'atomName'. molmodel-3.1.0/src/Compound.cpp:1164:17: style: Variable 'bondCenter' can be declared as reference to const [constVariableReference] molmodel-3.1.0/src/Compound.cpp:2493:22: style: Variable 'residue' can be declared as reference to const [constVariableReference] molmodel-3.1.0/src/Compound.cpp:649:35: style: Variable 'bondCenterInfo' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/src/Compound.cpp:2210:124: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] molmodel-3.1.0/src/Compound.cpp:3006:124: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] molmodel-3.1.0/src/Pdb.cpp:27:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:37:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:54:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:84:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residueNumber [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:93:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable coordinates [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:146:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable writeExtraPrecision [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:148:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable writeExtraPrecision [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:152:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomName [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:161:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomName [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:172:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomName [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:196:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable right [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:275:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable locations [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:279:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable locations [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:322:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable locationIndicesById [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:387:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:465:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residueName [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:477:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residueName [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:502:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residueName [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:553:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:571:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:587:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:639:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomIndicesByName [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:646:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomIndicesByName [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:667:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residueNumber [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:690:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residueNumber [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:705:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:729:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residues [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:734:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residues [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:739:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residues [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:754:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residueIndicesById [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:774:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chainIndicesById [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:788:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chainIndicesById [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:819:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chains [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:824:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chains [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:829:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chains [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:843:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:866:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chainIndicesById [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:878:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UndefinedPdbChainId [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:923:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CIF [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:939:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable models [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:944:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable models [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:965:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:1052:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable models [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Pdb.cpp:1064:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/PeriodicVmdReporter.cpp:30:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable blockWaitingForVmdConnection [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/PeriodicVmdReporter.cpp:25:9: style: The scope of the variable 'checkFrequency' can be reduced. [variableScope] molmodel-3.1.0/src/Pdb.cpp:247:51: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/Pdb.cpp:396:32: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/Pdb.cpp:434:60: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/Pdb.cpp:341:13: style: Statements following noreturn function 'exit()' will never be executed. [unreachableCode] molmodel-3.1.0/src/Representation.h:123:1: style: The class 'Atom' does not declare a constructor although it has private member variables which likely require initialization. [noConstructor] molmodel-3.1.0/src/PDBReader.cpp:78:38: performance: Function parameter 'extension' should be passed by const reference. [passedByValue] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:146:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chargedAtomTypeIndex [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1797:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Nm2Ang [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1969:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HalfMatrix [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:2017:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Dynamics [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:2343:84: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:2383:87: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:2396:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:2605:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable k [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:2679:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable InvalidAtomIndex [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/VanderWallSphere.cpp:26:21: style: Parameter 'particleForces' can be declared as reference to const [constParameterReference] molmodel-3.1.0/src/VanderWallSphere.cpp:27:12: style: Parameter 'mobilityForces' can be declared as reference to const [constParameterReference] molmodel-3.1.0/src/VelocityRescalingThermostat.cpp:66:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SimTK_BOLTZMANN_CONSTANT_MD [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/VelocityRescalingThermostat.cpp:71:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Velocity [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/VelocityRescalingThermostat.cpp:111:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable impl [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/VelocityRescalingThermostat.cpp:117:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable impl [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/VelocityRescalingThermostat.cpp:121:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Tb [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/VelocityRescalingThermostat.cpp:128:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Tb [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/VelocityRescalingThermostat.cpp:134:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable numExcludedDofs [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/VelocityRescalingThermostat.cpp:143:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable numExcludedDofs [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/VelocityRescalingThermostat.cpp:45:5: style: Class 'VelocityRescalingThermostatImpl' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/src/VmdConnection.cpp:34:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/VmdConnection.cpp:45:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/VmdConnection.cpp:65:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/VmdConnection.cpp:98:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clientSocket [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/VmdConnection.cpp:103:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clientSocket [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/VmdConnection.cpp:111:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clientSocket [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/VmdConnection.cpp:117:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable socketNumber [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/Representation.cpp:70:17: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/Representation.cpp:71:17: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/Representation.cpp:191:0: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm] molmodel-3.1.0/src/Representation.cpp:199:0: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm] molmodel-3.1.0/src/Representation.cpp:217:0: style: Consider using std::find_if algorithm instead of a raw loop. [useStlAlgorithm] molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.h:414:11: performance:inconclusive: Technically the member function 'SimTK::CpuImplicitSolvent::computeAceNonPolarForce' can be static (but you may consider moving to unnamed namespace). [functionStatic] molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.cpp:789:25: note: Technically the member function 'SimTK::CpuImplicitSolvent::computeAceNonPolarForce' can be static (but you may consider moving to unnamed namespace). molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.h:414:11: note: Technically the member function 'SimTK::CpuImplicitSolvent::computeAceNonPolarForce' can be static (but you may consider moving to unnamed namespace). molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.h:70:7: style: Class 'SimTKOpenMMLog' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.cpp:887:15: style: The scope of the variable 'forceConversion' can be reduced. [variableScope] molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.cpp:888:15: style: The scope of the variable 'lengthConversion' can be reduced. [variableScope] molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.cpp:871:25: style: Local variable 'message' shadows outer variable [shadowVariable] molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.cpp:868:22: note: Shadowed declaration molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.cpp:871:25: note: Shadow variable molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.cpp:876:25: style: Local variable 'message' shadows outer variable [shadowVariable] molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.cpp:868:22: note: Shadowed declaration molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.cpp:876:25: note: Shadow variable molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.h:388:96: performance: Function parameter 'delimiter' should be passed by const reference. [passedByValue] molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.cpp:1009:57: performance: Function parameter 'infoFileName' should be passed by const reference. [passedByValue] molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.cpp:849:31: style: Variable 'implicitSolventParameters' can be declared as pointer to const [constVariablePointer] molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.cpp:1059:30: style: Variable 'fileName' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.cpp:797:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.h:360:19: performance:inconclusive: Technically the member function 'SimTK::ImplicitSolventParameters::getStringTab' can be static (but you may consider moving to unnamed namespace). [functionStatic] molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.cpp:812:40: note: Technically the member function 'SimTK::ImplicitSolventParameters::getStringTab' can be static (but you may consider moving to unnamed namespace). molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.h:360:19: note: Technically the member function 'SimTK::ImplicitSolventParameters::getStringTab' can be static (but you may consider moving to unnamed namespace). molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.cpp:442:15: warning: Either the condition '_atomicRadii==NULL' is redundant or there is possible null pointer dereference: _atomicRadii. [nullPointerRedundantCheck] molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.cpp:439:21: note: Assuming that condition '_atomicRadii==NULL' is not redundant molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.cpp:442:15: note: Null pointer dereference molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.cpp:442:15: error: Null pointer dereference [nullPointer] molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.cpp:489:23: style: The scope of the variable 'methodName' can be reduced. [variableScope] molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.cpp:536:23: style: Variable 'methodName' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/src/gbsa/ObcParameters.cpp:542:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/gbsa/ObcParameters.cpp:628:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/gbsa/ObcParameters.h:258:11: performance:inconclusive: Technically the member function 'SimTK::ObcParameters::mapGmxAtomNameToTinkerAtomNumber' can be static (but you may consider moving to unnamed namespace). [functionStatic] molmodel-3.1.0/src/gbsa/ObcParameters.cpp:487:20: note: Technically the member function 'SimTK::ObcParameters::mapGmxAtomNameToTinkerAtomNumber' can be static (but you may consider moving to unnamed namespace). molmodel-3.1.0/src/gbsa/ObcParameters.h:258:11: note: Technically the member function 'SimTK::ObcParameters::mapGmxAtomNameToTinkerAtomNumber' can be static (but you may consider moving to unnamed namespace). molmodel-3.1.0/src/gbsa/ObcParameters.cpp:381:15: warning: Either the condition '_scaledRadiusFactors==NULL' is redundant or there is possible null pointer dereference: _scaledRadiusFactors. [nullPointerRedundantCheck] molmodel-3.1.0/src/gbsa/ObcParameters.cpp:378:29: note: Assuming that condition '_scaledRadiusFactors==NULL' is not redundant molmodel-3.1.0/src/gbsa/ObcParameters.cpp:381:15: note: Null pointer dereference molmodel-3.1.0/src/gbsa/ObcParameters.cpp:381:15: error: Null pointer dereference [nullPointer] molmodel-3.1.0/src/gbsa/ObcParameters.cpp:354:23: style: Variable 'methodName' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/src/gbsa/CpuObc.cpp:708:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HalfPlusDiagonal [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.cpp:258:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.cpp:288:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.cpp:318:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.cpp:233:20: style: Variable 'simTKOpenMMLog' can be declared as pointer to const [constVariablePointer] molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:315:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WriteDebugFile [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:888:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dec [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:911:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dec [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:982:19: warning: Either the condition 'file' is redundant or there is possible null pointer dereference: file. [nullPointerRedundantCheck] molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:984:8: note: Assuming that condition 'file' is not redundant molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:982:19: note: Null pointer dereference molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:157:31: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:410:21: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:415:27: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:545:24: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:1034:20: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:849:13: style: The scope of the variable 'ch2' can be reduced. [variableScope] molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:967:11: style: The scope of the variable 'bufferLen' can be reduced. [variableScope] molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:1075:16: style: The scope of the variable 'spanp' can be reduced. [variableScope] molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:1076:8: style: The scope of the variable 'c' can be reduced. [variableScope] molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:541:24: style: Checking if unsigned expression 'bytesToAllocate' is less than zero. [unsignedLessThanZero] molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:878:56: performance: Function parameter 'stringToCheck' should be passed by const reference. [passedByValue] molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:901:59: performance: Function parameter 'stringToCheck' should be passed by const reference. [passedByValue] molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:86:77: style: Parameter 'point' can be declared as pointer to const [constParameterPointer] molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:589:55: style: Parameter 'vectorToRemove' can be declared as pointer to const [constParameterPointer] molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:620:61: style: Parameter 'vectorX' can be declared as pointer to const [constParameterPointer] molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:621:61: style: Parameter 'vectorY' can be declared as pointer to const [constParameterPointer] molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:651:62: style: Parameter 'matrixX' can be declared as pointer to const [constParameterPointer] molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:652:62: style: Parameter 'vectorY' can be declared as pointer to const [constParameterPointer] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1251:10: performance:inconclusive: Technically the member function 'DuMMBody::realizeTopologicalCache' can be static (but you may consider moving to unnamed namespace). [functionStatic] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:2795:16: note: Technically the member function 'DuMMBody::realizeTopologicalCache' can be static (but you may consider moving to unnamed namespace). molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1251:10: note: Technically the member function 'DuMMBody::realizeTopologicalCache' can be static (but you may consider moving to unnamed namespace). molmodel-3.1.0/src/TinkerAmber99.cpp:1626:108: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Any [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:86:9: style: Condition 'printCrapToTheScreen' is always false [knownConditionTrueFalse] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:85:33: note: Assignment 'printCrapToTheScreen=false', assigned value is 0 molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:86:9: note: Condition 'printCrapToTheScreen' is always false molmodel-3.1.0/src/gbsa/cpuObcInterface.cpp:88:85: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ObcTypeII [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/gbsa/cpuObcInterface.cpp:76:23: style: The scope of the variable 'methodName' can be reduced. [variableScope] molmodel-3.1.0/src/gbsa/cpuObcInterface.cpp:155:54: style:inconclusive: Function 'cpuCalculateImplicitSolventForces' argument 2 names different: declaration 'partialChargesIn' definition 'partialCharges'. [funcArgNamesDifferent] molmodel-3.1.0/src/gbsa/cpuObcInterface.h:111:66: note: Function 'cpuCalculateImplicitSolventForces' argument 2 names different: declaration 'partialChargesIn' definition 'partialCharges'. molmodel-3.1.0/src/gbsa/cpuObcInterface.cpp:155:54: note: Function 'cpuCalculateImplicitSolventForces' argument 2 names different: declaration 'partialChargesIn' definition 'partialCharges'. molmodel-3.1.0/src/gbsa/cpuObcInterface.cpp:70:53: style: Parameter 'atomicRadii' can be declared as pointer to const [constParameterPointer] molmodel-3.1.0/src/gbsa/cpuObcInterface.cpp:70:78: style: Parameter 'obcScaleFactors' can be declared as pointer to const [constParameterPointer] molmodel-3.1.0/src/gbsa/cpuObcInterface.cpp:370:29: style: Variable 'methodName' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1293:41: style:inconclusive: Function 'calcBondStretch' argument 1 names different: declaration 'a1' definition 'a1num'. [funcArgNamesDifferent] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1871:33: note: Function 'calcBondStretch' argument 1 names different: declaration 'a1' definition 'a1num'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1293:41: note: Function 'calcBondStretch' argument 1 names different: declaration 'a1' definition 'a1num'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1296:41: style:inconclusive: Function 'calcBondStretch' argument 4 names different: declaration 'scaleFactor' definition 'bondStretchScaleFactor'. [funcArgNamesDifferent] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1874:33: note: Function 'calcBondStretch' argument 4 names different: declaration 'scaleFactor' definition 'bondStretchScaleFactor'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1296:41: note: Function 'calcBondStretch' argument 4 names different: declaration 'scaleFactor' definition 'bondStretchScaleFactor'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1297:41: style:inconclusive: Function 'calcBondStretch' argument 5 names different: declaration 'customScaleFactor' definition 'customBondStretchScaleFactor'. [funcArgNamesDifferent] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1875:33: note: Function 'calcBondStretch' argument 5 names different: declaration 'customScaleFactor' definition 'customBondStretchScaleFactor'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1297:41: note: Function 'calcBondStretch' argument 5 names different: declaration 'customScaleFactor' definition 'customBondStretchScaleFactor'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1363:41: style:inconclusive: Function 'calcBondBend' argument 1 names different: declaration 'a1' definition 'a1num'. [funcArgNamesDifferent] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1879:33: note: Function 'calcBondBend' argument 1 names different: declaration 'a1' definition 'a1num'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1363:41: note: Function 'calcBondBend' argument 1 names different: declaration 'a1' definition 'a1num'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1366:41: style:inconclusive: Function 'calcBondBend' argument 4 names different: declaration 'scaleFactor' definition 'bondBendScaleFactor'. [funcArgNamesDifferent] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1882:33: note: Function 'calcBondBend' argument 4 names different: declaration 'scaleFactor' definition 'bondBendScaleFactor'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1366:41: note: Function 'calcBondBend' argument 4 names different: declaration 'scaleFactor' definition 'bondBendScaleFactor'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1367:41: style:inconclusive: Function 'calcBondBend' argument 5 names different: declaration 'customScaleFactor' definition 'customBondBendScaleFactor'. [funcArgNamesDifferent] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1883:33: note: Function 'calcBondBend' argument 5 names different: declaration 'customScaleFactor' definition 'customBondBendScaleFactor'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1367:41: note: Function 'calcBondBend' argument 5 names different: declaration 'customScaleFactor' definition 'customBondBendScaleFactor'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1423:41: style:inconclusive: Function 'calcBondTorsion' argument 1 names different: declaration 'a1' definition 'a1num'. [funcArgNamesDifferent] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1887:33: note: Function 'calcBondTorsion' argument 1 names different: declaration 'a1' definition 'a1num'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1423:41: note: Function 'calcBondTorsion' argument 1 names different: declaration 'a1' definition 'a1num'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1426:41: style:inconclusive: Function 'calcBondTorsion' argument 4 names different: declaration 'scaleFactor' definition 'bondTorsionScaleFactor'. [funcArgNamesDifferent] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1890:33: note: Function 'calcBondTorsion' argument 4 names different: declaration 'scaleFactor' definition 'bondTorsionScaleFactor'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1426:41: note: Function 'calcBondTorsion' argument 4 names different: declaration 'scaleFactor' definition 'bondTorsionScaleFactor'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1427:41: style:inconclusive: Function 'calcBondTorsion' argument 5 names different: declaration 'customScaleFactor' definition 'customBondTorsionScaleFactor'. [funcArgNamesDifferent] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1891:33: note: Function 'calcBondTorsion' argument 5 names different: declaration 'customScaleFactor' definition 'customBondTorsionScaleFactor'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1427:41: note: Function 'calcBondTorsion' argument 5 names different: declaration 'customScaleFactor' definition 'customBondTorsionScaleFactor'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1485:41: style:inconclusive: Function 'calcAmberImproperTorsion' argument 1 names different: declaration 'a1' definition 'a1num'. [funcArgNamesDifferent] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1895:33: note: Function 'calcAmberImproperTorsion' argument 1 names different: declaration 'a1' definition 'a1num'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1485:41: note: Function 'calcAmberImproperTorsion' argument 1 names different: declaration 'a1' definition 'a1num'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1488:41: style:inconclusive: Function 'calcAmberImproperTorsion' argument 4 names different: declaration 'scaleFactor' definition 'amberImproperTorsionScaleFactor'. [funcArgNamesDifferent] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1898:33: note: Function 'calcAmberImproperTorsion' argument 4 names different: declaration 'scaleFactor' definition 'amberImproperTorsionScaleFactor'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1488:41: note: Function 'calcAmberImproperTorsion' argument 4 names different: declaration 'scaleFactor' definition 'amberImproperTorsionScaleFactor'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1562:45: style:inconclusive: Function 'calcBodySubsetNonbondedForces' argument 1 names different: declaration 'inclBodIx' definition 'dummBodIx'. [funcArgNamesDifferent] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1765:49: note: Function 'calcBodySubsetNonbondedForces' argument 1 names different: declaration 'inclBodIx' definition 'dummBodIx'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1562:45: note: Function 'calcBodySubsetNonbondedForces' argument 1 names different: declaration 'inclBodIx' definition 'dummBodIx'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1680:41: style:inconclusive: Function 'calcNonbondedForces' argument 2 names different: declaration 'inclAtomForces_G' definition 'inclAtomForce_G'. [funcArgNamesDifferent] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1905:33: note: Function 'calcNonbondedForces' argument 2 names different: declaration 'inclAtomForces_G' definition 'inclAtomForce_G'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1680:41: note: Function 'calcNonbondedForces' argument 2 names different: declaration 'inclAtomForces_G' definition 'inclAtomForce_G'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:2058:25: style:inconclusive: Function 'scaleBondedAtoms' argument 1 names different: declaration 'atom' definition 'a'. [funcArgNamesDifferent] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1749:49: note: Function 'scaleBondedAtoms' argument 1 names different: declaration 'atom' definition 'a'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:2058:25: note: Function 'scaleBondedAtoms' argument 1 names different: declaration 'atom' definition 'a'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:2087:25: style:inconclusive: Function 'unscaleBondedAtoms' argument 1 names different: declaration 'atom' definition 'a'. [funcArgNamesDifferent] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1752:49: note: Function 'unscaleBondedAtoms' argument 1 names different: declaration 'atom' definition 'a'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:2087:25: note: Function 'unscaleBondedAtoms' argument 1 names different: declaration 'atom' definition 'a'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:2421:17: style:inconclusive: Function 'calculateAtomForces' argument 4 names different: declaration 'scale' definition 'builtinScale'. [funcArgNamesDifferent] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:478:21: note: Function 'calculateAtomForces' argument 4 names different: declaration 'scale' definition 'builtinScale'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:2421:17: note: Function 'calculateAtomForces' argument 4 names different: declaration 'scale' definition 'builtinScale'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:2692:64: style:inconclusive: Function 'placeAtom' argument 2 names different: declaration 'stationInNm' definition 'station'. [funcArgNamesDifferent] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1079:59: note: Function 'placeAtom' argument 2 names different: declaration 'stationInNm' definition 'station'. molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:2692:64: note: Function 'placeAtom' argument 2 names different: declaration 'stationInNm' definition 'station'. molmodel-3.1.0/src/imd.cpp:91:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/imd.cpp:110:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/gbsa/CpuObc.cpp:527:30: style:inconclusive: Member variable 'ParallelTask1::bornForces' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/src/gbsa/CpuObc.cpp:454:25: note: Member variable 'ParallelTask1::bornForces' is in the wrong place in the initializer list. molmodel-3.1.0/src/gbsa/CpuObc.cpp:527:30: note: Member variable 'ParallelTask1::bornForces' is in the wrong place in the initializer list. molmodel-3.1.0/src/gbsa/CpuObc.cpp:526:30: style:inconclusive: Member variable 'ParallelTask1::obcEnergy' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/src/gbsa/CpuObc.cpp:454:49: note: Member variable 'ParallelTask1::obcEnergy' is in the wrong place in the initializer list. molmodel-3.1.0/src/gbsa/CpuObc.cpp:526:30: note: Member variable 'ParallelTask1::obcEnergy' is in the wrong place in the initializer list. molmodel-3.1.0/src/gbsa/CpuObc.cpp:532:22: style:inconclusive: Member variable 'ParallelTask1::one' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/src/gbsa/CpuObc.cpp:455:9: note: Member variable 'ParallelTask1::one' is in the wrong place in the initializer list. molmodel-3.1.0/src/gbsa/CpuObc.cpp:532:22: note: Member variable 'ParallelTask1::one' is in the wrong place in the initializer list. molmodel-3.1.0/src/gbsa/CpuObc.cpp:615:33: style:inconclusive: Member variable 'ParallelTask2::bornForces' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/src/gbsa/CpuObc.cpp:552:65: note: Member variable 'ParallelTask2::bornForces' is in the wrong place in the initializer list. molmodel-3.1.0/src/gbsa/CpuObc.cpp:615:33: note: Member variable 'ParallelTask2::bornForces' is in the wrong place in the initializer list. molmodel-3.1.0/src/gbsa/CpuObc.cpp:618:22: style:inconclusive: Member variable 'ParallelTask2::one' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/src/gbsa/CpuObc.cpp:553:9: note: Member variable 'ParallelTask2::one' is in the wrong place in the initializer list. molmodel-3.1.0/src/gbsa/CpuObc.cpp:618:22: note: Member variable 'ParallelTask2::one' is in the wrong place in the initializer list. molmodel-3.1.0/src/gbsa/CpuObc.cpp:758:21: warning: The class 'CpuObc' defines member function with name 'getStateString' also defined in its parent class 'CpuImplicitSolvent'. [duplInheritedMember] molmodel-3.1.0/src/gbsa/CpuImplicitSolvent.h:446:19: note: Parent function 'CpuImplicitSolvent::getStateString' molmodel-3.1.0/src/gbsa/CpuObc.cpp:758:21: note: Derived function 'CpuObc::getStateString' molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:383:43: performance: Searching before insertion is not necessary. [stlFindInsert] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:420:43: performance: Searching before insertion is not necessary. [stlFindInsert] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:455:43: performance: Searching before insertion is not necessary. [stlFindInsert] molmodel-3.1.0/src/gbsa/CpuObc.cpp:1135:23: style: Condition 'atomI==-1' is always false [knownConditionTrueFalse] molmodel-3.1.0/src/gbsa/CpuObc.cpp:1071:21: note: Assignment 'atomI=0', assigned value is 0 molmodel-3.1.0/src/gbsa/CpuObc.cpp:1135:23: note: Condition 'atomI==-1' is always false molmodel-3.1.0/src/gbsa/CpuObc.cpp:1302:11: style: Condition 'atomI==-1' is always false [knownConditionTrueFalse] molmodel-3.1.0/src/gbsa/CpuObc.cpp:1228:21: note: Assignment 'atomI=0', assigned value is 0 molmodel-3.1.0/src/gbsa/CpuObc.cpp:1302:11: note: Condition 'atomI==-1' is always false molmodel-3.1.0/src/gbsa/CpuObc.cpp:1302:26: style: Condition 'atomJ==-1' is always false [knownConditionTrueFalse] molmodel-3.1.0/src/gbsa/CpuObc.cpp:1239:24: note: Assignment 'atomJ=0', assigned value is 0 molmodel-3.1.0/src/gbsa/CpuObc.cpp:1302:26: note: Condition 'atomJ==-1' is always false molmodel-3.1.0/src/gbsa/CpuObc.cpp:1326:22: style: Condition 'atomI>=0' is always true [knownConditionTrueFalse] molmodel-3.1.0/src/gbsa/CpuObc.cpp:1228:21: note: Assignment 'atomI=0', assigned value is 0 molmodel-3.1.0/src/gbsa/CpuObc.cpp:1326:22: note: Condition 'atomI>=0' is always true molmodel-3.1.0/src/gbsa/CpuObc.cpp:1218:28: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/gbsa/CpuObc.cpp:1354:13: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/gbsa/CpuObc.cpp:1354:13: portability:inconclusive: Casting from double * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast] molmodel-3.1.0/src/imd.cpp:38:15: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:50:4: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:51:4: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:52:4: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:53:4: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:69:10: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:125:25: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:131:25: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:137:25: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:143:25: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:151:25: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:157:25: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:164:15: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:165:16: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:176:15: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:177:16: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:187:15: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:188:16: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:198:20: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:207:20: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:241:20: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:242:20: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:247:24: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:252:24: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/imd.cpp:242:20: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast] molmodel-3.1.0/src/imd.cpp:252:24: portability:inconclusive: Casting from float * to char * is not portable due to different binary data representations on different platforms. [invalidPointerCast] molmodel-3.1.0/src/imd.cpp:40:8: style: The scope of the variable 'N' can be reduced. [variableScope] molmodel-3.1.0/src/imd.cpp:86:9: style: The scope of the variable 'nread' can be reduced. [variableScope] molmodel-3.1.0/src/imd.cpp:105:9: style: The scope of the variable 'nwritten' can be reduced. [variableScope] molmodel-3.1.0/src/imd.cpp:54:10: error: Uninitialized variable: n [uninitvar] molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:93:77: performance: Prefer prefix ++/-- operators for non-primitive types. [postfixOperator] molmodel-3.1.0/src/gbsa/CpuObc.cpp:805:22: style: The scope of the variable 'scaledRadii' can be reduced. [variableScope] molmodel-3.1.0/src/vmdsock.cpp:105:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PF_INET [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/vmdsock.cpp:115:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PF_INET [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/vmdsock.cpp:205:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable timeval [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/vmdsock.cpp:222:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable timeval [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/gbsa/CpuObc.cpp:825:25: style: Local variable 'message' shadows outer variable [shadowVariable] molmodel-3.1.0/src/gbsa/CpuObc.cpp:822:22: note: Shadowed declaration molmodel-3.1.0/src/gbsa/CpuObc.cpp:825:25: note: Shadow variable molmodel-3.1.0/src/gbsa/CpuObc.cpp:830:25: style: Local variable 'message' shadows outer variable [shadowVariable] molmodel-3.1.0/src/gbsa/CpuObc.cpp:822:22: note: Shadowed declaration molmodel-3.1.0/src/gbsa/CpuObc.cpp:830:25: note: Shadow variable molmodel-3.1.0/src/vmdsock.cpp:84:5: style: Obsolescent function 'gethostbyname' called. It is recommended to use 'getaddrinfo' instead. [prohibitedgethostbynameCalled] molmodel-3.1.0/src/gbsa/CpuObc.cpp:723:16: style: Variable 'obcChain' can be declared as pointer to const [constVariablePointer] molmodel-3.1.0/src/gbsa/CpuObc.cpp:798:31: style: Variable 'implicitSolventParameters' can be declared as pointer to const [constVariablePointer] molmodel-3.1.0/src/vmdsock.cpp:69:8: warning: Either the condition 's!=NULL' is redundant or there is possible null pointer dereference: s. [nullPointerRedundantCheck] molmodel-3.1.0/src/vmdsock.cpp:66:9: note: Assuming that condition 's!=NULL' is not redundant molmodel-3.1.0/src/vmdsock.cpp:69:8: note: Null pointer dereference molmodel-3.1.0/src/vmdsock.cpp:65:8: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/vmdsock.cpp:79:19: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/vmdsock.cpp:109:26: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/vmdsock.cpp:113:19: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/vmdsock.cpp:118:23: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/vmdsock.cpp:122:19: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/vmdsock.cpp:128:34: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/vmdsock.cpp:142:23: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/vmdsock.cpp:144:14: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/vmdsock.cpp:154:19: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/vmdsock.cpp:163:19: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/vmdsock.cpp:173:20: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/vmdsock.cpp:185:20: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/vmdsock.cpp:198:19: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/vmdsock.cpp:205:10: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/vmdsock.cpp:215:19: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/vmdsock.cpp:222:10: style: C-style pointer casting [cstyleCast] molmodel-3.1.0/src/vmdsock.cpp:81:19: style: Variable 'h' can be declared as pointer to const [constVariablePointer] molmodel-3.1.0/src/vmdsock.cpp:122:14: style: Variable 's' can be declared as pointer to const [constVariablePointer] molmodel-3.1.0/src/vmdsock.cpp:154:14: style: Variable 's' can be declared as pointer to const [constVariablePointer] molmodel-3.1.0/src/vmdsock.cpp:163:14: style: Variable 's' can be declared as pointer to const [constVariablePointer] molmodel-3.1.0/src/vmdsock.cpp:198:14: style: Variable 's' can be declared as pointer to const [constVariablePointer] molmodel-3.1.0/src/vmdsock.cpp:215:14: style: Variable 's' can be declared as pointer to const [constVariablePointer] molmodel-3.1.0/tests/TestAtomTargetLocations.cpp:66:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PDB [valueFlowBailoutIncompleteVar] molmodel-3.1.0/src/gbsa/CpuObc.cpp:671:41: style: Variable 'electricConstant' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/src/gbsa/CpuObc.cpp:726:42: style: Variable 'alphaObc' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/src/gbsa/CpuObc.cpp:727:42: style: Variable 'betaObc' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/src/gbsa/CpuObc.cpp:728:42: style: Variable 'gammaObc' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/src/gbsa/CpuObc.cpp:649:28: style: Variable 'one' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/src/gbsa/CpuObc.cpp:650:28: style: Variable 'two' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/src/gbsa/CpuObc.cpp:651:28: style: Variable 'three' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/src/gbsa/CpuObc.cpp:652:28: style: Variable 'four' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/src/gbsa/CpuObc.cpp:653:28: style: Variable 'half' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/src/gbsa/CpuObc.cpp:654:28: style: Variable 'fourth' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/src/gbsa/CpuObc.cpp:655:28: style: Variable 'eighth' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/src/gbsa/CpuObc.cpp:902:22: style: Unused variable: header [unusedVariable] molmodel-3.1.0/src/gbsa/CpuObc.cpp:955:22: style: Unused variable: header [unusedVariable] molmodel-3.1.0/src/gbsa/CpuObc.cpp:1041:41: style: Variable 'electricConstant' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/tests/TestBiopolymer.cpp:41:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestBiotypeSelfCode.cpp:22:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestBodyIds.cpp:55:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestCompoundTransforms.cpp:31:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Position [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestCompoundTransforms.cpp:65:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Position [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestCompoundTransforms.cpp:113:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestDihedrals2.cpp:55:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PDB [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestEthane.cpp:43:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestEthane.cpp:52:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestEthane.cpp:61:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestEthane.cpp:82:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestEthane.cpp:92:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestEthane.cpp:101:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestFitMagnesiums.cpp:32:75: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PDB [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestFitMagnesiums.cpp:89:79: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PDB [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestFitMagnesiums.cpp:127:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestForeignBodyIds.cpp:86:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestGbsa.cpp:59:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestGetAtomName.cpp:45:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestDuMMForces.cpp:58:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Dynamics [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestDuMMForces.cpp:64:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Dynamics [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestDuMMForces.cpp:314:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Free [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestDuMMForces.cpp:553:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Rigid [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestDuMMForces.cpp:756:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Rigid [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestDuMMForces.cpp:775:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Dynamics [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestLoadVariantRnaAtomNames.cpp:150:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PDB [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestLoadPdb.cpp:25:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestLoadPdb.cpp:128:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestLoadPdb.cpp:213:26: style: Parameter 'argv' can be declared as const array [constParameter] molmodel-3.1.0/tests/TestLoadPdb.cpp:112:15: style: Variable 'startTime' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/tests/TestLoadPdb.cpp:208:15: style: Variable 'startTime' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/tests/TestMgSolvationEnergy.cpp:61:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Dynamics [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestMethanol.cpp:100:120: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Yellow [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestDuMMForces.cpp:402:10: style:inconclusive: Member variable 'HarmonicBondStretch::idealLength' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/tests/TestDuMMForces.cpp:388:33: note: Member variable 'HarmonicBondStretch::idealLength' is in the wrong place in the initializer list. molmodel-3.1.0/tests/TestDuMMForces.cpp:402:10: note: Member variable 'HarmonicBondStretch::idealLength' is in the wrong place in the initializer list. molmodel-3.1.0/tests/TestDuMMForces.cpp:616:10: style:inconclusive: Member variable 'HarmonicBondBend::idealAngle' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/tests/TestDuMMForces.cpp:602:49: note: Member variable 'HarmonicBondBend::idealAngle' is in the wrong place in the initializer list. molmodel-3.1.0/tests/TestDuMMForces.cpp:616:10: note: Member variable 'HarmonicBondBend::idealAngle' is in the wrong place in the initializer list. molmodel-3.1.0/tests/TestDuMMForces.cpp:90:5: style: Class 'SodiumChlorideSystem' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/tests/TestDuMMForces.cpp:172:5: style: Class 'ArgonSystem' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/tests/TestDuMMForces.cpp:273:5: style: Class 'OxygenSystem' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/tests/TestDuMMForces.cpp:409:5: style: Class 'CustomOxygenSystem' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/tests/TestDuMMForces.cpp:477:5: style: Class 'WaterSystem' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/tests/TestDuMMForces.cpp:623:5: style: Class 'CustomWaterSystem' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/tests/TestDuMMForces.cpp:686:5: style: Class 'HydrogenPeroxideSystem' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/tests/TestDuMMForces.cpp:869:5: style: Class 'CustomHydrogenPeroxideSystem' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/tests/TestOxygenMolecule.cpp:67:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestOxygenMolecule.cpp:83:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestPartitionerDihedrals.cpp:60:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestPdb.cpp:65:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PDB [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestPdb.cpp:117:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PDB [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestPdb.cpp:197:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestPositiveControl.cpp:6:3: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestProtein.cpp:70:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestProtein.cpp:126:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestPartitionerDihedrals.cpp:90:41: style: C-style reference casting [cstyleCast] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:83:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Dynamics [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:117:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Pi [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestProteinDihedrals.cpp:324:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PDB [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:181:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SimTK_BOLTZMANN_CONSTANT_MD [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:340:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Dynamics [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:362:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable daltons [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:367:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable angstroms [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:461:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Velocity [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:521:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:610:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:629:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestProtein.cpp:74:16: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled] molmodel-3.1.0/tests/TestProtein.cpp:75:22: style: Obsolete function 'std::asctime' called. It is recommended to use 'strftime' instead. [prohibitedasctimeCalled] molmodel-3.1.0/tests/TestProtein.cpp:78:16: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled] molmodel-3.1.0/tests/TestProtein.cpp:79:22: style: Obsolete function 'std::asctime' called. It is recommended to use 'strftime' instead. [prohibitedasctimeCalled] molmodel-3.1.0/tests/TestProtein.cpp:93:16: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled] molmodel-3.1.0/tests/TestProtein.cpp:94:22: style: Obsolete function 'std::asctime' called. It is recommended to use 'strftime' instead. [prohibitedasctimeCalled] molmodel-3.1.0/tests/TestProtein.cpp:101:16: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled] molmodel-3.1.0/tests/TestProtein.cpp:102:22: style: Obsolete function 'std::asctime' called. It is recommended to use 'strftime' instead. [prohibitedasctimeCalled] molmodel-3.1.0/tests/TestProtein.cpp:72:17: style: Variable 'timeinfo' can be declared as pointer to const [constVariablePointer] molmodel-3.1.0/tests/TestRna.cpp:59:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestRiboseMobilizer.cpp:68:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Rad2Deg [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestRiboseMobilizer.cpp:140:89: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable YAxis [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestProteinDihedrals.cpp:20:31: style: Variable 'vpfString' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/tests/TestProteinDihedrals.cpp:278:36: style: Variable 'gbpFrag2String' is assigned a value that is never used. [unreadVariable] molmodel-3.1.0/tests/TestSanityDuMM.cpp:10:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestSerine.cpp:50:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestRiboseMobilizer.cpp:45:21: style:inconclusive: Member variable 'PeriodicTorsionMeasurer::compound' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/tests/TestRiboseMobilizer.cpp:25:11: note: Member variable 'PeriodicTorsionMeasurer::compound' is in the wrong place in the initializer list. molmodel-3.1.0/tests/TestRiboseMobilizer.cpp:45:21: note: Member variable 'PeriodicTorsionMeasurer::compound' is in the wrong place in the initializer list. molmodel-3.1.0/tests/TestShortPdbLines.cpp:13:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PDB [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestShortPdbLines.cpp:25:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PDB [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestShortPdbLines.cpp:40:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestSetTorsion.cpp:10:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Pi [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestSetTorsion.cpp:31:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Pi [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestTinkerAmber.cpp:10:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestTorsionPartitioner.cpp:67:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestVelocityRescalingThermostat.cpp:102:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Dynamics [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestVelocityRescalingThermostat.cpp:160:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestVelocityRescalingThermostat.cpp:165:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestWriteDefaultPdb.cpp:57:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PDB [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestVelocityRescalingThermostat.cpp:94:17: style:inconclusive: Member variable 'EnergyMonitor::eventCount' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/tests/TestVelocityRescalingThermostat.cpp:96:91: note: Member variable 'EnergyMonitor::eventCount' is in the wrong place in the initializer list. molmodel-3.1.0/tests/TestVelocityRescalingThermostat.cpp:94:17: note: Member variable 'EnergyMonitor::eventCount' is in the wrong place in the initializer list. molmodel-3.1.0/tests/TestVelocityRescalingThermostat.cpp:52:5: style: Class 'BetweenBodyForce' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/tests/TestVelocityRescalingThermostat.cpp:96:5: style: Class 'EnergyMonitor' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/tests/TestWriteSimtimePdb.cpp:87:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/RemoveMassCenterDrift.cpp:29:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Velocity [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/RemoveMassCenterDrift.cpp:85:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Pi [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestVelocityRescalingThermostat.cpp:57:88: style: Parameter 'particleForces' can be declared as reference to const [constParameterReference] molmodel-3.1.0/tests/TestVelocityRescalingThermostat.cpp:57:112: style: Parameter 'mobilityForces' can be declared as reference to const [constParameterReference] molmodel-3.1.0/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:36:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Velocity [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:70:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Velocity [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:147:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:176:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Velocity [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:203:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Velocity [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/RemoveMassCenterDrift.cpp:46:2: style: Class 'SaveState' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:103:5: warning: Member variable 'HarmonicOscillator::reporter' is not initialized in the constructor. [uninitMemberVar] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:364:5: warning: Member variable 'ArgonGasSphere::reporter' is not initialized in the constructor. [uninitMemberVar] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:319:9: warning: Member variable 'ArgonReporter::nDofs' is not initialized in the constructor. [uninitMemberVar] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:319:9: warning: Member variable 'ArgonReporter::nConstraints' is not initialized in the constructor. [uninitMemberVar] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:60:21: style:inconclusive: Member variable 'OscillatorReporter::eventCount' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:71:15: note: Member variable 'OscillatorReporter::eventCount' is in the wrong place in the initializer list. molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:60:21: note: Member variable 'OscillatorReporter::eventCount' is in the wrong place in the initializer list. molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:310:21: style:inconclusive: Member variable 'ArgonReporter::eventCount' is in the wrong place in the initializer list. [initializerList] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:321:15: note: Member variable 'ArgonReporter::eventCount' is in the wrong place in the initializer list. molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:310:21: note: Member variable 'ArgonReporter::eventCount' is in the wrong place in the initializer list. molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:286:10: performance:inconclusive: Technically the member function 'HarmonicOscillator::getTime' can be static (but you may consider moving to unnamed namespace). [functionStatic] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:578:11: performance:inconclusive: Technically the member function 'ArgonGasSphere::getTime' can be static (but you may consider moving to unnamed namespace). [functionStatic] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:103:5: style: Class 'HarmonicOscillator' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:364:5: style: Class 'ArgonGasSphere' has a constructor with 1 argument that is not explicit. [noExplicitConstructor] molmodel-3.1.0/tests/adhoc/TestMemoryUse.cpp:101:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Position [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/TestMemoryUse.cpp:159:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:327:36: style: Local variable 'system' shadows outer variable [shadowVariable] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:583:29: note: Shadowed declaration molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:327:36: note: Shadow variable molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:328:43: style: Local variable 'matter' shadows outer variable [shadowVariable] molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:584:29: note: Shadowed declaration molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:328:43: note: Shadow variable molmodel-3.1.0/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:66:57: style: Parameter 'shouldTerminate' can be declared as reference to const [constParameterReference] molmodel-3.1.0/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:63:31: error: Uninitialized variable: dummy [uninitvar] molmodel-3.1.0/tests/adhoc/TestSimpleProtein.cpp:27:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Infinity [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/TestSimpleProtein.cpp:78:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Velocity [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/TestSimpleProtein.cpp:108:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Pi [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/TestWriteLargerPdb.cpp:57:8: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/TestSimpleProtein.cpp:74:57: style: Parameter 'shouldTerminate' can be declared as reference to const [constParameterReference] molmodel-3.1.0/tests/adhoc/TestWriteLargerPdb.cpp:61:19: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled] molmodel-3.1.0/tests/adhoc/TestWriteLargerPdb.cpp:62:25: style: Obsolete function 'std::asctime' called. It is recommended to use 'strftime' instead. [prohibitedasctimeCalled] molmodel-3.1.0/tests/adhoc/TestWriteLargerPdb.cpp:65:19: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled] molmodel-3.1.0/tests/adhoc/TestWriteLargerPdb.cpp:66:25: style: Obsolete function 'std::asctime' called. It is recommended to use 'strftime' instead. [prohibitedasctimeCalled] molmodel-3.1.0/tests/adhoc/TestWriteLargerPdb.cpp:78:19: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled] molmodel-3.1.0/tests/adhoc/TestWriteLargerPdb.cpp:79:25: style: Obsolete function 'std::asctime' called. It is recommended to use 'strftime' instead. [prohibitedasctimeCalled] molmodel-3.1.0/tests/adhoc/TestWriteLargerPdb.cpp:85:19: portability: Non reentrant function 'localtime' called. For threadsafe applications it is recommended to use the reentrant replacement function 'localtime_r'. [prohibitedlocaltimeCalled] molmodel-3.1.0/tests/adhoc/TestWriteLargerPdb.cpp:86:25: style: Obsolete function 'std::asctime' called. It is recommended to use 'strftime' instead. [prohibitedasctimeCalled] molmodel-3.1.0/tests/adhoc/TestWriteLargerPdb.cpp:59:20: style: Variable 'timeinfo' can be declared as pointer to const [constVariablePointer] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:177:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atoms [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:223:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Position [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:252:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable parentIx [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:343:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Ang2Nm [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:358:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable parentIx [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:442:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Ang2Nm [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:445:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Ang2Nm [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:448:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:482:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:521:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:669:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LorentzBerthelot [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:879:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable InvalidClusterIndex [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:1002:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SpaceRotationSequence [valueFlowBailoutIncompleteVar] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:342:10: performance:inconclusive: Technically the member function 'OxygenMolecule::getNominalOOBondLength' can be static (but you may consider moving to unnamed namespace). [functionStatic] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:441:10: performance:inconclusive: Technically the member function 'EthaneMolecule::getNominalCCBondLength' can be static (but you may consider moving to unnamed namespace). [functionStatic] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:444:10: performance:inconclusive: Technically the member function 'EthaneMolecule::getNominalCHBondLength' can be static (but you may consider moving to unnamed namespace). [functionStatic] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:447:10: performance:inconclusive: Technically the member function 'EthaneMolecule::getNominalHCCBondAngle' can be static (but you may consider moving to unnamed namespace). [functionStatic] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:221:10: style: The function 'setMoleculeTransform' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:66:18: note: Virtual function in base class molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:221:10: note: Function in derived class molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:265:10: style: The function 'setDefaultInternalState' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:79:18: note: Virtual function in base class molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:265:10: note: Function in derived class molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:403:10: style: The function 'setDefaultInternalState' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:79:18: note: Virtual function in base class molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:403:10: note: Function in derived class molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:461:10: style: The function 'setDefaultInternalState' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:79:18: note: Virtual function in base class molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:461:10: note: Function in derived class molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:496:10: style: The function 'setDefaultInternalState' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:79:18: note: Virtual function in base class molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:496:10: note: Function in derived class molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:509:10: style: The function 'setDefaultInternalState' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:79:18: note: Virtual function in base class molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:509:10: note: Function in derived class molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:871:73: style:inconclusive: Function 'EthaneMolecule' argument 2 names different: declaration 'parentMobilizerFrame' definition 'parentTransform'. [funcArgNamesDifferent] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:430:61: note: Function 'EthaneMolecule' argument 2 names different: declaration 'parentMobilizerFrame' definition 'parentTransform'. molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:871:73: note: Function 'EthaneMolecule' argument 2 names different: declaration 'parentMobilizerFrame' definition 'parentTransform'. molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:831:22: style: Local variable 's' shadows outer variable [shadowVariable] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:742:11: note: Shadowed declaration molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:831:22: note: Shadow variable molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:1097:34: style: Local variable 'b' shadows outer variable [shadowVariable] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:1087:26: note: Shadowed declaration molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:1097:34: note: Shadow variable molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:846:20: style: Modulo of one is always equal to zero [moduloofone] molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:829:24: style: Variable 'flag' is assigned a value that is never used. [unreadVariable] diff: head molmodel-3.1.0/examples/ExampleFoldPolyalanine.cpp:101:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/examples/ExampleFoldPolyalanine.cpp:149:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:216:100: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Rigid [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/examplesNotReadyYet/ExampleMeasureActualStepSize.cpp:49:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/AtomSubsystem.cpp:120:83: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] 2.13.0 molmodel-3.1.0/src/AtomSubsystem.cpp:129:49: style: Variable 'atom' is assigned a value that is never used. [unreadVariable] head molmodel-3.1.0/src/AtomSubsystem.cpp:158:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomsByBody [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/AtomSubsystem.cpp:162:74: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/AtomSubsystem.cpp:185:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable systemBodyIxToLocalBodyIx [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/AtomSubsystem.cpp:199:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atoms [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/AtomSubsystem.cpp:203:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atoms [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/AtomSubsystem.cpp:225:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bonds [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/AtomSubsystem.cpp:231:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bonds [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/AtomSubsystem.cpp:241:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomPositionCacheIndex [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/AtomSubsystem.cpp:252:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomBodyStationCacheIndex [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/AtomSubsystem.cpp:263:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomVelocityCacheIndex [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/AtomSubsystem.cpp:298:81: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/AtomSubsystem.cpp:339:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable N_SQUARED [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/AtomSubsystem.cpp:408:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable body1 [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/AtomSubsystem.cpp:421:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomsByBody [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/AtomSubsystem.cpp:440:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable square_nanometers [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/AtomSubsystem.cpp:490:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bUseVoxelHash [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/AtomSubsystem.cpp:557:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bUseVoxelHash [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/AtomSubsystem.cpp:613:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable state [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/AtomSubsystem.cpp:619:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable currentPair [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/AtomSubsystem.cpp:624:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable currentPair [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Biotype.cpp:173:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Any [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Biotype.cpp:291:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Biotype.cpp:303:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Any [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Biotype.cpp:318:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Biotype.cpp:324:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Biotype.cpp:330:73: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Biotype.cpp:341:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Any [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Biotype.cpp:484:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Any [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Compound.cpp:1028:97: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residueNumber [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Compound.cpp:1324:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Compound.cpp:2192:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Position [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Compound.cpp:2352:65: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable synonyms [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Compound.cpp:2399:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Compound.cpp:2403:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Compound.cpp:2433:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomIdsByName [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Compound.cpp:2489:61: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Any [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Compound.cpp:2503:15: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residueIdsByName [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Compound.cpp:2579:17: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Compound.cpp:2759:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable AminoAcidResidue [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Compound.cpp:2824:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Compound.cpp:2833:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Compound.cpp:2990:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Position [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Compound.cpp:3069:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NaN [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Compound.cpp:814:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Compound.cpp:853:75: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Compound.cpp:874:81: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Compound.cpp:903:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Compound.cpp:908:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Compound.cpp:933:56: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Compound.cpp:983:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundAtom.h:169:35: style: C-style reference casting [cstyleCast] head molmodel-3.1.0/src/CompoundAtom.h:203:42: style: C-style reference casting [cstyleCast] head molmodel-3.1.0/src/CompoundAtom.h:350:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundAtom.h:487:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Pi [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundAtom.h:497:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Pi [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundAtom.h:51:31: style: C-style reference casting [cstyleCast] head molmodel-3.1.0/src/CompoundAtom.h:579:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundAtom.h:605:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundAtom.h:632:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundAtom.h:659:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundAtom.h:706:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NaN [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundAtom.h:721:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable ZAxis [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundAtom.h:759:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable XAxis [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundRep.h:1130:83: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundRep.h:1348:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundRep.h:1372:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundRep.h:1415:39: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundRep.h:1443:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundRep.h:1806:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundRep.h:1812:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundRep.h:187:68: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable first [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundRep.h:1894:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundRep.h:2151:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundRep.h:2323:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundRep.h:2356:47: style: C-style reference casting [cstyleCast] head molmodel-3.1.0/src/CompoundRep.h:2373:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Position [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundRep.h:2389:47: style: C-style reference casting [cstyleCast] head molmodel-3.1.0/src/CompoundRep.h:2503:18: style: The destructor '~BiopolymerResidueRep' overrides a destructor in a base class but is not marked with a 'override' specifier. [missingOverride] molmodel-3.1.0/src/CompoundRep.h:120:14: note: Virtual destructor in base class molmodel-3.1.0/src/CompoundRep.h:2503:18: note: Destructor in derived class head molmodel-3.1.0/src/CompoundRep.h:462:72: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundRep.h:484:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundRep.h:644:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Pi [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundRep.h:684:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Pi [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundRep.h:709:76: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundRep.h:727:82: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundRep.h:773:76: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundRep.h:778:40: style: C-style reference casting [cstyleCast] head molmodel-3.1.0/src/CompoundRep.h:953:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Position [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundRep.h:961:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Velocity [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundRep.h:969:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Acceleration [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundSystem.cpp:139:28: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/CompoundSystem.cpp:154:37: style: C-style reference casting [cstyleCast] head molmodel-3.1.0/src/CompoundSystem.cpp:79:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:101:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomClasses [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1066:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gbsaSolventDielectric [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1069:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gbsaSoluteDielectric [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:107:78: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1100:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inclList [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1109:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inclList [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1120:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inclList [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1127:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inclList [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1134:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inclList [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1142:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inclList [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1150:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inclList [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1160:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inclList [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1176:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inclList [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1186:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable inclList [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1203:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atoms [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1209:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chargedAtomTypes [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1214:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chargedAtomTypes [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1263:84: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable vdwGlobalScaleFactor [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1264:84: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable coulombGlobalScaleFactor [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1265:84: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable gbsaGlobalScaleFactor [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1266:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bondStretchGlobalScaleFactor [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1267:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bondBendGlobalScaleFactor [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1268:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable bondTorsionGlobalScaleFactor [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1269:97: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable amberImproperTorsionGlobalScaleFactor [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1270:94: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable customBondStretchGlobalScaleFactor [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1271:94: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable customBondBendGlobalScaleFactor [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1272:94: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable customBondTorsionGlobalScaleFactor [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1275:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable tracing [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1279:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable useMultithreadedComputation [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1283:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable useMultithreadedComputation [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1286:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable usingMultithreaded [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1289:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable numThreadsRequested [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1293:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable numThreadsRequested [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1296:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable numThreadsInUse [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1300:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable wantOpenMMAcceleration [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1304:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable wantOpenMMAcceleration [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1307:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable allowOpenMMReference [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1311:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable allowOpenMMReference [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1314:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable usingOpenMM [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1317:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable openMMPlatformInUse [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1570:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atoms [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1603:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Green [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:1853:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable forcefieldName [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:255:88: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:321:91: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NaN [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:478:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:94:47: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atoms [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystem.cpp:98:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomClasses [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:146:49: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chargedAtomTypeIndex [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1797:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Nm2Ang [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:1969:66: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable HalfMatrix [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:2017:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Dynamics [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:2343:84: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:2383:87: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:2396:55: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:2605:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable k [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.cpp:2679:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable InvalidAtomIndex [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1056:43: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable InvalidAtomIndex [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1112:62: style: Parameter 'mm' can be declared as reference to const [constParameterReference] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1116:36: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1125:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1401:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable WaldmanHagler [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1508:79: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1516:79: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1532:94: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1539:94: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1582:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clusterIndex [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1627:41: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomIndex [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:1709:42: style: Parameter 's' can be declared as reference to const [constParameterReference] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:415:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:458:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:489:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Rad2Deg [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:542:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Pi [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:555:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Pi [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:567:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Rad2Deg [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:612:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable periodicity [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:619:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable periodicity [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:675:46: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/DuMMForceFieldSubsystemRep.h:811:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable NaN [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Element.cpp:490:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable impl [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/MolecularMechanicsSystem.cpp:112:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Position [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/MolecularMechanicsSystem.cpp:170:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Position [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/MolecularMechanicsSystem.cpp:91:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable molecularMechanicsSub [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/MolecularMechanicsSystem.cpp:95:62: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable molecularMechanicsSub [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/PDBReader.cpp:108:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/PDBReader.cpp:217:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chains [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/PDBReader.cpp:329:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chains [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/PDBReader.cpp:371:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable impl [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/PDBReader.cpp:375:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable impl [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/PDBReader.cpp:64:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/PDBReader.cpp:79:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/PDBReader.cpp:89:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:1052:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable models [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:1064:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:146:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable writeExtraPrecision [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:148:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable writeExtraPrecision [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:152:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomName [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:161:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomName [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:172:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomName [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:196:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable right [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:275:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable locations [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:279:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable locations [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:322:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable locationIndicesById [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:37:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:387:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:465:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residueName [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:477:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residueName [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:502:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residueName [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:54:18: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:553:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:571:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable second [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:587:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:639:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomIndicesByName [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:646:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable atomIndicesByName [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:667:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residueNumber [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:690:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residueNumber [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:705:58: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:729:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residues [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:734:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residues [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:739:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residues [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:754:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residueIndicesById [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:774:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chainIndicesById [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:788:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chainIndicesById [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:819:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chains [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:824:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chains [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:829:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chains [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:843:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:84:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable residueNumber [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:866:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable chainIndicesById [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:878:33: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable UndefinedPdbChainId [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:923:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable CIF [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:939:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable models [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:93:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable coordinates [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:944:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable models [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Pdb.cpp:965:22: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/Util.h:11:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable npos [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/VanderWallSphere.cpp:26:21: style: Parameter 'particleForces' can be declared as reference to const [constParameterReference] head molmodel-3.1.0/src/VanderWallSphere.cpp:27:12: style: Parameter 'mobilityForces' can be declared as reference to const [constParameterReference] head molmodel-3.1.0/src/VelocityRescalingThermostat.cpp:111:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable impl [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/VelocityRescalingThermostat.cpp:117:12: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable impl [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/VelocityRescalingThermostat.cpp:121:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Tb [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/VelocityRescalingThermostat.cpp:128:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Tb [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/VelocityRescalingThermostat.cpp:134:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable numExcludedDofs [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/VelocityRescalingThermostat.cpp:143:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable numExcludedDofs [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/VelocityRescalingThermostat.cpp:71:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Velocity [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/VmdConnection.cpp:103:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clientSocket [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/VmdConnection.cpp:111:20: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clientSocket [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/VmdConnection.cpp:117:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable socketNumber [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/VmdConnection.cpp:45:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/VmdConnection.cpp:65:13: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cerr [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/VmdConnection.cpp:98:21: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable clientSocket [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/gbsa/ObcParameters.cpp:628:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable endl [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/gbsa/ObcParameters.h:231:11: style: The function 'setAtomicRadii' overrides a function in a base class but is not marked with a 'override' specifier. [missingOverride] molmodel-3.1.0/src/gbsa/ImplicitSolventParameters.h:336:19: note: Virtual function in base class molmodel-3.1.0/src/gbsa/ObcParameters.h:231:11: note: Function in derived class head molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.cpp:288:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/gbsa/SimTKOpenMMLog.cpp:318:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable stderr [valueFlowBailoutIncompleteVar] 2.13.0 molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:761:11: style: C-style pointer casting [cstyleCast] head molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:888:52: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dec [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/gbsa/SimTKOpenMMUtilities.cpp:911:59: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable dec [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/imd.cpp:110:11: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable errno [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/vmdsock.cpp:115:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PF_INET [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/vmdsock.cpp:205:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable timeval [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/src/vmdsock.cpp:222:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable timeval [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestCompoundTransforms.cpp:113:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestCompoundTransforms.cpp:65:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Position [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestDuMMForces.cpp:314:50: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Free [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestDuMMForces.cpp:553:45: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Rigid [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestDuMMForces.cpp:64:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Dynamics [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestDuMMForces.cpp:756:44: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Rigid [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestDuMMForces.cpp:775:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Dynamics [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestEthane.cpp:101:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestEthane.cpp:52:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestEthane.cpp:61:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestEthane.cpp:82:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestEthane.cpp:92:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestFitMagnesiums.cpp:127:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestFitMagnesiums.cpp:89:79: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PDB [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestForeignBodyIds.cpp:86:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] 2.13.0 molmodel-3.1.0/tests/TestForeignBodyIds.cpp:86:40: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestLoadPdb.cpp:128:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestLoadPdb.cpp:213:26: style: Parameter 'argv' can be declared as const array [constParameter] head molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:117:70: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Pi [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:181:24: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SimTK_BOLTZMANN_CONSTANT_MD [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:340:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Dynamics [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:362:53: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable daltons [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:367:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable angstroms [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:461:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Velocity [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:521:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:610:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestNoseHooverThermostat.cpp:629:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestOxygenMolecule.cpp:83:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestPartitionerDihedrals.cpp:60:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] 2.13.0 molmodel-3.1.0/tests/TestPartitionerDihedrals.cpp:60:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestPartitionerDihedrals.cpp:90:41: style: C-style reference casting [cstyleCast] head molmodel-3.1.0/tests/TestPdb.cpp:117:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PDB [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestPdb.cpp:197:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestProtein.cpp:126:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestProtein.cpp:70:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] 2.13.0 molmodel-3.1.0/tests/TestProtein.cpp:70:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestRiboseMobilizer.cpp:140:89: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable YAxis [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestRna.cpp:59:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] 2.13.0 molmodel-3.1.0/tests/TestRna.cpp:59:25: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestSetTorsion.cpp:31:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Pi [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestShortPdbLines.cpp:25:67: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable PDB [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestShortPdbLines.cpp:40:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestVelocityRescalingThermostat.cpp:160:10: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestVelocityRescalingThermostat.cpp:165:5: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/TestVelocityRescalingThermostat.cpp:57:112: style: Parameter 'mobilityForces' can be declared as reference to const [constParameterReference] head molmodel-3.1.0/tests/TestVelocityRescalingThermostat.cpp:57:88: style: Parameter 'particleForces' can be declared as reference to const [constParameterReference] head molmodel-3.1.0/tests/TestWriteSimtimePdb.cpp:87:0: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] 2.13.0 molmodel-3.1.0/tests/TestWriteSimtimePdb.cpp:87:29: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/adhoc/RemoveMassCenterDrift.cpp:85:54: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Pi [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:147:14: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:176:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Velocity [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:203:34: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Velocity [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:63:31: error: Uninitialized variable: dummy [uninitvar] head molmodel-3.1.0/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:66:57: style: Parameter 'shouldTerminate' can be declared as reference to const [constParameterReference] head molmodel-3.1.0/tests/adhoc/RemoveMassCenterDriftWithOptimizer.cpp:70:38: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Velocity [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:1002:30: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable SpaceRotationSequence [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:223:35: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Position [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:252:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable parentIx [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:343:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Ang2Nm [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:358:57: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable parentIx [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:442:26: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Ang2Nm [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:445:23: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Ang2Nm [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:448:31: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:482:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:521:42: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Deg2Rad [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:669:51: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable LorentzBerthelot [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/adhoc/TestEthaneFromSimbody.cpp:879:48: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable InvalidClusterIndex [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/adhoc/TestMemoryUse.cpp:159:9: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable cout [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/adhoc/TestSimpleProtein.cpp:108:27: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Pi [valueFlowBailoutIncompleteVar] head molmodel-3.1.0/tests/adhoc/TestSimpleProtein.cpp:74:57: style: Parameter 'shouldTerminate' can be declared as reference to const [constParameterReference] head molmodel-3.1.0/tests/adhoc/TestSimpleProtein.cpp:78:32: debug: valueFlowConditionExpressions bailout: Skipping function due to incomplete variable Velocity [valueFlowBailoutIncompleteVar] DONE