Index

A

activity() (pycatkin.classes.system.System method) add_energy_landscape() (pycatkin.classes.system.System method)

add_reaction() (pycatkin.classes.system.System method) add_reactor() (pycatkin.classes.system.System method) add_state() (pycatkin.classes.system.System method)

C

calc_electronic_energy() (pycatkin.classes.state.ScalingState method) (pycatkin.classes.state.State method) calc_free_energy() (pycatkin.classes.state.ScalingState method) (pycatkin.classes.state.State method) calc_rate_constants() (pycatkin.classes.reaction.Reaction method) calc_reaction_energy() (pycatkin.classes.reaction.Reaction method) (pycatkin.classes.reaction.ReactionDerivedReaction method) (pycatkin.classes.reaction.UserDefinedReaction method) calc_rotational_contrib() (pycatkin.classes.state.State method)

calc_translational_contrib() (pycatkin.classes.state.State method) calc_vibrational_contrib() (pycatkin.classes.state.State method) calc_zpe() (pycatkin.classes.state.State method) check_rate_constants() (pycatkin.classes.system.System method) Cite CO oxidation in a reactor CO oxidation volcano plot Code overview construct_energy_landscape() (pycatkin.classes.energy.Energy method) CSTReactor (class in pycatkin.classes.reactor)

D

degree_of_rate_control() (pycatkin.classes.system.System method) Direct methane to methanol

draw_energy_landscape() (pycatkin.classes.energy.Energy method) draw_energy_landscape_simple() (pycatkin.classes.energy.Energy method)

E

Energy (class in pycatkin.classes.energy)

evaluate_energy_span_model() (pycatkin.classes.energy.Energy method)

F

find_steady() (pycatkin.classes.system.System method)

G

get_atoms() (pycatkin.classes.state.State method) get_correlated_state_noises() (pycatkin.classes.uncertainty.Uncertainty method) get_dynamic_indices() (pycatkin.classes.reactor.CSTReactor method) (pycatkin.classes.reactor.InfiniteDilutionReactor method) (pycatkin.classes.reactor.Reactor method) get_free_energy() (pycatkin.classes.state.State method) get_mean_property_value() (pycatkin.classes.uncertainty.Uncertainty method)

get_noise() (pycatkin.classes.uncertainty.Uncertainty method) get_noisy_sys_samples() (pycatkin.classes.uncertainty.Uncertainty method) get_potential_energy() (pycatkin.classes.state.State method) get_reaction_barriers() (pycatkin.classes.reaction.Reaction method) get_reaction_energy() (pycatkin.classes.reaction.Reaction method) get_vibrations() (pycatkin.classes.state.State method) Glossary

I

InfiniteDilutionReactor (class in pycatkin.classes.reactor)

Installation

J

jacobian() (pycatkin.classes.reactor.CSTReactor method) (pycatkin.classes.reactor.InfiniteDilutionReactor method) (pycatkin.classes.reactor.Reactor method)

L

Literature

M

module pycatkin.classes.energy pycatkin.classes.reaction pycatkin.classes.reactor pycatkin.classes.state pycatkin.classes.system pycatkin.classes.uncertainty pycatkin.constants pycatkin.functions

N

names_to_indices() (pycatkin.classes.system.System method)

P

plot_transient() (pycatkin.classes.system.System method) pycatkin.classes.energy module pycatkin.classes.reaction module pycatkin.classes.reactor module pycatkin.classes.state module

pycatkin.classes.system module pycatkin.classes.uncertainty module pycatkin.constants module pycatkin.functions module

R

Reaction (class in pycatkin.classes.reaction) reaction_derivatives() (pycatkin.classes.system.System method) reaction_terms() (pycatkin.classes.system.System method) ReactionDerivedReaction (class in pycatkin.classes.reaction)

Reactor (class in pycatkin.classes.reactor) rhs() (pycatkin.classes.reactor.CSTReactor method) (pycatkin.classes.reactor.InfiniteDilutionReactor method) (pycatkin.classes.reactor.Reactor method) run_and_return_tof() (pycatkin.classes.system.System method)

S

save_energy() (pycatkin.classes.state.State method) save_pdb() (pycatkin.classes.state.ScalingState method) (pycatkin.classes.state.State method) save_pickle() (pycatkin.classes.energy.Energy method) (pycatkin.classes.reaction.Reaction method) (pycatkin.classes.reactor.Reactor method) (pycatkin.classes.state.ScalingState method) (pycatkin.classes.state.State method) (pycatkin.classes.system.System method) save_vibrations() (pycatkin.classes.state.State method)

ScalingState (class in pycatkin.classes.state) set_correlated_state_noises() (pycatkin.classes.uncertainty.Uncertainty method) set_energy_modifier() (pycatkin.classes.state.State method) set_indices() (pycatkin.classes.reactor.Reactor method) set_parameters() (pycatkin.classes.system.System method) set_scaling() (pycatkin.classes.reactor.Reactor method) solve_odes() (pycatkin.classes.system.System method) species_jacobian() (pycatkin.classes.system.System method) species_odes() (pycatkin.classes.system.System method) State (class in pycatkin.classes.state) System (class in pycatkin.classes.system)

U

Uncertainty (class in pycatkin.classes.uncertainty)

UserDefinedReaction (class in pycatkin.classes.reaction)

V

view_atoms() (pycatkin.classes.state.ScalingState method) (pycatkin.classes.state.State method)

W

write_results() (pycatkin.classes.system.System method)