scine_puffin.utilities.rms_input_file_creator¶

Functions

`create_arrhenius_reaction_entry`(...[, type_str])	Create a reaction entry in the RMS format assuming that the rate constant is given by the Arrhenius equation: k = a / T^n exp(-e_a/(k_B T)).
`create_rms_phase_entry`(aggregate_str_ids, ...)	Create all entries for the species in the RMS input dictionary (this is the 'Phase' dictionary in RMS).
`create_rms_reaction_entry`(prefactors, ...)	Create the reaction entries for the RMS input dictionary assuming Arrhenius kinetics and that all reactions are Elementary Reactions (according to the RMS definition): k = a / T^n exp(-e_a/(k_B T))
`create_rms_units_entry`([units])	Create the 'units' entry in the RMS input dictionary.
`create_rms_yml_file`(aggregate_str_ids, ...)	Write the yml file input for RMS.
`create_single_species_entry`(name, h, s)	Get an entry for a species in the RMS format.
`create_solvent_entry`(solvent, ...)	Create the entry for the solvent.
`get_default_viscosity`(solvent_name)	Getter for tabulated solvent viscosity (in Pa s).
`get_ideal_dilute_solution`(rms_species, ...)	Getter for the ideal dilute solution phase object of RMS.
`get_ideal_surface`(rms_species, ...)	Getter for the ideal surface RMS phase object.
`resolve_rms_phase`(phase_name, rms_species, ...)	Resolve the RMS phase model by string.
`resolve_rms_solver`(solver_name, reactor)	Resolve the solver for the ODE system by string.

scine_puffin.utilities.rms_input_file_creator.create_arrhenius_reaction_entry(reactant_names: List[str], product_names: List[str], e_a: float, n: float, a: float, type_str: str = 'ElementaryReaction') → Dict[str, Any][source]¶

Create a reaction entry in the RMS format assuming that the rate constant is given by the Arrhenius equation: k = a / T^n exp(-e_a/(k_B T)).

Parameters:

reactant_namesList[str]: Species names of the reactions LHS (the names must correspond to an entry in the RMS phase dictionary).
product_namesList[str]: Species names of the reactions RHS (the names must correspond to an entry in the RMS phase dictionary).
e_afloat: Activation energy in J/mol.
nfloat: Temperature exponent.
afloat: Arrhenius prefactor.
type_strstr (default ‘ElementaryReaction’): Type of the reaction entry (see the RMS documentation for other options).

Returns:

Dict[str, Any]: The reaction entry.

scine_puffin.utilities.rms_input_file_creator.create_rms_phase_entry(aggregate_str_ids: List[str], enthalpies: List[float], entropies: List[float], solvent_name: str | None = None) → List[Dict][source]¶

Create all entries for the species in the RMS input dictionary (this is the ‘Phase’ dictionary in RMS).

Parameters:

aggregate_str_idsList[str]: The aggregate IDs as strings.
enthalpiesList[float]: The aggregate enthalpies (same ordering as for the aggregate_str_ids) in J/mol.
entropiesList[float]: The aggregate entropies (note the ordering) in J/mol/K.
solvent_nameOptional[str] (default None): The name of an additional solvent species that is added to the species if provided.

Returns:

The species a list of one dictionary.

scine_puffin.utilities.rms_input_file_creator.create_rms_reaction_entry(prefactors: List[float], temperature_exponents: List[float], activation_energies: List[float] | ndarray, reactant_list: List[Tuple[List[str], List[str]]]) → List[Dict[str, Any]][source]¶

Create the reaction entries for the RMS input dictionary assuming Arrhenius kinetics and that all reactions are Elementary Reactions (according to the RMS definition): k = a / T^n exp(-e_a/(k_B T))

The parameters are given as lists. The ordering in all lists must be the same.

Parameters:

prefactorsList[float]: Arrhenius prefactors (a in the equation above).
temperature_exponentsList[float]: Temperature exonents (n in the equation above).
activation_energiesUnion[List[float], np.ndarray]: Activation energies (e_a in the equation above).
reactant_listList[Tuple[List[str], List[str]]]: LHS (tuple[0]) and RHS (tuple[1]) of all reactions.

Returns:

List[Dict[str, Any]]: All reaction entries as a list of dictionaries.

scine_puffin.utilities.rms_input_file_creator.create_rms_units_entry(units: Dict | None = None) → Dict[source]¶

Create the ‘units’ entry in the RMS input dictionary. See the RMS documentation for supported units.

Parameters:

unitsOptional[Dict] (default None): The units as a dictionary.

Returns:

Dict: If no units were provided, an empty dictionary is returned.

scine_puffin.utilities.rms_input_file_creator.create_rms_yml_file(aggregate_str_ids: List[str], enthalpies: List[float], entropies: List[float], prefactors: List[float], temperature_exponents: List[float], activation_energies: List[float] | ndarray, reactants: List[Tuple[List[str], List[str]]], file_name: str, solvent_name: str | None = None, solvent_viscosity: float | None = None, solvent_aggregate_index: int | None = None) → None[source]¶

Write the yml file input for RMS.

Parameters:

aggregate_str_idsList[str]: The list of aggregate string ids to be added as RMS species.
enthalpiesList[float]: The list of enthalpies for the aggregates (in J/mol).
entropiesList[float]: The list of the aggregates entropies (in J/mol/K).
prefactorsList[float]: The list of the Arrhenius prefactors.
temperature_exponentsList[float]: The list of the temperature exponents.
activation_energiesUnion[List[float], np.ndarray]: The activation energies in J/mol.
reactantsList[Tuple[List[str], List[str]]]: LHS (tuple[0]) and RHS (tuple[1]) of all reactions.
file_namestr: The filename for the yml file.
solvent_nameOptional[str] (default None): The solvent name.
solvent_viscosityOptional[float] (default None): The solvent’s viscosity in Pa s.
solvent_aggregate_indexOptional[int] (default None): The index of the solvent in the aggregte id list. This is only required if the solvent is a reacting species.

scine_puffin.utilities.rms_input_file_creator.create_single_species_entry(name: str, h: float, s: float)[source]¶

Get an entry for a species in the RMS format.

We could extend this function to use the heat capacity of the species or directly insert the NASA polynomials. This would be interesting for non-constant temperature simulations.

Parameters:

namestr: The species name (unique identifier).
hfloat: The species enthalpy in J/mol.
sfloat: The species entropy in J/mol/K.

Returns:

The species entry.

scine_puffin.utilities.rms_input_file_creator.create_solvent_entry(solvent: str, solvent_viscosity: float | None, solvent_id_str: str | None) → Dict[source]¶

Create the entry for the solvent.

Parameters:

solventstr: The solvent name (e.g., water) to extract tabulated viscosity values.
solvent_viscosityOptional[float]: The solvent’s viscosity in Pa s.
solvent_id_strOptional[str]: The string id of the solvent compound. Only required if the solvent is a reacting species.

Returns:

Dict: The solvent entry as a dictionary.

scine_puffin.utilities.rms_input_file_creator.get_default_viscosity(solvent_name: str) → float[source]¶

Getter for tabulated solvent viscosity (in Pa s). Tabulated values are at 25 celsius.

Source: https://hbcp.chemnetbase.com/faces/contents/InteractiveTable.xhtml Accessed on 23.01.2023, 14:00

Parameters:

solvent_namestr: The solvent’s name.

Returns:

float: The solvent’s viscosity (in Pa s).

scine_puffin.utilities.rms_input_file_creator.get_ideal_dilute_solution(rms_species: Any, rms_reactions: Any, rms_solvent: Any, diffusion_limited: bool) → Any[source]¶

Getter for the ideal dilute solution phase object of RMS.

Parameters:

rms_speciesRMS species object: The RMS species.
rms_reactionsRMS Reaction list: The RMS reactions.
rms_solventRMS solvent object: The RMS solvetn object.
diffusion_limitedbool: If true, diffusion limitations are enforced.

Returns:

Any: The rms.IdealDiluteSolution object.

scine_puffin.utilities.rms_input_file_creator.get_ideal_surface(rms_species, rms_reactions, diffusion_limited: bool, site_density: float | None)[source]¶

Getter for the ideal surface RMS phase object.

Parameters:

rms_speciesRMS species object: The RMS species.
rms_reactionsRMS Reaction list object: The RMS reactions.
diffusion_limitedbool: If true, diffusion limitations are enforced.
site_densityfloat: The site density for surface reactions.

Returns:

The rms.IdealSurface object.

scine_puffin.utilities.rms_input_file_creator.resolve_rms_phase(phase_name: str, rms_species: Any, rms_reactions: Any, rms_solvent: Any, diffusion_limited: bool, site_density: float | None) → Any[source]¶

Resolve the RMS phase model by string.

Parameters:

phase_namestr: The name of the phase. Options are ‘ideal_gas’ and ‘ideal_dilute_solution’.
rms_speciesRMS species object: The RMS species.
rms_reactionsRMS Reaction list: The RMS reactions.
rms_solventRMS solvent object: The RMS solvetn object.
diffusion_limitedbool: If true, diffusion limitations are enforced.
site_densityOptional[float]: The site density for surface reactions.

Returns:

Any: Returns the RMS phase object.

scine_puffin.utilities.rms_input_file_creator.resolve_rms_solver(solver_name: str, reactor: Any)[source]¶

Resolve the solver for the ODE system by string.

Parameters:

solver_namestr: The solver name.
reactorrms.Reactor: The julia RMS reactor object.

Returns:

Returns the selected ODE solver as a julia Differential Equation object.