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 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)
])
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))
# You can specify the notation for the reaction!
rxn = Reaction.from_string(reaction_str='H2 ++ 0.5O2 --> H2O_TS --> H2O',
species=species_dict,
species_delimiter='++',
reaction_delimiter='-->')
# When reprinting it, it will converts it to the standard notation
print('Creating Reaction object using custom string notation: {}'.format(rxn))
# ## Calculate Thermodynamic Reaction Properties
# With the reaction object specified, we can now calculate reaction properties. Let us calculate the standard formation enthalpy and standard entropy.
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)