arkane.PressureDependenceJob¶
- class arkane.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, sensitivity_conditions=None, sensitivity_perturbation=0)¶
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.
- property Plist¶
The pressures at which the k(T,P) values are computed.
- property Pmax¶
The maximum pressure at which the computed k(T,P) values are valid, or
None
if not defined.
- property Pmin¶
The minimum pressure at which the computed k(T,P) values are valid, or
None
if not defined.
- property Tlist¶
The temperatures at which the k(T,P) values are computed.
- property Tmax¶
The maximum temperature at which the computed k(T,P) values are valid, or
None
if not defined.
- property 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(output_directory, file_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.
- execute(output_file, plot, file_format='pdf', print_summary=True)¶
Execute a PressureDependenceJob
- fit_interpolation_model(Tdata, Pdata, kdata, k_units)¶
Fit an interpolation model to a pressure dependent rate
- fit_interpolation_models()¶
Fit all pressure dependent rates with interpolation models
- generate_P_list()¶
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.
- generate_T_list()¶
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.
- initialize()¶
Initialize a PressureDependenceJob
- property maximum_grain_size¶
The maximum allowed energy grain size, or
None
if not defined.
- plot(output_directory)¶
Plot pressure dependent rates
- save(output_file)¶
Save the output of a pressure dependent job
- save_input_file(path)¶
Save an Arkane input file for the pressure dependence job to path on disk.