rmgpy.pdep.
Network
(label='', isomers=None, reactants=None, products=None, pathReactions=None, bathGas=None)¶A representation of a unimolecular reaction network. The attributes are:
Attribute | Description |
---|---|
isomers | A list of the unimolecular isomers in the network |
reactants | A list of the bimolecular reactant channels in the network |
products | A list of the bimolecular product channels in the network |
pathReactions | A list of “path” reaction objects that connect adjacent isomers (the high-pressure-limit) |
bathGas | A dictionary of the bath gas species (keys) and their mole fractions (values) |
netReactions | A list of “net” reaction objects that connect any pair of isomers |
T | The current temperature in K |
P | The current pressure in bar |
Elist | The current array of energy grains in kJ/mol |
Jlist | The current array of total angular momentum quantum numbers |
Nisom | The number of unimolecular isomers in the network |
Nreac | The number of bimolecular reactant channels in the network |
Nprod | The number of bimolecular product channels in the network |
Ngrains | The number of energy grains |
NJ | The number of angular momentum grains |
activeKRotor | True if the K-rotor is treated as active, False if treated as adiabatic |
activeJRotor | True if the J-rotor is treated as active, False if treated as adiabatic |
rmgmode | True if in RMG mode, False otherwise |
applyChemicallySignificantEigenvaluesMethod
(lumpingOrder=None)¶Compute the phenomenological rate coefficients \(k(T,P)\) at the current conditions using the chemically-significant eigenvalues method. If a lumpingOrder is provided, the algorithm will attempt to lump the configurations (given by index) in the order provided, and return a reduced set of \(k(T,P)\) values.
applyModifiedStrongCollisionMethod
(efficiencyModel='default')¶Compute the phenomenological rate coefficients \(k(T,P)\) at the current conditions using the modified strong collision method.
applyReservoirStateMethod
()¶Compute the phenomenological rate coefficients \(k(T,P)\) at the current conditions using the reservoir state method.
calculateCollisionModel
()¶Calculate the matrix of first-order rate coefficients for collisional population transfer between grains for each isomer, including the corresponding collision frequencies.
calculateDensitiesOfStates
()¶Calculate the densities of states of each configuration that has states data. The densities of states are computed such that they can be applied to each temperature in the range of interest by interpolation.
calculateEquilibriumRatios
()¶Return an array containing the fraction of each isomer and reactant channel present at equilibrium, as determined from the Gibbs free energy and using the concentration equilibrium constant \(K_\mathrm{c}\). These values are ratios, and the absolute magnitude is not guaranteed; however, the implementation scales the elements of the array so that they sum to unity.
calculateMicrocanonicalRates
()¶Calculate and return arrays containing the microcanonical rate coefficients \(k(E)\) for the isomerization, dissociation, and association path reactions in the network.
getAllSpecies
()¶Return a list of all unique species in the network, including all isomers, reactant and product channels, and bath gas species.
initialize
(Tmin, Tmax, Pmin, Pmax, maximumGrainSize=0.0, minimumGrainCount=0, activeJRotor=True, activeKRotor=True, rmgmode=False)¶Initialize a pressure dependence calculation by computing several quantities that are independent of the conditions. You must specify the temperature and pressure ranges of interesting using Tmin and Tmax in K and Pmin and Pmax in Pa. You must also specify the maximum energy grain size grainSize in J/mol and/or the minimum number of grains grainCount.
invalidate
()¶Mark the network as in need of a new calculation to determine the pressure-dependent rate coefficients
mapDensitiesOfStates
()¶Map the overall densities of states to the current energy grains. Semi-logarithmic interpolation will be used if the grain sizes of Elist0 and Elist do not match; this should not be a significant source of error as long as the grain sizes are sufficiently small.
printSummary
(level=20)¶Print a formatted list of information about the current network. Each molecular configuration - unimolecular isomers, bimolecular reactant channels, and bimolecular product channels - is given along with its energy on the potential energy surface. The path reactions connecting adjacent molecular configurations are also given, along with their energies on the potential energy surface. The level parameter controls the level of logging to which the summary is written, and is DEBUG by default.
selectEnergyGrains
(T, grainSize=0.0, grainCount=0)¶Select a suitable list of energies to use for subsequent calculations. This is done by finding the minimum and maximum energies on the potential energy surface, then adding a multiple of \(k_\mathrm{B} T\) onto the maximum energy.
You must specify either the desired grain spacing grainSize in J/mol or the desired number of grains Ngrains, as well as a temperature T in K to use for the equilibrium calculation. You can specify both grainSize and grainCount, in which case the one that gives the more accurate result will be used (i.e. they represent a maximum grain size and a minimum number of grains). An array containing the energy grains in J/mol is returned.
setConditions
(T, P, ymB=None)¶Set the current network conditions to the temperature T in K and pressure P in Pa. All of the internal variables are updated accordingly if they are out of date. For example, those variables that depend only on temperature will not be recomputed if the temperature is the same.
solveFullME
(tlist, x0)¶Directly solve the full master equation using a stiff ODE solver. Pass the reaction network to solve, the temperature T in K and pressure P in Pa to solve at, the energies Elist in J/mol to use, the output time points tlist in s, the initial total populations x0, the full master equation matrix M, the accounting matrix indices relating isomer and energy grain indices to indices of the master equation matrix, and the densities of states densStates in mol/J of each isomer. Returns the times in s, population distributions for each isomer, and total population profiles for each configuration.
solveReducedME
(tlist, x0)¶Directly solve the reduced master equation using a stiff ODE solver. Pass the output time points tlist in s and the initial total populations x0. Be sure to run one of the methods for generating \(k(T,P)\) values before calling this method. Returns the times in s, population distributions for each isomer, and total population profiles for each configuration.