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.

active_j_rotor

‘bool’

Type:

active_j_rotor

active_k_rotor

‘bool’

Type:

active_k_rotor

calculate_collision_frequency(self, double T, double P, dict bath_gas) → 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 bath_gas 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.

calculate_density_of_states(self, ndarray e_list, bool active_j_rotor=True, bool active_k_rotor=True, bool rmgmode=False)

Calculate the density (and sum) of states for the configuration at the given energies above the ground state e_list in J/mol. The active_j_rotor and active_k_rotor 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.

dens_states

numpy.ndarray

Type:

dens_states

e_list

numpy.ndarray

Type:

e_list

energy_correction

‘float’

Type:

energy_correction

generate_collision_matrix(self, double T, ndarray dens_states, ndarray e_list, ndarray j_list=None) → ndarray

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

get_enthalpy(self, double T) → double

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

get_entropy(self, double T) → double

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

get_free_energy(self, double T) → double

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

get_heat_capacity(self, double T) → double

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

has_statmech(self) → bool

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

has_thermo(self) → bool

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

is_bimolecular(self) → bool

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

is_termolecular(self) → bool

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

is_transition_state(self) → bool

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

is_unimolecular(self) → bool

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

map_density_of_states(self, ndarray e_list, ndarray j_list=None)

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

map_sum_of_states(self, ndarray e_list, ndarray j_list=None)

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

species

list

Type:

species

sum_states

numpy.ndarray

Type:

sum_states