A representation of a Reaction Mechanism Generator (RMG) job. The attributes are:
|inputFile||The path to the input file|
|databaseDirectory||The directory containing the RMG database|
|thermoLibraries||The thermodynamics libraries to load|
|reactionLibraries||The kinetics libraries to load|
|statmechLibraries||The statistical mechanics libraries to load|
|seedMechanisms||The seed mechanisms included in the model|
|kineticsFamilies||The kinetics families to use for reaction generation|
|kineticsDepositories||The kinetics depositories to use for looking up kinetics in each family|
|kineticsEstimator||The method to use to estimate kinetics: ‘group additivity’ or ‘rate rules’|
|solvent||If solvation estimates are required, the name of the solvent.|
|reactionModel||The core-edge reaction model generated by this job|
|reactionSystems||A list of the reaction systems used in this job|
|database||The RMG database used in this job|
|absoluteTolerance||The absolute tolerance used in the ODE/DAE solver|
|relativeTolerance||The relative tolerance used in the ODE/DAE solver|
|sensitivityAbsoluteTolerance||The absolute tolerance used in the ODE/DAE solver for the sensitivities|
|sensitivityRelativeTolerance||The relative tolerance used in the ODE/DAE solver for the sensitivities|
|fluxToleranceKeepInEdge||The relative species flux below which species are discarded from the edge|
|fluxToleranceMoveToCore||The relative species flux above which species are moved from the edge to the core|
|fluxToleranceInterrupt||The relative species flux above which the simulation will halt|
|maximumEdgeSpecies||The maximum number of edge species allowed at any time|
|minCoreSizeForPrune||Minimum number of core species before pruning is allowed|
|minSpeciesExistIterationsForPrune||Minimum number of iterations a species must exist before it can be pruned|
|filterReactions||Specify whether to filter reactions during model enlarging step|
|unimolecularThreshold||Array of flags indicating whether a species is above the unimolecular reaction threshold|
|bimolecularaThreshold||Array of flags indicating whether two species are above the bimolecular reaction threshold|
|unimolecularReact||Array of flags indicating whether a species should react unimolecularly in the enlarge step|
|bimolecularReact||Array of flags indicating whether two species should react in the enlarge step|
|termination||A list of termination targets (i.e
|speciesConstraints||Dictates the maximum number of atoms, carbons, electrons, etc. generated by RMG|
|outputDirectory||The directory used to save output files|
|verbosity||The level of logging verbosity for console output|
|saveRestartPeriod||The time period to periodically save a restart file (
|units||The unit system to use to save output files (currently must be ‘si’)|
|pressureDependence||Whether to process unimolecular (pressure-dependent) reaction networks|
|quantumMechanics||Whether to apply quantum mechanical calculations instead of group additivity to certain molecular types.|
|wallTime||The maximum amount of CPU time in the form DD:HH:MM:SS to expend on this job; used to stop gracefully so we can still get profiling information|
|initializationTime||The time at which the job was initiated, in seconds since the epoch (i.e. from time.time())|
|done||Whether the job has completed (there is nothing new to add)|
Check for a few common mistakes in the input file.
Check unwanted use of libraries: Liquid phase libraries in Gas phase simulation. Loading a Liquid phase library obtained in another solvent than the one defined in the input file. Other checks can be added here.
Clear all loaded information about the job (except the file paths).
Execute an RMG job using the command-line arguments args as returned
Complete the model generation.
Convert a chemkin mechanism chem.inp file to a cantera mechanism file chem.cti and save it in the cantera directory
Initialize an RMG job using the command-line arguments args as returned
Load an RMG job from the input file located at inputFile, or from the inputFile attribute if not given as a parameter.
Load an RMG-Java job from the input file located at inputFile, or from the inputFile attribute if not given as a parameter.
Load a restart file at path on disk.
Load an Thermo Estimation job from a thermo input file located at inputFile, or from the inputFile attribute if not given as a parameter.
Output a header containing identifying information about RMG to the log.
Read a meaningful line from an RMG-Java condition file object f, returning the line with any comments removed.
Attaches listener classes depending on the options found in the RMG input file.
Saves the output HTML, the Chemkin file, and the Restart file (if appropriate).
The restart file is only saved if self.saveRestartPeriod or self.done.
Save an RMG job to the input file located at path, or from the outputFile attribute if not given as a parameter.
Set up a logger for RMG to use to print output to stdout. The
verbose parameter is an integer specifying the amount of log text seen
at the console; the levels correspond to those of the
Uses gprof2dot to create a graphviz dot file of the profiling information.
This requires the gprof2dot package available via pip install gprof2dot. Render the result using the program ‘dot’ via a command like dot -Tps2 input.dot -o output.ps2.
Rendering the ps2 file to pdf requires an external pdf converter ps2pdf output.ps2 which produces a output.ps2.pdf file.