def setUp(self):
slope = 0.5
intercept = 10. # kcal/mol
del_E = -1. # kcal/mol
del_E_eV = del_E * c.convert_unit(initial='kcal/mol',
final='eV/molecule')
E_surf = -2. # kcal/mol
E_surf_eV = E_surf * c.convert_unit(initial='kcal/mol',
final='eV/molecule')
E_gas = -3. # kcal/mol
E_gas_eV = E_gas * c.convert_unit(initial='kcal/mol',
final='eV/molecule')
species = {
'A(g)_shomate':
Shomate(name='A(g)_shomate',
T_low=100.,
T_high=500.,
a=np.zeros(8)),
'A(g)_statmech':
StatMech(),
'*':
StatMech(),
'A*':
StatMech(U=del_E_eV, H=del_E_eV, **presets['constant']),
'surf':
StatMech(U=E_surf_eV, H=E_surf_eV, **presets['constant']),
'gas':
StatMech(U=E_gas_eV, H=E_gas_eV, **presets['constant'])
}
reaction_shomate = Reaction.from_string('A(g)_shomate + * = A*',
species)
reaction_statmech = Reaction.from_string('A(g)_statmech + * = A*',
species)
self.lsr_const = LSR(slope=slope,
intercept=intercept,
reaction=del_E,
surf_species=E_surf,
gas_species=E_gas)
self.lsr_shomate = LSR(slope=slope,
intercept=intercept,
reaction=reaction_shomate,
surf_species=species['surf'],
gas_species=species['gas'])
self.lsr_statmech = LSR(slope=slope,
intercept=intercept,
reaction=reaction_statmech,
surf_species=species['surf'],
gas_species=species['gas'])
def from_string(cls,
reaction_str,
species,
species_delimiter='+',
reaction_delimiter='=',
notes=None,
beta=1,
is_adsorption=False,
sticking_coeff=0.5,
direction=None,
id=None):
"""Create a reaction object using the reaction string
Parameters
----------
reaction_str : str
Reaction string.
species : dict
Dictionary using the names as keys. If you have a list of
species, use pmutt.pmutt_list_to_dict to make a dict.
species_delimiter : str, optional
Delimiter that separate species. Leading and trailing spaces
will be trimmed. Default is '+'
reaction_delimiter : str, optional
Delimiter that separate states of the reaction. Leading and
trailing spaces will be trimmed. Default is '='
notes : str or dict, optional
Other notes such as the source of the reaction. Default is None
beta : float, optional
Power to raise the temperature in the rate expression.
Default is 1
is_adsorption : bool, optional
If True, the reaction represents an adsorption. Default is False
sticking_coeff : float, optional
Sticking coefficient. Only relevant if ``is_adsorption`` is
True. Default is 0.5
gas_phase : bool
True if the reaction has only gas-phase species. This attribute
is determined based on the reactants and products
Returns
-------
SurfaceReaction : :class:`~pmutt.omkm.SurfaceReaction` object
"""
rxn = Reaction.from_string(reaction_str=reaction_str,
species=species,
species_delimiter=species_delimiter,
reaction_delimiter=reaction_delimiter)
return cls(reactants=rxn.reactants,
reactants_stoich=rxn.reactants_stoich,
products=rxn.products,
products_stoich=rxn.products_stoich,
transition_state=rxn.transition_state,
transition_state_stoich=rxn.transition_state_stoich,
notes=notes,
beta=beta,
is_adsorption=is_adsorption,
sticking_coeff=sticking_coeff,
direction=direction,
id=id)
def read_reactions(filename,
species,
species_delimiter='.',
reaction_delimiter='>>',
raise_error=True,
raise_warning=True):
"""Reads reactions from RING output file.
Parameters
----------
filename : str
Input filename
species : dict
Dictionary using the names as keys. If you have a list of
species, use pmutt.pmutt_list_to_dict to make a dict.
species_delimiter : str, optional
Delimiter that separate species. Leading and trailing spaces
will be trimmed. Default is '.'
reaction_delimiter : str, optional
Delimiter that separate states of the reaction. Leading and
trailing spaces will be trimmed. Default is '>>'
raise_error : bool, optional
If True, raises an error if the transition state is not located in
species. Default is True
raise_warning : bool, optional
Only relevant if raise_error is False. Raises a warning if the
transition state is not located in species. Default is True
Returns
-------
reactions : list of :class:`~pmutt.reaction.Reaction` objects
Reactions
"""
rxns = []
with open(filename, 'r') as f_ptr:
for line in f_ptr:
# Skip lines that do not have a reaction
if reaction_delimiter not in line:
continue
reaction_str = line.replace('\n', '')
rxn = Reaction.from_string(reaction_str=reaction_str,
species=species,
species_delimiter=species_delimiter,
reaction_delimiter=reaction_delimiter,
raise_error=raise_error,
raise_warning=raise_warning)
rxns.append(rxn)
return Reactions(reactions=rxns)
def _float_to_reaction(self, val):
"""Converts a float to a :class:`~pmutt.reaction.Reaction` object
Parameters
----------
val : float
Value (in kcal/mol)
Returns
-------
obj : :class:`~pmutt.reaction.Reaction` object
:class:`~pmutt.reaction.Reaction` object that gives the val
when `get_delta_E` is called
"""
reactant = StatMech()
product = self._float_to_specie(val=val)
return Reaction(reactants=[reactant], reactants_stoich=[1.],
products=[product], products_stoich=[1.])
def setUp(self):
self.species_dict = {
'H2O':
Nasa(name='H2O',
T_low=200.,
T_mid=1000.,
T_high=3500.,
elements={
'H': 2,
'O': 1
},
a_low=[
4.19864056E+00, -2.03643410E-03, 6.52040211E-06,
-5.48797062E-09, 1.77197817E-12, -3.02937267E+04,
-8.49032208E-01
],
a_high=[
3.03399249E+00, 2.17691804E-03, -1.64072518E-07,
-9.70419870E-11, 1.68200992E-14, -3.00042971E+04,
4.96677010E+00
]),
'H2':
Nasa(name='H2',
T_low=200.,
T_mid=1000.,
T_high=3500.,
elements={'H': 2},
a_low=[
2.34433112E+00, 7.98052075E-03, -1.94781510E-05,
2.01572094E-08, -7.37611761E-12, -9.17935173E+02,
6.83010238E-01
],
a_high=[
3.33727920E+00, -4.94024731E-05, 4.99456778E-07,
-1.79566394E-10, 2.00255376E-14, -9.50158922E+02,
-3.20502331E+00
]),
'O2':
Nasa(name='O2',
T_low=200.,
T_mid=1000.,
T_high=3500.,
elements={'O': 2},
a_low=[
3.78245636E+00, -2.99673416E-03, 9.84730201E-06,
-9.68129509E-09, 3.24372837E-12, -1.06394356E+03,
3.65767573E+00
],
a_high=[
3.28253784E+00, 1.48308754E-03, -7.57966669E-07,
2.09470555E-10, -2.16717794E-14, -1.08845772E+03,
5.45323129E+00
]),
'O':
Nasa(name='O',
T_low=200.,
T_mid=1000.,
T_high=3500.,
elements={'O': 1},
a_low=[
3.16826710E+00, -3.27931884E-03, 6.64306396E-06,
-6.12806624E-09, 2.11265971E-12, 2.91222592E+04,
2.05193346E+00
],
a_high=[
2.56942078E+00, -8.59741137E-05, 4.19484589E-08,
-1.00177799E-11, 1.22833691E-15, 2.92175791E+04,
4.78433864E+00
]),
'H':
Nasa(name='H',
T_low=200.,
T_mid=1000.,
T_high=3500.,
elements={'H': 1},
a_low=[
2.50000000E+00, 7.05332819E-13, -1.99591964E-15,
2.30081632E-18, -9.27732332E-22, 2.54736599E+04,
-4.46682853E-01
],
a_high=[
2.50000001E+00, -2.30842973E-11, 1.61561948E-14,
-4.73515235E-18, 4.98197357E-22, 2.54736599E+04,
-4.46682914E-01
]),
'OH':
Nasa(name='OH',
T_low=200.,
T_mid=1000.,
T_high=3500.,
elements={
'O': 1,
'H': 1
},
a_high=[
3.09288767E+00, 5.48429716E-04, 1.26505228E-07,
-8.79461556E-11, 1.17412376E-14, 3.85865700E+03,
4.47669610E+00
],
a_low=[
3.99201543E+00, -2.40131752E-03, 4.61793841E-06,
-3.88113333E-09, 1.36411470E-12, 3.61508056E+03,
-1.03925458E-01
])
}
self.reactions = Reactions(reactions=[
Reaction.from_string('O+2H=H2O', self.species_dict),
Reaction.from_string('O+H2=H2O', self.species_dict),
Reaction.from_string('OH+H=H2O', self.species_dict),
Reaction.from_string('OH+0.5H2=H2O', self.species_dict),
Reaction.from_string('0.5O+2H=H2O', self.species_dict),
Reaction.from_string('0.5O2+H2=H2O', self.species_dict)
])
self.reactions_dict = {
'class':
"<class 'pmutt.reaction.Reactions'>",
'reactions': [{
'class':
"<class 'pmutt.reaction.Reaction'>",
'products': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.03399249, 0.00217691804, -1.64072518e-07,
-9.7041987e-11, 1.68200992e-14, -30004.2971, 4.9667701
],
'a_low': [
4.19864056, -0.0020364341, 6.52040211e-06,
-5.48797062e-09, 1.77197817e-12, -30293.7267,
-0.849032208
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 2,
'O': 1
},
'name':
'H2O',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa'
}],
'products_stoich': [1.0],
'reactants': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
2.56942078, -8.59741137e-05, 4.19484589e-08,
-1.00177799e-11, 1.22833691e-15, 29217.5791, 4.78433864
],
'a_low': [
3.1682671, -0.00327931884, 6.64306396e-06,
-6.12806624e-09, 2.11265971e-12, 29122.2592, 2.05193346
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'O': 1
},
'name':
'O',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa'
}, {
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
2.50000001, -2.30842973e-11, 1.61561948e-14,
-4.73515235e-18, 4.98197357e-22, 25473.6599,
-0.446682914
],
'a_low': [
2.5, 7.05332819e-13, -1.99591964e-15, 2.30081632e-18,
-9.27732332e-22, 25473.6599, -0.446682853
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 1
},
'name':
'H',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa'
}],
'reactants_stoich': [1.0, 2.0],
'transition_state':
None,
'transition_state_stoich':
None
}, {
'class':
"<class 'pmutt.reaction.Reaction'>",
'products': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.03399249, 0.00217691804, -1.64072518e-07,
-9.7041987e-11, 1.68200992e-14, -30004.2971, 4.9667701
],
'a_low': [
4.19864056, -0.0020364341, 6.52040211e-06,
-5.48797062e-09, 1.77197817e-12, -30293.7267,
-0.849032208
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 2,
'O': 1
},
'name':
'H2O',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa'
}],
'products_stoich': [1.0],
'reactants': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
2.56942078, -8.59741137e-05, 4.19484589e-08,
-1.00177799e-11, 1.22833691e-15, 29217.5791, 4.78433864
],
'a_low': [
3.1682671, -0.00327931884, 6.64306396e-06,
-6.12806624e-09, 2.11265971e-12, 29122.2592, 2.05193346
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'O': 1
},
'name':
'O',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa'
}, {
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.3372792, -4.94024731e-05, 4.99456778e-07,
-1.79566394e-10, 2.00255376e-14, -950.158922,
-3.20502331
],
'a_low': [
2.34433112, 0.00798052075, -1.9478151e-05,
2.01572094e-08, -7.37611761e-12, -917.935173,
0.683010238
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 2
},
'name':
'H2',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa'
}],
'reactants_stoich': [1.0, 1.0],
'transition_state':
None,
'transition_state_stoich':
None
}, {
'class':
"<class 'pmutt.reaction.Reaction'>",
'products': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.03399249, 0.00217691804, -1.64072518e-07,
-9.7041987e-11, 1.68200992e-14, -30004.2971, 4.9667701
],
'a_low': [
4.19864056, -0.0020364341, 6.52040211e-06,
-5.48797062e-09, 1.77197817e-12, -30293.7267,
-0.849032208
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 2,
'O': 1
},
'name':
'H2O',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa'
}],
'products_stoich': [1.0],
'reactants': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.09288767, 0.000548429716, 1.26505228e-07,
-8.79461556e-11, 1.17412376e-14, 3858.657, 4.4766961
],
'a_low': [
3.99201543, -0.00240131752, 4.61793841e-06,
-3.88113333e-09, 1.3641147e-12, 3615.08056,
-0.103925458
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 1,
'O': 1
},
'name':
'OH',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa',
}, {
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
2.50000001, -2.30842973e-11, 1.61561948e-14,
-4.73515235e-18, 4.98197357e-22, 25473.6599,
-0.446682914
],
'a_low': [
2.5, 7.05332819e-13, -1.99591964e-15, 2.30081632e-18,
-9.27732332e-22, 25473.6599, -0.446682853
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 1
},
'name':
'H',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa',
}],
'reactants_stoich': [1.0, 1.0],
'transition_state':
None,
'transition_state_stoich':
None
}, {
'class':
"<class 'pmutt.reaction.Reaction'>",
'products': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.03399249, 0.00217691804, -1.64072518e-07,
-9.7041987e-11, 1.68200992e-14, -30004.2971, 4.9667701
],
'a_low': [
4.19864056, -0.0020364341, 6.52040211e-06,
-5.48797062e-09, 1.77197817e-12, -30293.7267,
-0.849032208
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 2,
'O': 1
},
'name':
'H2O',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa',
}],
'products_stoich': [1.0],
'reactants': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.09288767, 0.000548429716, 1.26505228e-07,
-8.79461556e-11, 1.17412376e-14, 3858.657, 4.4766961
],
'a_low': [
3.99201543, -0.00240131752, 4.61793841e-06,
-3.88113333e-09, 1.3641147e-12, 3615.08056,
-0.103925458
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 1,
'O': 1
},
'name':
'OH',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa',
}, {
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.3372792, -4.94024731e-05, 4.99456778e-07,
-1.79566394e-10, 2.00255376e-14, -950.158922,
-3.20502331
],
'a_low': [
2.34433112, 0.00798052075, -1.9478151e-05,
2.01572094e-08, -7.37611761e-12, -917.935173,
0.683010238
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 2
},
'name':
'H2',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa',
}],
'reactants_stoich': [1.0, 0.5],
'transition_state':
None,
'transition_state_stoich':
None
}, {
'class':
"<class 'pmutt.reaction.Reaction'>",
'products': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.03399249, 0.00217691804, -1.64072518e-07,
-9.7041987e-11, 1.68200992e-14, -30004.2971, 4.9667701
],
'a_low': [
4.19864056, -0.0020364341, 6.52040211e-06,
-5.48797062e-09, 1.77197817e-12, -30293.7267,
-0.849032208
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 2,
'O': 1
},
'name':
'H2O',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa',
}],
'products_stoich': [1.0],
'reactants': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
2.56942078, -8.59741137e-05, 4.19484589e-08,
-1.00177799e-11, 1.22833691e-15, 29217.5791, 4.78433864
],
'a_low': [
3.1682671, -0.00327931884, 6.64306396e-06,
-6.12806624e-09, 2.11265971e-12, 29122.2592, 2.05193346
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'O': 1
},
'name':
'O',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa',
}, {
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
2.50000001, -2.30842973e-11, 1.61561948e-14,
-4.73515235e-18, 4.98197357e-22, 25473.6599,
-0.446682914
],
'a_low': [
2.5, 7.05332819e-13, -1.99591964e-15, 2.30081632e-18,
-9.27732332e-22, 25473.6599, -0.446682853
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 1
},
'name':
'H',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa',
}],
'reactants_stoich': [0.5, 2.0],
'transition_state':
None,
'transition_state_stoich':
None
}, {
'class':
"<class 'pmutt.reaction.Reaction'>",
'products': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.03399249, 0.00217691804, -1.64072518e-07,
-9.7041987e-11, 1.68200992e-14, -30004.2971, 4.9667701
],
'a_low': [
4.19864056, -0.0020364341, 6.52040211e-06,
-5.48797062e-09, 1.77197817e-12, -30293.7267,
-0.849032208
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 2,
'O': 1
},
'name':
'H2O',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa',
}],
'products_stoich': [1.0],
'reactants': [{
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.28253784, 0.00148308754, -7.57966669e-07,
2.09470555e-10, -2.16717794e-14, -1088.45772,
5.45323129
],
'a_low': [
3.78245636, -0.00299673416, 9.84730201e-06,
-9.68129509e-09, 3.24372837e-12, -1063.94356,
3.65767573
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'O': 2
},
'name':
'O2',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa',
}, {
'T_high':
3500.0,
'T_low':
200.0,
'T_mid':
1000.0,
'a_high': [
3.3372792, -4.94024731e-05, 4.99456778e-07,
-1.79566394e-10, 2.00255376e-14, -950.158922,
-3.20502331
],
'a_low': [
2.34433112, 0.00798052075, -1.9478151e-05,
2.01572094e-08, -7.37611761e-12, -917.935173,
0.683010238
],
'class':
"<class 'pmutt.empirical.nasa.Nasa'>",
'elements': {
'H': 2
},
'name':
'H2',
'notes':
None,
'phase':
None,
'statmech_model':
None,
'misc_models':
None,
'cat_site':
None,
'n_sites':
None,
'smiles':
None,
'type':
'nasa',
}],
'reactants_stoich': [0.5, 1.0],
'transition_state':
None,
'transition_state_stoich':
None
}]
}
species_pathway = {
'A': StatMech(G=1., **presets['constant']),
'A_TS1': StatMech(G=3., **presets['constant']),
'A_TS2': StatMech(G=2., **presets['constant']),
'B': StatMech(G=-1., **presets['constant']),
'C': StatMech(G=2., **presets['constant']),
'C_TS': StatMech(G=2.5, **presets['constant']),
'D': StatMech(G=0., **presets['constant']),
}
self.rxn_pathway1 = Reactions(reactions=[
Reaction.from_string('A = A_TS1 = B', species_pathway),
Reaction.from_string('B = C', species_pathway),
Reaction.from_string('C = C_TS = D', species_pathway)
])
self.rxn_pathway2 = Reactions(reactions=[
Reaction.from_string('A = A_TS2 = B', species_pathway),
Reaction.from_string('B = C', species_pathway),
Reaction.from_string('C = C_TS = D', species_pathway)
])
# Add it to the dictionary
species_dict['H2O_TS'] = H2O_TS
# (Optional) Print the new dictionary to see the new entry
pprint(species_dict)
# ## Initialize Reaction Manually
# Let us initialize the reaction manually. You will have to feed the reactants, transition states, products and their stoichiometries.
# In[3]:
from pmutt.reaction import Reaction
rxn = Reaction(reactants=[species_dict['H2'], species_dict['O2']],
reactants_stoich=[1., 0.5],
products=[species_dict['H2O']],
products_stoich=[1.],
transition_state=species_dict['H2O_TS'],
transition_state_stoich=[1.])
# (Optional) Converting a Reaction object to a string will give its stoichiometric formula
print('Creating Reaction object manually: {}'.format(rxn))
# ## Initialize Reaction Using Strings
# Initializing manually is cumbersome and prone to error. Instead, we can use ``.from_string()`` to initialize the reaction more easily.
# In[4]:
rxn = Reaction.from_string(reaction_str='H2 + 0.5O2 = H2O_TS = H2O',
species=species_dict)
# See that you get the same stoichiometry as before
print('Creating Reaction object using default string notation: {}'.format(rxn))
200.123762, 196.698042, 195.736534, 75.269065, 72.94012,
70.402739, 68.651958, 65.289743, 64.556735, 63.904694,
60.051442, 58.698334, 55.589005, 52.608038, 43.883525
],
**presets['harmonic']),
}
# ## Create Reactions for Phase Diagram
# The reactions will be initialized and put in a list. Notice that the stoichiometric coefficient of CO changes for higher coverages. If you are unfamiliar with initializing reactions, see the Reactions example.
# In[2]:
from pmutt.reaction import Reaction
reactions = [
Reaction.from_string('Pt = Pt', species), # Clean surface
Reaction.from_string('Pt + CO = CO(S) 1/16ML fcc', species),
Reaction.from_string('Pt + CO = CO(S) 1/16ML br', species),
Reaction.from_string('Pt + CO = CO(S) 1/16ML top', species),
Reaction.from_string('Pt + 2CO = CO(S) 1/8ML', species),
Reaction.from_string('Pt + 3CO = CO(S) 3/16ML', species),
Reaction.from_string('Pt + 8CO = CO(S) 1/2ML', species)
]
# ## Create PhaseDiagram Object
# Now we have everything we need to create the ``PhaseDiagram`` object.
# In[3]:
from pmutt.reaction.phasediagram import PhaseDiagram
# You can also evaluate reactions properties. The most straightforward way to do this is to initialize using strings.
# In[15]:
from pmutt.io.thermdat import read_thermdat
from pmutt import pmutt_list_to_dict
from pmutt.reaction import Reaction
# Get a dictionary of species
thermdat_H2O_path = os.path.join(notebook_folder, 'thermdat_H2O')
species_list = read_thermdat(thermdat_H2O_path)
species_dict = pmutt_list_to_dict(species_list)
# Initialize the reaction
rxn_H2O = Reaction.from_string('H2 + 0.5O2 = H2O', species=species_dict)
# Calculate reaction properties
H_rxn = rxn_H2O.get_delta_H(T=298., units='kJ/mol')
S_rxn = rxn_H2O.get_delta_S(T=298., units='J/mol/K')
print('H_rxn(T=298) = {:.1f} kJ/mol'.format(H_rxn))
print('S_rxn(T=298) = {:.2f} J/mol/K'.format(S_rxn))
# ## Exercise
# Write a script to calculate the Enthalpy of adsorption (in kcal/mol) of H2O on Cu(111) at T = 298 K. Some important details are given below.
#
# ### Information Required
# #### H2O:
# - ideal gas
# - atoms: You can use "ase.build.molecule" to generate a water molecule like we did with ethane, propane, and butane.
-3.3518122405333548e-09, 7.58446718337381e-13, -191086.2004520406,
0.6858235504924011
]),
'NH3':
Shomate(name='NH3',
T_low=300.,
T_high=1000.,
a=[
18.792357134351683, 44.82725349479501, -10.05898449447048,
0.3711633831565547, 0.2969942466370908, -1791.225746924463,
203.9035662274934, 1784.714638346206
]),
}
# Define the formation of water reaction
rxn = Reaction.from_string('1.5H2 + 0.5N2 = NH3', species)
# Calculate forward change in enthalpy
H_rxn_fwd = rxn.get_delta_H(units='kcal/mol', T=300.)
print('Delta H_fwd(T = 300 K) = {:.1f} kcal/mol'.format(H_rxn_fwd))
# Calculate reverse change in enthalpy
H_rxn_rev = rxn.get_delta_H(units='kcal/mol', T=300., rev=True)
print('Delta H_rev(T = 300 K) = {:.1f} kcal/mol'.format(H_rxn_rev))
# Calculate enthalpy of reactants
H_react = rxn.get_H_state(units='kcal/mol', T=300., state='reactants')
print('H_reactants(T = 300 K) = {:.1f} kcal/mol'.format(H_react))
# <a id='section_11'></a>
atoms=molecule('H2O'),
potentialenergy=-14.2209,
symmetrynumber=2,
spin=0,
references=refs,
vib_wavenumbers=[3825.434, 3710.264, 1582.432],
**presets['idealgas'])
H2O_TS_statmech = StatMech(name='H2O',
elements={
'H': 2,
'O': 1
},
phase='G',
atoms=molecule('H2O'),
potentialenergy=0.,
symmetrynumber=2,
spin=0,
references=refs,
vib_wavenumbers=[3825.434, 3710.264, 1582.432],
**presets['idealgas'])
species = {
'H2': H2_shomate,
'H2O': H2O_statmech,
'O2': O2_nasa,
'H2O_TS': H2O_TS_statmech,
}
rxn = Reaction.from_string('H2 + 0.5O2 = H2O_TS = H2O', species)
4.050329990684662, -0.0029677854067980108, 5.323485005316287e-06,
-3.3518122405333548e-09, 7.58446718337381e-13, -191086.2004520406,
0.6858235504924011
]),
'NH3':
Shomate(name='NH3',
T_low=300.,
T_high=1000.,
a=[
18.792357134351683, 44.82725349479501, -10.05898449447048,
0.3711633831565547, 0.2969942466370908, -1791.225746924463,
203.9035662274934, 1784.714638346206
]),
}
# Define the formation of ammonia reaction
rxn = Reaction.from_string('1.5H2 + 0.5N2 = NH3', species)
# Now we can calculate thermodynamic properties of the reaction.
# In[13]:
'''Forward change in enthalpy'''
H_rxn_fwd = rxn.get_delta_H(units='kcal/mol', T=300.)
print('Delta H_fwd(T = 300 K) = {:.1f} kcal/mol'.format(H_rxn_fwd))
'''Reverse change in entropy'''
S_rxn_rev = rxn.get_delta_S(units='cal/mol/K', T=300., rev=True)
print('Delta S_rev(T = 300 K) = {:.1f} cal/mol/K'.format(S_rxn_rev))
'''Gibbs energy of reactants'''
G_react = rxn.get_G_state(units='kcal/mol', T=300., state='reactants')
print('G_reactants(T = 300 K) = {:.1f} kcal/mol'.format(G_react))
def setUp(self):
self.T = c.T0('K')
# Factor to convert potential energy to dimensionless number
dim_factor = c.R('eV/K')*self.T
self.m = 0.5 # BEP Slope
self.c = 20. # BEP Intercept in kcal/mol
species = {
'H2': StatMech(name='H2', potentialenergy=2.*dim_factor,
**presets['electronic']),
'O2': StatMech(name='O2', potentialenergy=4.*dim_factor,
**presets['electronic']),
'H2O': StatMech(name='H2O', potentialenergy=3.*dim_factor,
**presets['electronic']),
'BEP': BEP(slope=self.m, intercept=self.c, name='BEP')
}
self.rxn_delta_H = Reaction.from_string(
reaction_str='H2 + 0.5O2 = BEP = H2O',
species=species,
bep_descriptor='delta_H')
self.bep_delta_H = self.rxn_delta_H.transition_state[0]
rxn_rev_delta_H = Reaction.from_string(
reaction_str='H2 + 0.5O2 = BEP = H2O',
species=species,
bep_descriptor='rev_delta_H')
self.bep_rev_delta_H = rxn_rev_delta_H.transition_state[0]
rxn_reactants_H = Reaction.from_string(
reaction_str='H2 + 0.5O2 = BEP = H2O',
species=species,
bep_descriptor='reactants_H')
self.bep_reactants_H = rxn_reactants_H.transition_state[0]
rxn_products_H = Reaction.from_string(
reaction_str='H2 + 0.5O2 = BEP = H2O',
species=species,
bep_descriptor='products_H')
self.bep_products_H = rxn_products_H.transition_state[0]
self.rxn_delta_E = Reaction.from_string(
reaction_str='H2 + 0.5O2 = BEP = H2O',
species=species,
bep_descriptor='delta_E')
self.bep_delta_E = self.rxn_delta_E.transition_state[0]
rxn_rev_delta_E = Reaction.from_string(
reaction_str='H2 + 0.5O2 = BEP = H2O',
species=species,
bep_descriptor='rev_delta_E')
self.bep_rev_delta_E = rxn_rev_delta_E.transition_state[0]
rxn_reactants_E = Reaction.from_string(
reaction_str='H2 + 0.5O2 = BEP = H2O',
species=species,
bep_descriptor='reactants_E')
self.bep_reactants_E = rxn_reactants_E.transition_state[0]
rxn_products_E = Reaction.from_string(
reaction_str='H2 + 0.5O2 = BEP = H2O',
species=species,
bep_descriptor='products_E')
self.bep_products_E = rxn_products_E.transition_state[0]
'O2':
O2,
}
# (Optional) Print the species dictionary
pprint(species)
# ## Create Reactions for Phase Diagram
# The reactions will be initialized and put in a list. Notice that the stiochiometric coefficient of O2 in all reactions is 1 to ensure consistency. If you are unfamiliar with initializing reactions, see the reactions example.
# In[2]:
from pmutt.reaction import Reaction
reactions = [
Reaction.from_string(reaction_str='2Fe+O2=2FeO', species=species),
Reaction.from_string(reaction_str='{}Fe+O2={}Fe2O3'.format(
4. / 3., 2. / 3.),
species=species),
Reaction.from_string(reaction_str='1.5Fe+O2=0.5Fe3O4', species=species)
]
# ## Create PhaseDiagram Object
# Now we have everything we need to create the ``PhaseDiagram`` object.
# In[3]:
from pmutt.reaction.phasediagram import PhaseDiagram
phase_diagram = PhaseDiagram(reactions=reactions)
def from_string(cls,
reaction_str,
species,
species_delimiter='+',
reaction_delimiter='=',
notes=None,
A=None,
beta=1,
Ea=None,
is_adsorption=False,
sticking_coeff=0.5,
direction=None,
id=None,
use_motz_wise=False):
"""Create a reaction object using the reaction string
Parameters
----------
reaction_str : str
Reaction string.
species : dict
Dictionary using the names as keys. If you have a list of
species, use pmutt.pmutt_list_to_dict to make a dict.
species_delimiter : str, optional
Delimiter that separate species. Leading and trailing spaces
will be trimmed. Default is '+'
reaction_delimiter : str, optional
Delimiter that separate states of the reaction. Leading and
trailing spaces will be trimmed. Default is '='
notes : str or dict, optional
Other notes such as the source of the reaction. Default is None
A : float, optional
Pre-exponential constant. If not specified, uses reaction to
determine value.
beta : float, optional
Power to raise the temperature in the rate expression. Default
is 1 if ``is_adsorption`` is False, 0 if ``is_adsorption``
is True.
Ea : float, optional
Activation energy. If not specified, uses reaction to determine
value.
is_adsorption : bool, optional
If True, the reaction represents an adsorption. Default is False
sticking_coeff : float, optional
Sticking coefficient. Only relevant if ``is_adsorption`` is
True. Default is 0.5
gas_phase : bool
True if the reaction has only gas-phase species. This attribute
is determined based on the reactants and products
use_motz_wise : bool, optional
Used when generating OpenMKM YAML file. If True, uses Motz-Wise
correction to sticking coefficient. Only applicable to
adsorption reactions. Default is False.
Returns
-------
SurfaceReaction : :class:`~pmutt.omkm.SurfaceReaction` object
"""
rxn = Reaction.from_string(reaction_str=reaction_str,
species=species,
species_delimiter=species_delimiter,
reaction_delimiter=reaction_delimiter)
return cls(reactants=rxn.reactants,
reactants_stoich=rxn.reactants_stoich,
products=rxn.products,
products_stoich=rxn.products_stoich,
transition_state=rxn.transition_state,
transition_state_stoich=rxn.transition_state_stoich,
notes=notes,
A=A,
beta=beta,
Ea=Ea,
is_adsorption=is_adsorption,
sticking_coeff=sticking_coeff,
direction=direction,
id=id,
use_motz_wise=use_motz_wise)