- a -

• addBondConstraint() : templateMolecule.cpp
• addStateConstraint() : templateMolecule.cpp
• assembleFullSymmetryList() : parseSymRxns.cpp
• assembleFullSymmetryListOnRxnCenter() : parseSymRxns.cpp
• assembleOffRxnCenterSymClasses() : parseSymRxns.cpp

- b -

• BroadcastString() : Scheduler.cpp , Scheduler.h

- c -

• clear_slave_data() : Scheduler.cpp
• clearMoleculeComplexIds() : NFoutput.cpp
• ConvergeAllData() : Scheduler.h , Scheduler.cpp
• ConvertBufferMapToString() : Scheduler.cpp , Scheduler.h
• convertModelScanToJobs() : Scheduler.h , Scheduler.cpp
• ConvertStringToBufferMap() : Scheduler.cpp , Scheduler.h
• ConvertStringToCString() : Scheduler.cpp , Scheduler.h
• createCompositeFunction() : parseFuncXML.cpp
• createFullSymMaps() : parseSymRxns.cpp
• createFunction() : parseFuncXML.cpp
• createLocalFunction() : parseFuncXML.cpp
• createMoleculeSymMap() : parseSymRxns.cpp
• createSymMap() : parseSymRxns.cpp

- d -

• dtoa() : Scheduler.cpp , Scheduler.h
• DynamicParallel() : Scheduler.cpp , Scheduler.h

- e -

• echo() : rnfRunner.cpp
• EmbarrassingParallel() : Scheduler.cpp , Scheduler.h
• endl() : NFstream.cpp , NFstream.h
• enterMainMenuLoop() : walk.cpp
• enterStepLoop() : walk.cpp
• equilibrate() : rnfRunner.cpp

- f -

• FinalizeMPI() : Scheduler.cpp , Scheduler.h
• findandreplace() : Scheduler.cpp , Scheduler.h

- g -

• getFileLine() : Scheduler.cpp , Scheduler.h
• getInput() : walk.cpp
• getPath() : Scheduler.cpp , Scheduler.h
• getPrintout() : walk.cpp
• getStringsFileline() : Scheduler.cpp , Scheduler.h
• getTestJobs() : Scheduler.cpp

- i -

• InitializeMPI() : Scheduler.cpp , Scheduler.h
• initSystemFromFlags() : NFsim.hh , NFsim.cpp
• isMoleculePermuationValid() : parseSymRxns.cpp
• itoa() : Scheduler.cpp , Scheduler.h

- j -

• job2str() : Scheduler.cpp

- l -

• load_to_buffer() : Scheduler.cpp , Scheduler.h

- m -

• main() : NFsim.cpp
• master_init() : Scheduler.cpp

- o -

• operator!=() : tinystr.h
• operator+() : tinystr.cpp , tinystr.h , tinystr.cpp , tinystr.h
• operator<() : tinystr.h
• operator<<() : system.cpp , complexList.cpp , NFstream.cpp , moleculeType.cpp , NFstream.h
• operator<=() : tinystr.h
• operator==() : tinystr.h
• operator>() : tinystr.h
• operator>=() : tinystr.h

- p -

• parseJobsFile() : Scheduler.cpp , Scheduler.h
• perr() : Scheduler.h , Scheduler.cpp
• print() : rnfRunner.cpp
• PrintFileBuffer() : Scheduler.cpp , Scheduler.h
• printFileLineOutput() : Scheduler.h
• printHelp() : NFsim.cpp
• printLogo() : NFsim.cpp
• printMainMenu() : walk.cpp
• printParallelJobOutput() : Scheduler.h , Scheduler.cpp
• printSpecificMolecule() : walk.cpp
• printSpecificMoleculeByUid() : walk.cpp
• printStepMenu() : walk.cpp
• push_stream() : Scheduler.h , Scheduler.cpp

- r -

• recv_from_master() : Scheduler.cpp , Scheduler.h
• recv_from_slave() : Scheduler.h , Scheduler.cpp
• runAgentCell() : agentcell.cpp , agentcell.hh
• runFromArgs() : NFsim.hh , NFsim.cpp
• runRNFscript() : NFsim.cpp

- s -

• schedulerInterpreter() : Scheduler.cpp , Scheduler.h
• send_to_master() : Scheduler.h , Scheduler.cpp
• send_to_slave() : Scheduler.cpp , Scheduler.h
• setParameter() : rnfRunner.cpp
• simulate() : rnfRunner.cpp
• slave_work() : Scheduler.cpp
• str2job() : Scheduler.cpp
• stringToStrings() : Scheduler.h , Scheduler.cpp

- t -

• test() : mttest.cpp
• TiXmlFOpen() : tinyxml.cpp

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