def test_force_pass_arguments(self):
self.assertEqual(
pmutt._force_pass_arguments(self.sum_fn, **{
'num1': 1,
'num2': 2
}), 3)
self.assertEqual(
pmutt._force_pass_arguments(self.kwargs_fn, **{'num1': 1}),
{'num1': 1})
self.assertEqual(
pmutt._force_pass_arguments(self.sum_class, **{
'num1': 1,
'num2': 2
}), self.sum_class(num1=1, num2=2))
self.assertEqual(
pmutt._force_pass_arguments(self.sum_class, **{
'num1': 1,
'num2': 2,
'num3': 3
}), self.sum_class(num1=1, num2=2))
self.assertEqual(
pmutt._force_pass_arguments(self.kwargs_class, **{
'num1': 1,
'num2': 2,
'num3': 3
}), self.kwargs_class(num1=1, num2=2, num3=3))
def get_state_quantity(species, stoich, method_name, **kwargs):
if method_name == 'get_q':
state_quantity = 1.
else:
state_quantity = 0.
for specie, coeff in zip(species, stoich):
# Process the inputs and methods for each specie
specie_kwargs = _get_specie_kwargs(specie.name, **kwargs)
method = getattr(specie, method_name)
if method_name == 'get_q':
state_quantity *= \
_force_pass_arguments(method, **specie_kwargs)**coeff
else:
state_quantity += \
_force_pass_arguments(method, **specie_kwargs)*coeff
return state_quantity
def write_thermo_yaml(phases=None,
species=None,
reactions=None,
lateral_interactions=None,
units=None,
filename=None,
T=300.,
P=1.,
newline='\n',
ads_act_method='get_H_act',
yaml_options={
'default_flow_style': None,
'indent': 2,
'sort_keys': False,
'width': 79
}):
"""Writes the units, phases, species, lateral interactions, reactions and
additional options in the CTI format for OpenMKM
Parameters
----------
phases : list of :class:`~pmutt.omkm.phase.Phase` objects
Phases to write in YAML file. The species should already be assigned.
species : list of :class:`~pmutt.empirical.nasa.Nasa`, :class:`~pmutt.empirical.nasa.Nasa9` or :class:`~pmutt.empirical.shomate.Shomate`
Species to write in YAML file.
reactions : list of :class:`~pmutt.omkm.reaction.SurfaceReaction`
Reactions to write in YAML file.
lateral_interactions : list of :class:`~pmutt.mixture.cov.PiecewiseCovEffect` objects, optional
Lateral interactions to include in YAML file. Default is None.
units : dict or :class:`~pmutt.omkm.units.Unit` object, optional
Units to write file. If a dict is inputted, the key is the quantity
and the value is the unit. If not specified, uses the default units
of :class:`~pmutt.omkm.units.Unit`.
filename: str, optional
Filename for the input.yaml file. If not specified, returns file
as str.
T : float, optional
Temperature in K. Default is 300 K.
P : float, optional
Pressure in atm. Default is 1 atm.
newline : str, optional
Type of newline to use. Default is Linux newline ('\\n')
ads_act_method : str, optional
Activation method to use for adsorption reactions. Accepted
options include 'get_H_act' and 'get_G_act'. Default is
'get_H_act'.
Returns
-------
lines_out : str
If ``filename`` is None, CTI file is returned.
"""
lines = [
_get_file_timestamp(comment_char='# '),
'# See documentation for OpenMKM YAML file here:',
'# https://vlachosgroup.github.io/openmkm/input',
]
yaml_dict = {}
'''Organize units units'''
if units is None:
units = Units()
elif isinstance(units, dict):
units = Units(**units)
units_out = units.to_omkm_yaml()
'''Pre-assign IDs for lateral interactions so phases can be written'''
if lateral_interactions is not None:
interactions_out = []
i = 0
for lat_interaction in lateral_interactions:
if lat_interaction.name is None:
lat_interaction.name = 'i_{:04d}'.format(i)
i += 1
interaction_dict = lat_interaction.to_omkm_yaml(units=units)
interactions_out.append(interaction_dict)
'''Pre-assign IDs for reactions so phases can be written'''
beps = []
if reactions is not None:
reactions_out = []
i = 0
for reaction in reactions:
# Assign reaction ID if not present
if reaction.id is None:
reaction.id = 'r_{:04d}'.format(i)
i += 1
# Write reaction
reaction_dict = reaction.to_omkm_yaml(units=units, T=T)
reactions_out.append(reaction_dict)
# Add unique BEP relationship if any
try:
bep = reaction.bep
except AttributeError:
pass
else:
if bep is not None and bep not in beps:
beps.append(bep)
'''Write phases'''
if phases is not None:
phases_out = []
for phase in phases:
phase_dict = _force_pass_arguments(phase.to_omkm_yaml, units=units)
phases_out.append(phase_dict)
# yaml_dict['phases'] = phases_out
'''Write species'''
if species is not None:
species_out = []
for ind_species in species:
ind_species_dict = _force_pass_arguments(ind_species.to_omkm_yaml,
units=units)
species_out.append(ind_species_dict)
# yaml_dict['species'] = species_out
'''Organize BEPs'''
if len(beps) > 0:
beps_out = []
i = 0
for bep in beps:
# Assign name if necessary
if bep.name is None:
bep.name = 'b_{:04d}'.format(i)
i += 1
bep_dict = _force_pass_arguments(bep.to_omkm_yaml, units=units)
beps_out.append(bep_dict)
# yaml_dict['beps'] = beps_out
'''Organize fields'''
fields = (
'units',
'phases',
'species',
'reactions',
'beps',
'interactions',
)
for field in fields:
try:
val = locals()['{}_out'.format(field)]
except:
pass
else:
# Create a YAML string
yaml_str = yaml.dump(data={field: val},
stream=None,
**yaml_options)
lines.extend([
'', '#' + '-' * 79, '# {}'.format(field.upper()),
'#' + '-' * 79, yaml_str
])
# yaml_dict[field] = val
# Convert to YAML format
# yaml_str = yaml.dump(data=yaml_dict, stream=None, **yaml_options)
# Remove redundant quotes
# yaml_str = yaml_str.replace('\'', '')
# lines.append(yaml_str)
lines_out = '\n'.join(lines)
# Remove redundant strings
lines_out = lines_out.replace('\'', '')
# Add spacing between list elements
lines_out = lines_out.replace('\n-', '\n\n-')
if filename is not None:
filename = Path(filename)
with open(filename, 'w', newline=newline) as f_ptr:
f_ptr.write(lines_out)
else:
# Or return as string
return lines_out
def write_cti(phases=None,
species=None,
reactions=None,
lateral_interactions=None,
units=None,
filename=None,
T=300.,
P=1.,
newline='\n',
use_motz_wise=False,
ads_act_method='get_H_act',
write_xml=True):
"""Writes the units, phases, species, lateral interactions, reactions and
additional options in the CTI format for OpenMKM
Parameters
----------
phases : list of :class:`~pmutt.omkm.phase.Phase` objects
Phases to write in CTI file. The species should already be assigned.
species : list of :class:`~pmutt.empirical.nasa.Nasa`, :class:`~pmutt.empirical.nasa.Nasa9` or :class:`~pmutt.empirical.shomate.Shomate`
Species to write in CTI file.
reactions : list of :class:`~pmutt.omkm.reaction.SurfaceReaction`
Reactions to write in CTI file.
lateral_interactions : list of :class:`~pmutt.mixture.cov.PiecewiseCovEffect` objects, optional
Lateral interactions to include in CTI file. Default is None.
units : dict or :class:`~pmutt.omkm.units.Unit` object, optional
Units to write file. If a dict is inputted, the key is the quantity
and the value is the unit. If not specified, uses the default units
of :class:`~pmutt.omkm.units.Unit`.
filename: str, optional
Filename for the input.cti file. If not specified, returns file
as str.
T : float, optional
Temperature in K. Default is 300 K.
P : float, optional
Pressure in atm. Default is 1 atm.
newline : str, optional
Type of newline to use. Default is Linux newline ('\\n')
use_motz_wise : bool, optional
Whether to use Motz-wise sticking coefficients or not. Default is
False
ads_act_method : str, optional
Activation method to use for adsorption reactions. Accepted
options include 'get_H_act' and 'get_G_act'. Default is
'get_H_act'.
write_xml : bool, optional
If True and ``filename`` is not ``None``, automatically generates
an XML file with the CTI file.
Returns
-------
lines_out : str
If ``filename`` is None, CTI file is returned.
"""
lines = [
_get_file_timestamp(comment_char='# '),
'# See documentation for OpenMKM CTI file here:',
'# https://vlachosgroup.github.io/openmkm/input'
]
'''Write units'''
lines.extend(['', '#' + '-' * 79, '# UNITS', '#' + '-' * 79])
if units is None:
units = Units()
elif isinstance(units, dict):
units = Units(**units)
lines.append(units.to_cti())
'''Pre-assign IDs for lateral interactions so phases can be written'''
if lateral_interactions is not None:
lat_inter_lines = []
i = 0
if lateral_interactions is not None:
for lat_interaction in lateral_interactions:
if lat_interaction.name is None:
lat_interaction.name = '{:04d}'.format(i)
i += 1
lat_inter_CTI = _force_pass_arguments(lat_interaction.to_cti,
units=units)
lat_inter_lines.append(lat_inter_CTI)
'''Pre-assign IDs for reactions so phases can be written'''
if reactions is not None:
beps = []
reaction_lines = []
i = 0
for reaction in reactions:
# Assign reaction ID if not present
if reaction.id is None:
reaction.id = '{:04d}'.format(i)
i += 1
# Write reaction
reaction_CTI = _force_pass_arguments(reaction.to_cti,
units=units,
T=T)
reaction_lines.append(reaction_CTI)
# Add unique BEP relationship if any
try:
bep = reaction.bep
except AttributeError:
pass
else:
if bep is not None and bep not in beps:
beps.append(bep)
'''Write phases'''
if phases is not None:
lines.extend(['', '#' + '-' * 79, '# PHASES', '#' + '-' * 79])
for phase in phases:
phase_CTI = _force_pass_arguments(phase.to_cti, units=units)
lines.append(phase_CTI)
'''Write species'''
if species is not None:
lines.extend(['', '#' + '-' * 79, '# SPECIES', '#' + '-' * 79])
for ind_species in species:
ind_species_CTI = _force_pass_arguments(ind_species.to_cti,
units=units)
lines.append(ind_species_CTI)
'''Write lateral interactions'''
if lateral_interactions is not None:
lines.extend(
['', '#' + '-' * 79, '# LATERAL INTERACTIONS', '#' + '-' * 79])
lines.extend(lat_inter_lines)
if reactions is not None:
'''Write reaction options'''
lines.extend(
['', '#' + '-' * 79, '# REACTION OPTIONS', '#' + '-' * 79])
if use_motz_wise:
lines.extend(['enable_motz_wise()\n'])
else:
lines.extend(['disable_motz_wise()\n'])
'''Write reactions'''
lines.extend(['', '#' + '-' * 79, '# REACTIONS', '#' + '-' * 79])
lines.extend(reaction_lines)
'''Write BEP Relationships'''
if len(beps) > 0:
lines.extend(
['', '#' + '-' * 79, '# BEP Relationships', '#' + '-' * 79])
# Only write each BEP once
i = 0
for bep in beps:
bep_CTI = _force_pass_arguments(bep.to_cti, units=units)
# Increment counter if necessary
if bep.name is None:
i += 1
lines.append(bep_CTI)
'''Write to file'''
lines_out = '\n'.join(lines)
if filename is not None:
filename = Path(filename)
with open(filename, 'w', newline=newline) as f_ptr:
f_ptr.write(lines_out)
'''Write XML file'''
if write_xml:
xml_filename = filename.with_suffix('.xml').as_posix()
convert(filename=filename, outName=xml_filename)
else:
# Or return as string
return lines_out
def _write_reaction_lines(reactions, species_delimiter, reaction_delimiter,
include_TS, stoich_format, act_method_name, act_unit,
float_format, column_delimiter, sden_operation,
**kwargs):
"""Write the reaction lines in the Chemkin format
Parameters
----------
reactions : list of :class:`~pmutt.reaction.ChemkinReaction` objects
Chemkin reactions to write in surf.inp file
species_delimiter : str
Delimiter to separate species when writing reactions
reaction_delimiter : str
Delimiter to separate reaction sides
act_method_name : str
Name of method to use to calculate activation function
act_unit : str
Units to calculate activation energy
float_format : str
String format to print floating numbers
stoich_format : str
String format to print stoichiometric coefficients
column_delimiter : str
Delimiter to separate columns
kwargs : keyword arguments
Parameters needed to calculate activation energy and preexponential
factor
Returns
-------
reaction_lines : str
Reactions represented in Chemkin format
"""
max_reaction_len = _get_max_reaction_len(
reactions=reactions,
species_delimiter=species_delimiter,
reaction_delimiter=reaction_delimiter,
stoich_format=stoich_format,
include_TS=include_TS)
float_field = '{:%s}' % float_format
reaction_lines = []
for reaction in reactions:
# Get reaction string
reaction_str = reaction.to_string(
species_delimiter=species_delimiter,
reaction_delimiter=reaction_delimiter,
stoich_format=stoich_format,
include_TS=include_TS).ljust(max_reaction_len)
# Calculate preexponential factor
if reaction.is_adsorption:
A = reaction.sticking_coeff
else:
# If using delta_G, take out entropic contribution in A
if act_method_name in ('get_GoRT_act', 'get_G_act',
'get_delta_GoRT', 'get_delta_G'):
include_entropy = False
else:
include_entropy = True
A = reaction.get_A(include_entropy=include_entropy,
sden_operation=sden_operation,
**kwargs)
A_str = float_field.format(A)
# Format beta value
beta_str = float_field.format(reaction.beta)
# Calculate activation energy
if act_method_name != 'get_EoRT_act' and \
act_method_name != 'get_E_act':
kwargs['activation'] = True
kwargs['units'] = act_unit
Ea_method = getattr(reaction, act_method_name)
try:
Ea = _force_pass_arguments(Ea_method, **kwargs)
except AttributeError:
Ea = 0.
Ea_str = float_field.format(Ea)
reaction_line = '{0}{4}{1}{4}{2}{4}{3}'.format(reaction_str, A_str,
beta_str, Ea_str,
column_delimiter)
if reaction.is_adsorption:
reaction_line = '{}\nSTICK'.format(reaction_line)
reaction_lines.append(reaction_line)
return reaction_lines
def write_EA(reactions,
conditions,
write_gas_phase=False,
filename='EAs.inp',
act_method_name='get_EoRT_act',
float_format=' .2E',
species_delimiter='+',
reaction_delimiter='<=>',
stoich_format='.0f',
newline='\n',
column_delimiter=' '):
"""Writes the EAs.inp or EAg.inp file for Chemkin
Parameters
----------
reactions : list of :class:`~pmutt.reaction.ChemkinReaction` objects
Reactions to write
conditions : list of dicts
Conditions to evaluate each reaction. The key of the dictionaries
should be a relevant quantity to evaluate the reaction (e.g. T, P)
write_gas_phase : bool, optional
If True, only gas phase reactions are written (including
adsorption). If False, only surface phase reactions are written.
Default is False
filename : str, optional
Filename for the EAs.inp file. Default is 'EAs.inp'
method_name : str, optional
Method to use to calculate values. Typical values are:
- 'get_EoRT_act' (default)
- 'get_HoRT_act'
- 'get_GoRT_act'
float_format : float, optional
Format to write numbers. Default is ' .2E' (scientific notation
rounded to 2 decimal places with a preceding space if the value is
positive)
stoich_format : float, optional
Format to write stoichiometric numbers. Default is '.0f' (integer)
newline : str, optional
Newline character to use. Default is the Linux newline character
column_delimiter : str, optional
Delimiter for columns. Default is ' '
"""
valid_reactions = []
for reaction in reactions:
# Skip gas-phase reactions if we want surface phase
if not write_gas_phase and reaction.gas_phase:
continue
# Skip surface-phase reactions if we want gas phase
if write_gas_phase and not reaction.gas_phase:
continue
valid_reactions.append(reaction)
n_reactions = len(valid_reactions)
# Add initial comment help line and number of reactions
lines = [
_get_filestamp(),
('!The first line is the number of reactions. Subsequent lines follow '
'the format'),
('!of rxn (from surf.out) followed by the EA/RT value at each run '
'condition.'),
('!There may be one slight deviation from surf.out: any repeated '
'species should'),
('!be included in the reaction string with a stoichiometric '
'coefficient equal to'),
('!the number of times the species appears in the reaction. '
'If not using'), '!MultiInput, then only the first value is used.',
' {} !Number of reactions'.format(n_reactions)
]
# Find length to pad reactions
max_rxn_len = _get_max_reaction_len(reactions=valid_reactions,
species_delimiter=species_delimiter,
reaction_delimiter=reaction_delimiter,
stoich_format=stoich_format,
include_TS=False)
rxn_padding = max_rxn_len + len(column_delimiter)
# Define string formats to use
float_field = '{:%s}' % float_format
str_field = '{:%d}' % rxn_padding
column_line = _write_column_line(padding=rxn_padding,
column_delimiter=column_delimiter,
float_format=float_format,
n_conditions=len(conditions))
lines.append(column_line)
# Add line for each reaction step
for reaction in valid_reactions:
line = [
str_field.format(
reaction.to_string(species_delimiter=species_delimiter,
reaction_delimiter=reaction_delimiter,
stoich_format=stoich_format,
include_TS=False))
]
for condition in conditions:
method = getattr(reaction, act_method_name)
quantity = _force_pass_arguments(method, **condition)
line.append(float_field.format(quantity))
lines.append(column_delimiter.join(line))
lines.append('EOF')
with open(filename, 'w', newline=newline) as f_ptr:
f_ptr.write('\n'.join(lines))
