rmgpy.cantherm.PressureDependenceJob

class rmgpy.cantherm.PressureDependenceJob(network, Tmin=None, Tmax=None, Tcount=0, Tlist=None, Pmin=None, Pmax=None, Pcount=0, Plist=None, maximumGrainSize=None, minimumGrainCount=0, method=None, interpolationModel=None, maximumAtoms=None, activeKRotor=True, activeJRotor=True, rmgmode=False)

A representation of a pressure dependence job. The attributes are:

Attribute Description
Tmin The minimum temperature at which to compute \(k(T,P)\) values
Tmax The maximum temperature at which to compute \(k(T,P)\) values
Tcount The number of temperatures at which to compute \(k(T,P)\) values
Pmin The minimum pressure at which to compute \(k(T,P)\) values
Pmax The maximum pressure at which to compute \(k(T,P)\) values
Pcount The number of pressures at which to compute \(k(T,P)\) values
Emin The minimum energy to use to compute \(k(T,P)\) values
Emax The maximum energy to use to compute \(k(T,P)\) values
maximumGrainSize The maximum energy grain size to use to compute \(k(T,P)\) values
minimumGrainCount The minimum number of energy grains to use to compute \(k(T,P)\) values
method The method to use to reduce the master equation to \(k(T,P)\) values
interpolationModel The interpolation model to fit to the computed \(k(T,P)\) values
maximumAtoms The maximum number of atoms to apply pressure dependence to (in RMG jobs)
activeKRotor A flag indicating whether to treat the K-rotor as active or adiabatic
activeJRotor A flag indicating whether to treat the J-rotor as active or adiabatic
rmgmode A flag that toggles “RMG mode”, described below
network The unimolecular reaction network
Tlist An array of temperatures at which to compute \(k(T,P)\) values
Plist An array of pressures at which to compute \(k(T,P)\) values
Elist An array of energies to use to compute \(k(T,P)\) values

In RMG mode, several alterations to the k(T,P) algorithm are made both for speed and due to the nature of the approximations used:

  • Densities of states are not computed for product channels
  • Arbitrary rigid rotor moments of inertia are included in the active modes; these cancel in the ILT and equilibrium expressions
  • k(E) for each path reaction is computed in the direction A -> products, where A is always an explored isomer; the high-P kinetics are reversed if necessary for this purpose
  • Thermodynamic parameters are always used to compute the reverse k(E) from the forward k(E) for each path reaction

RMG mode should be turned off by default except in RMG jobs.

Plist

The pressures at which the k(T,P) values are computed.

Pmax

The maximum pressure at which the computed k(T,P) values are valid, or None if not defined.

Pmin

The minimum pressure at which the computed k(T,P) values are valid, or None if not defined.

Tlist

The temperatures at which the k(T,P) values are computed.

Tmax

The maximum temperature at which the computed k(T,P) values are valid, or None if not defined.

Tmin

The minimum temperature at which the computed k(T,P) values are valid, or None if not defined.

copy()

Return a copy of the pressure dependence job.

draw(outputDirectory, format='pdf')

Generate a PDF drawing of the pressure-dependent reaction network. This requires that Cairo and its Python wrapper be available; if not, the drawing is not generated.

You may also generate different formats of drawings, by changing format to one of the following: pdf, svg, png.

generatePressureList()

Returns an array of pressures based on the interpolation model, minimum and maximum pressures Pmin and Pmax in Pa, and the number of pressures Pcount. For Chebyshev polynomials a Gauss-Chebyshev distribution is used; for all others a linear distribution on an logarithmic pressure domain is used. Note that the Gauss-Chebyshev grid does not place Pmin and Pmax at the endpoints, yet the interpolation is still valid up to these values.

generateTemperatureList()

Returns an array of temperatures based on the interpolation model, minimum and maximum temperatures Tmin and Tmax in K, and the number of temperatures Tcount. For Chebyshev polynomials a Gauss-Chebyshev distribution is used; for all others a linear distribution on an inverse temperature domain is used. Note that the Gauss-Chebyshev grid does not place Tmin and Tmax at the endpoints, yet the interpolation is still valid up to these values.

maximumGrainSize

The maximum allowed energy grain size, or None if not defined.

saveInputFile(path)

Save a CanTherm input file for the pressure dependence job to path on disk.