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 test_from_dict(self):
self.assertEqual(Reactions.from_dict(self.reactions_dict),
self.reactions)
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)
])
from pmutt.io.thermdat import read_thermdat
# Find the location of Jupyter notebook
# Note that normally Python scripts have a __file__ variable but Jupyter notebook doesn't.
# Using pathlib can overcome this limiation
notebook_folder = Path().resolve()
'''Read the thermdat file and convert it to a dictionary'''
NH3_species_list = read_thermdat(os.path.join(notebook_folder, 'thermdat_NH3'))
NH3_species = pmutt_list_to_dict(NH3_species_list)
'''Initialize the reaction'''
rxns = Reactions(reactions=[
Reaction.from_string('0.5N2 + 1.5H2 = 0.5TS4_N2 + 1.5H2 = N(S1) + 1.5H2',
NH3_species),
Reaction.from_string('N(S1) + 1.5H2 = N(S1) + 3H(S1)', NH3_species),
Reaction.from_string('N(S1) + 3H(S1) = TS3_NH + 2H(S1) = NH(S1) + 2H(S1)',
NH3_species),
Reaction.from_string('NH(S1) + 2H(S1) = TS2_NH2 + H(S1) = NH2(S1) + H(S1)',
NH3_species),
Reaction.from_string('NH2(S1) + H(S1) = TS1_NH3 = NH3(S1)', NH3_species),
Reaction.from_string('NH3(S1) = NH3', NH3_species)
])
'''Plot the reaction coordinate diagram'''
# Enthalpy coordinate diagram
fig1, ax1 = rxns.plot_coordinate_diagram(method_name='get_H',
units='eV',
T=300.)
# Gibbs energy coordinate diagram on the same plot
fig1, ax1 = rxns.plot_coordinate_diagram(method_name='get_G',
units='eV',
T=300.,
figure=fig1,
# In[4]:
from pmutt import pmutt_list_to_dict
from pmutt.reaction import ChemkinReaction, Reactions
# Convert list of Nasa polynomials to dictionary of Nasa polynomials
species_dict = pmutt_list_to_dict(species)
reactions_data = read_excel(io=excel_path, sheet_name='reactions')
reactions_list = []
for reaction_data in reactions_data:
reaction = ChemkinReaction.from_string(species=species_dict,
**reaction_data)
reactions_list.append(reaction)
reactions = Reactions(reactions=reactions_list)
# ## Writing Chemkin files
# Now that we have all the required objects, we can write the output files. All outputs can be found in the [./outputs folder](https://github.com/VlachosGroup/pmutt/blob/master/docs/source/examples_jupyter/chemkin_io/outputs).
# ### Writing thermdat
# In[5]:
from pmutt.io.thermdat import write_thermdat
write_thermdat(filename='./outputs/thermdat', nasa_species=species)
# The thermdat file written in shown below.
# ```
# THERMO ALL