Index

_

__getattr__() (catmap.analyze.matrix_map.MatrixMap method) (catmap.ReactionModelWrapper method) (catmap.analyze.mechanism.MechanismAnalysis method) (catmap.analyze.scaling.ScalingAnalysis method) (catmap.analyze.vector_map.VectorMap method) (catmap.mappers.mapper_base.MapperBase method) (catmap.mappers.min_resid_mapper.MinResidMapper method) (catmap.parsers.parser_base.ParserBase method) (catmap.parsers.table_parser.TableParser method) (catmap.scalers.generalized_linear_scaler.GeneralizedLinearScaler method) (catmap.scalers.null_scaler.NullScaler method) (catmap.scalers.scaler_base.ScalerBase method) (catmap.scalers.thermodynamic_scaler.ThermodynamicScaler method) (catmap.solvers.integrated_rate_control_solver.IntegratedRateControlSolver method) (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.solver_base.SolverBase method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method) (catmap.thermodynamics.first_order_interactions.FirstOrderInteractions method) (catmap.thermodynamics.second_order_interactions.SecondOrderInteractions method) __getattribute__() (catmap.analyze.matrix_map.MatrixMap method) (catmap.ReactionModelWrapper method) (catmap.analyze.mechanism.MechanismAnalysis method) (catmap.analyze.scaling.ScalingAnalysis method) (catmap.analyze.vector_map.VectorMap method) (catmap.mappers.mapper_base.MapperBase method) (catmap.mappers.min_resid_mapper.MinResidMapper method) (catmap.parsers.parser_base.ParserBase method) (catmap.parsers.table_parser.TableParser method) (catmap.scalers.generalized_linear_scaler.GeneralizedLinearScaler method) (catmap.scalers.null_scaler.NullScaler method) (catmap.scalers.scaler_base.ScalerBase method) (catmap.scalers.thermodynamic_scaler.ThermodynamicScaler method) (catmap.solvers.integrated_rate_control_solver.IntegratedRateControlSolver method) (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.solver_base.SolverBase method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method) (catmap.thermodynamics.first_order_interactions.FirstOrderInteractions method) (catmap.thermodynamics.second_order_interactions.SecondOrderInteractions method) __init__() (catmap.analyze.analysis_base.MapPlot method) (catmap.analyze.analysis_base.MechanismPlot method) (catmap.analyze.analysis_base.ScalingPlot method) (catmap.analyze.matrix_map.MatrixMap method) (catmap.analyze.mechanism.MechanismAnalysis method) (catmap.analyze.scaling.ScalingAnalysis method) (catmap.analyze.vector_map.VectorMap method) (catmap.mappers.mapper_base.MapperBase method) (catmap.mappers.min_resid_mapper.MinResidMapper method) (catmap.model.ReactionModel method) (catmap.parsers.parser_base.ParserBase method) (catmap.parsers.table_parser.TableParser method) (catmap.scalers.generalized_linear_scaler.GeneralizedLinearScaler method) (catmap.scalers.null_scaler.NullScaler method) (catmap.scalers.scaler_base.ScalerBase method) (catmap.scalers.thermodynamic_scaler.ThermodynamicScaler method) (catmap.solvers.integrated_rate_control_solver.IntegratedRateControlSolver method) (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.solver_base.NewtonRoot method) (catmap.solvers.solver_base.SolverBase method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method) (catmap.thermodynamics.first_order_interactions.FirstOrderInteractions method) (catmap.thermodynamics.second_order_interactions.SecondOrderInteractions method) __iter__() (catmap.solvers.solver_base.NewtonRoot method) __module__ (catmap.analyze.analysis_base.MapPlot attribute) (catmap.ReactionModelWrapper attribute) (catmap.analyze.analysis_base.MechanismPlot attribute) (catmap.analyze.analysis_base.ScalingPlot attribute) (catmap.analyze.matrix_map.MatrixMap attribute) (catmap.analyze.mechanism.MechanismAnalysis attribute) (catmap.analyze.scaling.ScalingAnalysis attribute) (catmap.analyze.vector_map.VectorMap attribute) (catmap.mappers.mapper_base.MapperBase attribute) (catmap.mappers.min_resid_mapper.MinResidMapper attribute) (catmap.model.ReactionModel attribute) (catmap.parsers.parser_base.ParserBase attribute) (catmap.parsers.table_parser.TableParser attribute) (catmap.scalers.generalized_linear_scaler.GeneralizedLinearScaler attribute) (catmap.scalers.null_scaler.NullScaler attribute) (catmap.scalers.scaler_base.ScalerBase attribute) (catmap.scalers.thermodynamic_scaler.ThermodynamicScaler attribute) (catmap.solvers.integrated_rate_control_solver.IntegratedRateControlSolver attribute) (catmap.solvers.mean_field_solver.MeanFieldSolver attribute) (catmap.solvers.solver_base.NewtonRoot attribute) (catmap.solvers.solver_base.SolverBase attribute) (catmap.solvers.steady_state_solver.SteadyStateSolver attribute) (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections attribute) (catmap.thermodynamics.first_order_interactions.FirstOrderInteractions attribute) (catmap.thermodynamics.second_order_interactions.SecondOrderInteractions attribute) __setattr__() (catmap.analyze.matrix_map.MatrixMap method) (catmap.ReactionModelWrapper method) (catmap.analyze.mechanism.MechanismAnalysis method) (catmap.analyze.scaling.ScalingAnalysis method) (catmap.analyze.vector_map.VectorMap method) (catmap.mappers.mapper_base.MapperBase method) (catmap.mappers.min_resid_mapper.MinResidMapper method) (catmap.parsers.parser_base.ParserBase method) (catmap.parsers.table_parser.TableParser method) (catmap.scalers.generalized_linear_scaler.GeneralizedLinearScaler method) (catmap.scalers.null_scaler.NullScaler method) (catmap.scalers.scaler_base.ScalerBase method) (catmap.scalers.thermodynamic_scaler.ThermodynamicScaler method) (catmap.solvers.integrated_rate_control_solver.IntegratedRateControlSolver method) (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.solver_base.SolverBase method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method) (catmap.thermodynamics.first_order_interactions.FirstOrderInteractions method) (catmap.thermodynamics.second_order_interactions.SecondOrderInteractions method)

_bar2Pa (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections attribute) _baseparse() (catmap.parsers.parser_base.ParserBase method) (catmap.parsers.table_parser.TableParser method) _get_echem_corrections() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method) _header() (catmap.model.ReactionModel method) _kJmol2eV (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections attribute) _token() (catmap.model.ReactionModel method)

A

add_dict_in_place() (in module catmap.functions) adsorption_to_reaction_energies() (catmap.model.ReactionModel method) approach_to_equilibrium_pressure() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method)

array_to_map() (catmap.model.ReactionModel static method) average_transition_state() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method)

B

bisect_descriptor_line() (catmap.mappers.min_resid_mapper.MinResidMapper method) bisect_interaction_strength() (catmap.solvers.steady_state_solver.SteadyStateSolver method)

boltzmann_coverages() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method) boltzmann_vector() (in module catmap.analyze.analysis_base)

C

cartesian_product() (in module catmap.functions) catmap (module) catmap.analyze (module) catmap.analyze.analysis_base (module) catmap.analyze.matrix_map (module) catmap.analyze.mechanism (module) catmap.analyze.scaling (module) catmap.analyze.vector_map (module) catmap.cli (module) catmap.data (module) catmap.data.hbond_data (module) catmap.data.parameter_data (module) catmap.data.regular_expressions (module) catmap.data.templates (module) catmap.functions (module) catmap.mappers (module) catmap.mappers.mapper_base (module) catmap.mappers.min_resid_mapper (module) catmap.model (module) catmap.parsers (module) catmap.parsers.parser_base (module)

catmap.parsers.table_parser (module) catmap.scalers (module) catmap.scalers.generalized_linear_scaler (module) catmap.scalers.null_scaler (module) catmap.scalers.scaler_base (module) catmap.scalers.thermodynamic_scaler (module) catmap.solvers (module) catmap.solvers.integrated_rate_control_solver (module) catmap.solvers.mean_field_solver (module) catmap.solvers.solver_base (module) catmap.solvers.steady_state_solver (module) catmap.thermodynamics (module) catmap.thermodynamics.enthalpy_entropy (module) catmap.thermodynamics.first_order_interactions (module) catmap.thermodynamics.second_order_interactions (module) compatibility_check() (catmap.model.ReactionModel method) compile() (catmap.solvers.integrated_rate_control_solver.IntegratedRateControlSolver method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) concentration_pressure() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method) constrain_coverages() (catmap.solvers.steady_state_solver.SteadyStateSolver method) constrained_relaxation() (in module catmap.functions) convert_formation_energies() (in module catmap.functions)

D

descriptor_space_analysis() (catmap.model.ReactionModel method)

draw() (catmap.analyze.analysis_base.MechanismPlot method) (catmap.analyze.mechanism.MechanismAnalysis method)

E

error_norm() (catmap.thermodynamics.first_order_interactions.FirstOrderInteractions method) (catmap.thermodynamics.second_order_interactions.SecondOrderInteractions method) estimate_hbond_corr() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method)

expression_string_to_list() (catmap.model.ReactionModel method)

F

fetch_all_output_variables() (in module catmap.functions) FirstOrderInteractions (class in catmap.thermodynamics.first_order_interactions) fit() (catmap.thermodynamics.first_order_interactions.FirstOrderInteractions method) (catmap.thermodynamics.second_order_interactions.SecondOrderInteractions method) fit_interaction_parameter() (catmap.thermodynamics.first_order_interactions.FirstOrderInteractions method) (catmap.thermodynamics.second_order_interactions.SecondOrderInteractions method) fit_old() (catmap.thermodynamics.first_order_interactions.FirstOrderInteractions method) (catmap.thermodynamics.second_order_interactions.SecondOrderInteractions method) fit_shomate() (in module catmap.thermodynamics.enthalpy_entropy)

fixed_enthalpy_entropy_adsorbate() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method) fixed_enthalpy_entropy_gas() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method) fixed_entropy_gas() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method) frozen_adsorbate() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method) frozen_fixed_entropy_gas() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method) frozen_gas() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method)

G

GeneralizedLinearScaler (class in catmap.scalers.generalized_linear_scaler) generate_echem_species_definitions() (catmap.model.ReactionModel method) generate_echem_TS() (catmap.model.ReactionModel method) generate_echem_TS_energies() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method) generate_hbond_dict() (in module catmap.data.hbond_data) generate_static_functions() (catmap.model.ReactionModel method) get_adsorbate_coefficient_matrix() (catmap.scalers.generalized_linear_scaler.GeneralizedLinearScaler method) get_apparent_activation_energy() (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) get_coefficient_matrix() (catmap.scalers.generalized_linear_scaler.GeneralizedLinearScaler method) get_colors() (in module catmap.analyze.analysis_base) get_composition() (in module catmap.functions) get_coverage() (catmap.solvers.steady_state_solver.SteadyStateSolver method) get_coverage_map() (catmap.mappers.min_resid_mapper.MinResidMapper method) get_directional_rates() (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) get_electronic_energies() (catmap.scalers.generalized_linear_scaler.GeneralizedLinearScaler method) (catmap.scalers.null_scaler.NullScaler method) (catmap.scalers.scaler_base.ScalerBase method) (catmap.scalers.thermodynamic_scaler.ThermodynamicScaler method) get_elem_ec() (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) get_empty_site_cvgs() (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) get_energetics() (catmap.scalers.generalized_linear_scaler.GeneralizedLinearScaler method) (catmap.scalers.null_scaler.NullScaler method) (catmap.scalers.scaler_base.ScalerBase method) (catmap.scalers.thermodynamic_scaler.ThermodynamicScaler method) get_energy_error() (catmap.thermodynamics.first_order_interactions.FirstOrderInteractions method) (catmap.thermodynamics.second_order_interactions.SecondOrderInteractions method) get_error() (catmap.analyze.scaling.ScalingAnalysis method) get_formation_energy_interaction_parameters() (catmap.scalers.generalized_linear_scaler.GeneralizedLinearScaler method) (catmap.scalers.thermodynamic_scaler.ThermodynamicScaler method) get_formation_energy_parameters() (catmap.scalers.generalized_linear_scaler.GeneralizedLinearScaler method) (catmap.scalers.thermodynamic_scaler.ThermodynamicScaler method) get_free_energies() (catmap.scalers.generalized_linear_scaler.GeneralizedLinearScaler method) (catmap.scalers.null_scaler.NullScaler method) (catmap.scalers.scaler_base.ScalerBase method) (catmap.scalers.thermodynamic_scaler.ThermodynamicScaler method) get_frequency_cutoff() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method) get_ideal_coverages() (catmap.solvers.steady_state_solver.SteadyStateSolver method) get_included_indices() (catmap.analyze.matrix_map.MatrixMap method) (catmap.analyze.vector_map.VectorMap method) get_initial_coverage() (catmap.mappers.min_resid_mapper.MinResidMapper method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) get_initial_coverage_from_map() (catmap.mappers.min_resid_mapper.MinResidMapper method) get_integrated_DRC_rate() (catmap.solvers.integrated_rate_control_solver.IntegratedRateControlSolver method) get_interacting_coverages() (catmap.solvers.steady_state_solver.SteadyStateSolver method) get_interacting_energies() (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.steady_state_solver.SteadyStateSolver method)

get_interaction_info() (catmap.thermodynamics.first_order_interactions.FirstOrderInteractions method) (catmap.thermodynamics.second_order_interactions.SecondOrderInteractions method) get_interaction_matrix() (catmap.thermodynamics.first_order_interactions.FirstOrderInteractions method) (catmap.thermodynamics.second_order_interactions.SecondOrderInteractions method) get_interaction_scaling_matrix() (catmap.thermodynamics.first_order_interactions.FirstOrderInteractions method) (catmap.thermodynamics.second_order_interactions.SecondOrderInteractions method) get_interaction_transition_state_scaling_matrix() (catmap.thermodynamics.first_order_interactions.FirstOrderInteractions method) (catmap.thermodynamics.second_order_interactions.SecondOrderInteractions method) get_labels() (catmap.analyze.matrix_map.MatrixMap method) (catmap.analyze.vector_map.VectorMap method) get_options() (in module catmap.cli) get_output_map() (catmap.mappers.mapper_base.MapperBase method) (catmap.mappers.min_resid_mapper.MinResidMapper method) get_point_coverage() (catmap.mappers.min_resid_mapper.MinResidMapper method) get_point_output() (catmap.mappers.mapper_base.MapperBase method) (catmap.mappers.min_resid_mapper.MinResidMapper method) get_pts_cols() (catmap.analyze.matrix_map.MatrixMap method) (catmap.analyze.vector_map.VectorMap method) get_rate() (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) get_rate_constants() (catmap.solvers.steady_state_solver.SteadyStateSolver method) get_rate_control() (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) get_residual() (catmap.solvers.steady_state_solver.SteadyStateSolver method) get_rxn_energy() (catmap.model.ReactionModel method) get_rxn_index_from_TS() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method) get_rxn_order() (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) get_rxn_parameters() (catmap.scalers.generalized_linear_scaler.GeneralizedLinearScaler method) (catmap.scalers.null_scaler.NullScaler method) (catmap.scalers.scaler_base.ScalerBase method) (catmap.scalers.thermodynamic_scaler.ThermodynamicScaler method) get_rxn_rates() (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) get_selectivity() (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) get_selectivity_control() (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) get_state_energy() (catmap.model.ReactionModel method) get_steady_state_coverage() (catmap.solvers.steady_state_solver.SteadyStateSolver method) get_thermodynamic_corrections() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method) get_thermodynamic_energies() (catmap.scalers.generalized_linear_scaler.GeneralizedLinearScaler method) (catmap.scalers.null_scaler.NullScaler method) (catmap.scalers.scaler_base.ScalerBase method) (catmap.scalers.thermodynamic_scaler.ThermodynamicScaler method) get_transition_state_coefficient_matrix() (catmap.scalers.generalized_linear_scaler.GeneralizedLinearScaler method) get_transition_state_scaling_matrix() (catmap.scalers.generalized_linear_scaler.GeneralizedLinearScaler method) get_TS_weight_matrix() (catmap.thermodynamics.first_order_interactions.FirstOrderInteractions method) (catmap.thermodynamics.second_order_interactions.SecondOrderInteractions method) get_turnover_frequency() (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) griddata() (in module catmap)

H

harmonic_adsorbate() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method) hbond_electrochemical() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method)

hbond_with_estimates_electrochemical() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method)

I

ideal_gas() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method) ideal_steady_state_function() (catmap.solvers.steady_state_solver.SteadyStateSolver method) ideal_steady_state_jacobian() (catmap.solvers.steady_state_solver.SteadyStateSolver method) include_labels_to_idxs() (catmap.analyze.matrix_map.MatrixMap method) (catmap.analyze.vector_map.VectorMap method)

IntegratedRateControlSolver (class in catmap.solvers.integrated_rate_control_solver) interacting_steady_state_function() (catmap.solvers.steady_state_solver.SteadyStateSolver method) interacting_steady_state_jacobian() (catmap.solvers.steady_state_solver.SteadyStateSolver method)

J

jacobian_equations() (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.steady_state_solver.SteadyStateSolver method)

L

label_maker() (catmap.analyze.mechanism.MechanismAnalysis method) linear_regression() (in module catmap.functions) linear_response() (catmap.thermodynamics.first_order_interactions.FirstOrderInteractions static method) (catmap.thermodynamics.second_order_interactions.SecondOrderInteractions static method)

load() (catmap.model.ReactionModel method) (in module catmap) load_data_file() (catmap.model.ReactionModel method) log() (catmap.model.ReactionModel method)

M

main() (in module catmap.cli) make_standalone() (catmap.model.ReactionModel method) map_to_array() (catmap.model.ReactionModel static method) MapperBase (class in catmap.mappers.mapper_base) MapPlot (class in catmap.analyze.analysis_base) match_keys() (in module catmap.cli) match_regex() (in module catmap.functions) MatrixMap (class in catmap.analyze.matrix_map)

maxsteps (catmap.solvers.solver_base.NewtonRoot attribute) MeanFieldSolver (class in catmap.solvers.mean_field_solver) MechanismAnalysis (class in catmap.analyze.mechanism) MechanismPlot (class in catmap.analyze.analysis_base) MinResidMapper (class in catmap.mappers.min_resid_mapper) model_summary() (catmap.model.ReactionModel method) multi_point_analysis() (catmap.model.ReactionModel method)

N

nearest_mapped_point() (catmap.model.ReactionModel method) NewtonRoot (class in catmap.solvers.solver_base)

NullScaler (class in catmap.scalers.null_scaler) numerical_jacobian() (in module catmap.functions)

O

offset_smooth_piecewise_linear() (in module catmap.functions) offset_smooth_piecewise_linear_response() (catmap.thermodynamics.second_order_interactions.SecondOrderInteractions static method)

optimize_analytical_function() (catmap.solvers.steady_state_solver.SteadyStateSolver method)

P

parameterize() (catmap.scalers.generalized_linear_scaler.GeneralizedLinearScaler method) parameterize_interactions() (catmap.thermodynamics.first_order_interactions.FirstOrderInteractions method) (catmap.thermodynamics.second_order_interactions.SecondOrderInteractions method) params_to_matrix() (catmap.thermodynamics.first_order_interactions.FirstOrderInteractions method) (catmap.thermodynamics.second_order_interactions.SecondOrderInteractions method) parse() (catmap.model.ReactionModel method) (catmap.parsers.table_parser.TableParser method) parse_constraint() (in module catmap.functions) parse_constraints() (catmap.scalers.generalized_linear_scaler.GeneralizedLinearScaler method) parse_coverage() (catmap.parsers.table_parser.TableParser method) parse_elementary_rxns() (catmap.model.ReactionModel method) parse_formation_energy() (catmap.parsers.table_parser.TableParser method) parse_frequencies() (catmap.parsers.table_parser.TableParser method) ParserBase (class in catmap.parsers.parser_base)

piecewise_linear_response() (catmap.thermodynamics.first_order_interactions.FirstOrderInteractions static method) (catmap.thermodynamics.second_order_interactions.SecondOrderInteractions static method) plot() (catmap.analyze.analysis_base.ScalingPlot method) (catmap.analyze.matrix_map.MatrixMap method) (catmap.analyze.mechanism.MechanismAnalysis method) (catmap.analyze.scaling.ScalingAnalysis method) (catmap.analyze.vector_map.VectorMap method) plot_descriptor_pts() (catmap.analyze.analysis_base.MapPlot method) (catmap.analyze.matrix_map.MatrixMap method) (catmap.analyze.mechanism.MechanismAnalysis method) (catmap.analyze.vector_map.VectorMap method) plot_separate() (catmap.analyze.analysis_base.MapPlot method) (catmap.analyze.matrix_map.MatrixMap method) (catmap.analyze.mechanism.MechanismAnalysis method) (catmap.analyze.vector_map.VectorMap method) plot_single() (catmap.analyze.analysis_base.MapPlot method) (catmap.analyze.matrix_map.MatrixMap method) (catmap.analyze.mechanism.MechanismAnalysis method) (catmap.analyze.vector_map.VectorMap method) plot_weighted() (catmap.analyze.analysis_base.MapPlot method) (catmap.analyze.matrix_map.MatrixMap method) (catmap.analyze.mechanism.MechanismAnalysis method) (catmap.analyze.vector_map.VectorMap method) plotter_scaling_function() (catmap.analyze.scaling.ScalingAnalysis method) plotter_x_axis_function() (catmap.analyze.scaling.ScalingAnalysis method) print_point() (catmap.model.ReactionModel static method) print_rxn() (catmap.model.ReactionModel method) process_resolution() (catmap.mappers.mapper_base.MapperBase method) (catmap.mappers.min_resid_mapper.MinResidMapper method)

R

rate_equation_term() (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) rate_equations() (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) reaction_energy_equations() (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) ReactionModel (class in catmap.model) ReactionModelWrapper (class in catmap)

required_interaction_parameters() (catmap.thermodynamics.first_order_interactions.FirstOrderInteractions method) (catmap.thermodynamics.second_order_interactions.SecondOrderInteractions method) retrieve_data() (catmap.model.ReactionModel method) reverse_rxn() (catmap.model.ReactionModel static method) run() (catmap.model.ReactionModel method)

S

same_rxn() (catmap.model.ReactionModel static method) save() (catmap.analyze.analysis_base.MapPlot method) (catmap.analyze.matrix_map.MatrixMap method) (catmap.analyze.mechanism.MechanismAnalysis method) (catmap.analyze.vector_map.VectorMap method) ScalerBase (class in catmap.scalers.scaler_base) scaling_coefficient_matrix() (in module catmap.functions) ScalingAnalysis (class in catmap.analyze.scaling) ScalingPlot (class in catmap.analyze.analysis_base) SecondOrderInteractions (class in catmap.thermodynamics.second_order_interactions) set_output_attrs() (catmap.scalers.generalized_linear_scaler.GeneralizedLinearScaler method) (catmap.scalers.null_scaler.NullScaler method) (catmap.scalers.scaler_base.ScalerBase method) (catmap.scalers.thermodynamic_scaler.ThermodynamicScaler method) (catmap.solvers.integrated_rate_control_solver.IntegratedRateControlSolver method) (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.solver_base.SolverBase method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) set_rxn_options() (catmap.model.ReactionModel method) sh() (in module catmap.cli) shomate_gas() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method)

simple_electrochemical() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method) single_point_analysis() (catmap.model.ReactionModel method) site_string_list() (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) smooth_piecewise_linear() (in module catmap.functions) smooth_piecewise_linear_response() (catmap.thermodynamics.first_order_interactions.FirstOrderInteractions static method) (catmap.thermodynamics.second_order_interactions.SecondOrderInteractions static method) SolverBase (class in catmap.solvers.solver_base) static_pressure() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method) SteadyStateSolver (class in catmap.solvers.steady_state_solver) substitutions_dict() (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) summary_text() (catmap.scalers.generalized_linear_scaler.GeneralizedLinearScaler method) (catmap.scalers.null_scaler.NullScaler method) (catmap.scalers.scaler_base.ScalerBase method) (catmap.scalers.thermodynamic_scaler.ThermodynamicScaler method) (catmap.solvers.mean_field_solver.MeanFieldSolver method) (catmap.solvers.steady_state_solver.SteadyStateSolver method) (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method)

T

TableParser (class in catmap.parsers.table_parser) texify() (catmap.model.ReactionModel method)

ThermoCorrections (class in catmap.thermodynamics.enthalpy_entropy) ThermodynamicScaler (class in catmap.scalers.thermodynamic_scaler)

U

update() (catmap.model.ReactionModel method)

update_descriptor_args() (catmap.analyze.analysis_base.MapPlot method) (catmap.analyze.matrix_map.MatrixMap method) (catmap.analyze.mechanism.MechanismAnalysis method) (catmap.analyze.vector_map.VectorMap method)

V

VectorMap (class in catmap.analyze.vector_map)

verify() (catmap.model.ReactionModel method)

Z

zero_point_adsorbate() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method)

zero_point_gas() (catmap.thermodynamics.enthalpy_entropy.ThermoCorrections method)