rmgpy.pdep.Configuration

class rmgpy.pdep.Configuration(*species)

A representation of a molecular configuration on a potential energy surface.

E0

The ground-state energy of the configuration in J/mol.

Elist

Elist: numpy.ndarray

activeJRotor

activeJRotor: ‘bool’

activeKRotor

activeKRotor: ‘bool’

calculateCollisionFrequency(self, double T, double P, dict bathGas) → double

Return the value of the collision frequency in Hz at the given temperature T in K and pressure P in Pa. If a dictionary bathGas of bath gas species and corresponding mole fractions is given, the collision parameters of the bas gas species will be averaged with those of the species before computing the collision frequency.

Only the Lennard-Jones collision model is currently supported.

calculateDensityOfStates(self, ndarray Elist, bool activeJRotor=True, bool activeKRotor=True, bool rmgmode=False)

Calculate the density (and sum) of states for the configuration at the given energies above the ground state Elist in J/mol. The activeJRotor and activeKRotor flags control whether the J-rotor and/or K-rotor are treated as active (and therefore included in the density and sum of states). The computed density and sum of states arrays are stored on the object for future use.

cleanup(self)

Delete intermediate arrays used in computing k(T,P) values.

densStates

densStates: numpy.ndarray

generateCollisionMatrix(self, double T, ndarray densStates, ndarray Elist, ndarray Jlist=None) → ndarray

Return the collisional energy transfer probabilities matrix for the configuration at the given temperature T in K using the given energies Elist in kJ/mol and total angular momentum quantum numbers Jlist. The density of states of the configuration densStates in mol/kJ is also required.

getEnthalpy(self, double T) → double

Return the enthalpy in kJ/mol at the specified temperature T in K.

getEntropy(self, double T) → double

Return the entropy in J/mol*K at the specified temperature T in K.

getFreeEnergy(self, double T) → double

Return the Gibbs free energy in kJ/mol at the specified temperature T in K.

getHeatCapacity(self, double T) → double

Return the constant-pressure heat capacity in J/mol*K at the specified temperature T in K.

hasStatMech(self) → bool

Return True if all species in the configuration have statistical mechanics parameters, or False otherwise.

hasThermo(self) → bool

Return True if all species in the configuration have thermodynamics parameters, or False otherwise.

isBimolecular(self) → bool

Return True if the configuration represents a bimolecular reactant or product channel, or False otherwise.

isTransitionState(self) → bool

Return True if the configuration represents a transition state, or False otherwise.

isUnimolecular(self) → bool

Return True if the configuration represents a unimolecular isomer, or False otherwise.

mapDensityOfStates(self, ndarray Elist, ndarray Jlist=None)

Return a mapping of the density of states for the configuration to the given energies Elist in J/mol and, if the J-rotor is not active, the total angular momentum quantum numbers Jlist.

mapSumOfStates(self, ndarray Elist, ndarray Jlist=None)

Return a mapping of the density of states for the configuration to the given energies Elist in J/mol and, if the J-rotor is not active, the total angular momentum quantum numbers Jlist.

species

species: list

sumStates

sumStates: numpy.ndarray