import numpy as np
from vunits import constants as c
from pmutt.statmech.lsr import LSR, ExtendedLSR
from pmutt.empirical.nasa import Nasa
from pmutt.empirical.shomate import Shomate
from pmutt.empirical.references import Reference, References
from pmutt.reaction import Reaction
from pmutt.reaction import ChemkinReaction, Reactions
from pmutt.mixture.cov import PiecewiseCovEffect
from pmutt.omkm.reaction import SurfaceReaction, BEP
from pgradd.GroupAdd.Library import GroupLibrary
import pgradd.ThermoChem
[docs]def initialize_references(refs_data):
"""Initialie reference species from spreadsheet data
Parameters
----------
refs_data : list of dicts
References data. Each element of the list has the keyword arguments
to create a `pMuTT Reference`_ object.
Returns
-------
refs : `pMuTT References`_ object
Initialized references.
.. _`pMuTT Reference`: https://vlachosgroup.github.io/pMuTT/api/empirical/references/pmutt.empirical.references.Reference.html
.. _`pMuTT References`: https://vlachosgroup.github.io/pMuTT/api/empirical/references/pmutt.empirical.references.References.html
"""
if len(refs_data) > 0:
refs = []
for ref_data in refs_data:
ref = Reference(**ref_data)
refs.append(ref)
refs = References(references=refs)
else:
refs = None
return refs
[docs]def initialize_nasa_species(nasas_data):
"""Initialize NASA polynomials from spreadsheet data
Parameters
----------
nasas_data : list of dicts
NASAs data. Each element of the list corresponds to the keyword
arguments that can initialize a `pMuTT Nasa`_ object.
Returns
-------
nasas_dict : dict of `pMuTT Nasa`_ objects
Initialized `pMuTT Nasa`_ objects where the ``name`` attribute is
the key.
.. _`pMuTT Nasa`: https://vlachosgroup.github.io/pMuTT/api/empirical/nasa/pmutt.empirical.nasa.Nasa.html
"""
nasa_species_dict = {}
for ind_nasa_species_data in nasas_data:
name = ind_nasa_species_data['name']
nasa_species_dict[name] = Nasa(**ind_nasa_species_data)
return nasa_species_dict
[docs]def initialize_shomate_species(shomates_data):
"""Initialize Shomate polynomials from spreadsheet data
Parameters
----------
shomates_data : list of dicts
Shomates data. Each element of the list corresponds to the keyword
arguments that can initialize a `pMuTT Shomate`_ object.
Returns
-------
shomates_dict : dict of `pMuTT Shomate`_ objects
Shomate species where the ``name`` attribute is the key.
.. _`pMuTT Shomate`: https://vlachosgroup.github.io/pMuTT/api/empirical/shomate/pmutt.empirical.shomate.Shomate.html
"""
shomate_species_dict = {}
for ind_shomate_species_data in shomates_data:
name = ind_shomate_species_data['name']
shomate_species_dict[name] = Shomate(**ind_shomate_species_data)
return shomate_species_dict
[docs]def initialize_ga_species(ga_data, descriptors=None, statmech_species=None,
ref_species=None):
"""Initialize group additivity species from spreadsheet data
Parameters
----------
ga_data : list of dicts
Group additivity data. Each element of the list corresponds to the
keyword arguments that can initialize a ``pGrAdd Group`` object.
descriptors : list of str, optional
Names of descriptors to use to adjust enthalpy. Default is None.
statmech_species : dict of `pMuTT StatMech`_ objects, optional
StatMech objects used to initialize LSRs. Default is None.
ref_species : dict of `pMuTT StatMech`_ objects, optional
Reference species to adjust the enthalpy. If the pGrAdd library
is over a particular surface, the reference species should
represent those species over that surface. Default is None.
Returns
-------
ga_species_dict : dict of `pMuTT Nasa`_ objects
Group additivity species converted to `pMuTT Nasa` objects where
the ``name`` attribute is the key.
.. _`pMuTT Nasa`: https://vlachosgroup.github.io/pMuTT/api/empirical/nasa/pmutt.empirical.nasa.Nasa.html
.. _`pMuTT StatMech`: https://vlachosgroup.github.io/pMuTT/api/statmech/statmech.html
"""
ga_species_dict = {}
for ind_ga_species_data in ga_data:
name = ind_ga_species_data['name']
# Create GA species
ga_lib = GroupLibrary.Load(ind_ga_species_data['library'])
ga_groups = ga_lib.GetDescriptors(ind_ga_species_data['smiles'])
ga_species = ga_lib.Estimate(ga_groups, 'thermochem')
# Calculate thermo properties
T = np.linspace(ind_ga_species_data.pop('T_low'),
ind_ga_species_data.pop('T_high'))
CpoR = [ga_species.get_CpoR(T=T_i) for T_i in T]
T_ref = T[0]
HoRT = ga_species.get_HoRT(T=T_ref)
SoR = ga_species.get_SoR(T=T_ref)
if 'reaction' in ind_ga_species_data:
ga_reaction = Reaction.from_string(ind_ga_species_data['reaction'],
species={**ga_species_dict,
**statmech_species})
ga_lsr = LSR(slope=ind_ga_species_data['slope'],
intercept=ind_ga_species_data['intercept'],
reaction=ga_reaction)
elif 'reactions' in ind_ga_species_data:
ga_reactions = []
for reaction_str in ind_ga_species_data['reactions']:
reaction = Reaction.from_string(reaction_str,
species={**ga_species_dict,
**statmech_species})
ga_reactions.append(reaction)
ga_lsr = ExtendedLSR(slopes=ind_ga_species_data['slopes'],
intercept=ind_ga_species_data['intercept'],
reactions=ga_reactions)
# Add enthalpy correction if LSR is used
try:
ga_lsr
except NameError:
pass
else:
# If piecewise, check if descriptor falls within value
if 'low_val' in ind_ga_species_data \
or 'high_val' in ind_ga_species_data:
ga_reaction_species = ga_reaction.get_species()
# Find the desciptor and its corresponding value
for descriptor in descriptors:
if descriptor.name in ga_reaction_species:
descriptor_val = descriptor.val
break
# Skips applying adjustment to enthalpy if descriptor value
# out of range
if descriptor_val < ind_ga_species_data['low_val']:
continue
if descriptor_val > ind_ga_species_data['high_val']:
continue
# Adjust binding energy by taking different between reference
# species and new species
# TODO Make ref_name more general
ref_name = name.replace('(S)', '(PT)')
BE_m = ga_lsr.get_H(T=T_ref, units='kcal/mol')
BE_ref = ref_species[ref_name].get_H(T=T_ref, units='kcal/mol')
delta_HoRT = (BE_m - BE_ref)/c.R('kcal/mol/K')/T_ref
HoRT = HoRT + delta_HoRT
# Create NASA polynomial from data
ga_species_dict[name] = Nasa.from_data(T=T,
CpoR=CpoR,
T_ref=T_ref,
HoRT_ref=HoRT,
SoR_ref=SoR,
**ind_ga_species_data)
return ga_species_dict
[docs]def initialize_lsr_species(lsr_data, statmech_species, references=None):
"""Initialize LSR species from spreadsheet data
Parameters
----------
lsr_data : list of dicts
Linear scaling relationship data. Each element of the list
corresponds to the keyword arguments that can initialize a
`pMuTT LSR`_ object.
statmech_species : dict of `pMuTT StatMech`_ objects
StatMech objects used to initialize LSRs. Default is None.
references : `pMuTT References`_ object, optional
References to use to adjust enthalpy when creating `pMuTT Nasa`_
objects. Default is None
Returns
-------
lsr_species_dict : dict of `pMuTT Nasa`_ objects
Linear scaling relationships converted to `pMuTT Nasa_` objects
where the ``name`` attribute is the key
.. _`pMuTT LSR`: https://vlachosgroup.github.io/pMuTT/api/statmech/elec/pmutt.statmech.lsr.LSR.html
.. _`pMuTT StatMech`: https://vlachosgroup.github.io/pMuTT/api/statmech/statmech.html
.. _`pMuTT Nasa`: https://vlachosgroup.github.io/pMuTT/api/empirical/nasa/pmutt.empirical.nasa.Nasa.html
.. _`pMuTT References`: https://vlachosgroup.github.io/pMuTT/api/empirical/references/pmutt.empirical.references.References.html
"""
lsr_species_dict = {}
for ind_lsr_species_data in lsr_data:
name = ind_lsr_species_data['name']
# Create the reaction
ind_lsr_species_data['reaction'] = Reaction.from_string(
reaction_str=ind_lsr_species_data['reaction'],
species=statmech_species)
# Create the surface species
try:
ind_lsr_species_data['surf_species'] = \
statmech_species[ind_lsr_species_data['surf_species']]
except KeyError:
ind_lsr_species_data['surf_species'] = 0.
# Create the gas species
try:
ind_lsr_species_data['gas_species'] = \
statmech_species[ind_lsr_species_data['gas_species']]
except KeyError:
ind_lsr_species_data['gas_species'] = 0.
'''Create a NASA polynomial from the data'''
lsr_species_dict[name] = Nasa.from_model(references=references,
**ind_lsr_species_data)
return lsr_species_dict
[docs]def initialize_extended_lsr_species(extended_lsr_data,
statmech_species,
references=None):
"""Initialize extended LSR species from spreadsheet data
Parameters
----------
extended_lsr_data : list of dicts
Extended linear scaling relationship data. Each element of the list
corresponds to the keyword arguments that can initialize a
`pMuTT ExtendedLSR`_ object.
statmech_species : dict of `pMuTT StatMech`_ objects
StatMech objects used to initialize Extended LSRs. Default is None.
references : `pMuTT References`_ object, optional
References to use to adjust enthalpy when creating `pMuTT Nasa`_
objects. Default is None
Returns
-------
lsr_species_dict : dict of `pMuTT Nasa`_ objects
Linear scaling relationships converted to `pMuTT Nasa_` objects
where the ``name`` attribute is the key.
.. _`pMuTT ExtendedLSR`: https://vlachosgroup.github.io/pMuTT/api/statmech/elec/pmutt.statmech.lsr.ExtendedLSR.html
.. _`pMuTT Nasa`: https://vlachosgroup.github.io/pMuTT/api/empirical/nasa/pmutt.empirical.nasa.Nasa.html
.. _`pMuTT StatMech`: https://vlachosgroup.github.io/pMuTT/api/statmech/statmech.html
.. _`pMuTT References`: https://vlachosgroup.github.io/pMuTT/api/empirical/references/pmutt.empirical.references.References.html
"""
lsr_species_dict = {}
for ind_lsr_species_data in extended_lsr_data:
name = ind_lsr_species_data['name']
reactions = []
for reaction_str in ind_lsr_species_data['reactions']:
reaction = Reaction.from_string(reaction_str=reaction_str,
species=statmech_species)
reactions.append(reaction)
ind_lsr_species_data['reactions'] = reactions
surf_species = []
if 'surf_species' in ind_lsr_species_data:
for ind_surf_species in ind_lsr_species_data['surf_species']:
# Create the surface species
try:
new_species = statmech_species[ind_surf_species]
except KeyError:
new_species = 0.
surf_species.append(new_species)
ind_lsr_species_data['surf_species'] = surf_species
gas_species = []
if 'gas_species' in ind_lsr_species_data:
for ind_gas_species in ind_lsr_species_data['gas_species']:
# Create the gasace species
try:
new_species = statmech_species[ind_gas_species]
except KeyError:
new_species = 0.
gas_species.append(new_species)
ind_lsr_species_data['gas_species'] = gas_species
'''Create a NASA polynomial from the data'''
lsr_species_dict[name] = Nasa.from_model(references=references,
**ind_lsr_species_data)
return lsr_species_dict
[docs]def initialize_bep_species(beps_data):
"""Initialize BEP species from spreadsheet data
Parameters
----------
beps_data : list of dict
BEP relationship data. Each element of the list correspond to the
keyword arguments that can initialize a `pMuTT BEP`_ object.
Returns
-------
beps_dict : dict of `pMuTT BEP`_ objects
Initialized BEP relationships where the ``name`` attribute is the
key.
.. _`pMuTT BEP`: https://vlachosgroup.github.io/pMuTT/api/reactions/bep/pmutt.reaction.bep.BEP.html
"""
beps_dict = {bep_data['name']: BEP(**bep_data) for bep_data in beps_data}
return beps_dict
[docs]def initialize_interactions(interactions_data):
"""Initialize lateral interactions from spreadsheet data
Parameters
----------
interactions_data : list of dict
Lateral interactions data. Each element of the list correspond to
the keyword arguments that can initialize a
`pMuTT PiecewiseCovEffect`_ object.
Returns
-------
interactions : list of `pMuTT PiecewiseCovEffect`_ objects
Initialized lateral interactions.
.. _`pMuTT PiecewiseCovEffect`: https://vlachosgroup.github.io/pMuTT/api/mixture/cov/pmutt.mixture.cov.PiecewiseCovEffect.html
"""
interactions = [PiecewiseCovEffect(**interaction_data) \
for interaction_data in interactions_data]
return interactions
[docs]def initialize_reactions(reactions_data, species):
"""Initialize reactions
Parameters
----------
reactions_data : list of dict
Reactions data. Each element of the list correspond to
the keyword arguments that can initialize a
`pMuTT SurfaceReaction`_ object using the ``from_string`` method.
species : dict of pMuTT Model objects
Species corresponding to the reaction strings in ``reaction_data``
Returns
-------
reactions : list of `pMuTT SurfaceReaction`_ objects
Surface reactions that can be written to OpenMKM format
.. _`pMuTT SurfaceReaction`: https://vlachosgroup.github.io/pMuTT/api/reactions/reactions/pmutt.omkm.reaction.SurfaceReaction.html#pmutt.omkm.reaction.SurfaceReaction
"""
reactions = [SurfaceReaction.from_string(species=species, **reaction_data) \
for reaction_data in reactions_data]
return reactions
[docs]def initialize_chemkin_reactions(reactions_data, species):
"""Initialize reactions
Parameters
----------
reactions_data : list of dict
Reactions data. Each element of the list correspond to
the keyword arguments that can initialize a
`pMuTT ChemkinReaction`_ object using the ``from_string`` method.
species : dict of pMuTT Model objects
Species corresponding to the reaction strings in ``reaction_data``
Returns
-------
reactions : list of `pMuTT ChemkinReaction`_ objects
Surface reactions that can be written to Chemkin format
.. _`pMuTT ChemkinReaction`: https://vlachosgroup.github.io/pMuTT/api/reactions/reactions/pmutt.reaction.ChemkinReaction.html#pmutt.reaction.ChemkinReaction
"""
reactions = Reactions([ChemkinReaction.from_string(species=species, **reaction_data) \
for reaction_data in reactions_data])
return reactions