# ## Initialize Species Used For Reaction # First, we need to describe our species as pMuTT objects. For this example, we will be importing the thermdat from the [combustion database by Berkeley](http://combustion.berkeley.edu/gri_mech/version30/files30/thermo30.dat). We will store the species in a dictionary for code clarity later on. # In[1]: from pprint import pprint from pMuTT.io_.thermdat import read_thermdat from pMuTT import pMuTT_list_to_dict # The output will be a list species_list = read_thermdat(filename='thermdat') # This function converts the list to a dict for easier usage downstream species_dict = pMuTT_list_to_dict(pMuTT_list=species_list, key='name') # (Optional) Print the species_dict to see what's in it pprint(species_dict) # To calculate transition state properties, we will need to represent the transition state species as a pMuTT object. For this example, we will create a new ``Nasa`` object based on the H2O entry but modify the a6 parameter arbitrarily to give it a higher enthalpy. # In[2]: from copy import deepcopy # Make a copy so we don't edit the original H2O H2O_TS = deepcopy(species_dict['H2O'])
import json
import numpy as np
from matplotlib import pyplot as plt
from pMuTT import pMuTT_list_to_dict
from pMuTT.reaction import Reaction
from pMuTT.io_.thermdat import read_thermdat
from pMuTT.io_.excel import read_excel
from pMuTT.io_.json import pMuTTEncoder
os.chdir(os.path.dirname(__file__))
'''Read species'''
nasa_species = read_thermdat('thermdat')
nasa_dict = pMuTT_list_to_dict(nasa_species)
'''Read reactions'''
rxns_data = read_excel('reactions.xlsx')
rxns = [Reaction.from_string(species=nasa_dict, **rxn_data) for rxn_data in rxns_data]
'''Save reactions as json'''
with open('reactions.json', 'w') as f_ptr:
json.dump(rxns, f_ptr, cls=pMuTTEncoder, indent=True)
'''
Get thermodynamics from Reaction
'''
T = np.linspace(200., 3500.)
for rxn in rxns:
HoRT_rxn = rxn.get_delta_HoRT(T=T)
def read_reactions(filename, species=None):
"""Directly read reactions from Chemkin gas.inp or surf.inp files
Parameters
----------
filename : str
Input filename for Chemkin surf or gas .inp file
species : list of :class:`~pMuTT.empirical.nasa.Nasa` objects
List of NASA objects containing thermodynamic properties for
all Reactants and Products in Reactions
default = None. Will not return React_obj and Prod_obj
Returns
-------
Reactions : list of reactions
Reactants : list of reactants found in reactions
React_obj : list of NASA polynomials for each Reactant
If species object list is supplied
React_stoic : list of reaction stoichiometries for Reactants
Products : list of products found in reactions
Prod_obj : list of NASA polynomials for each Product
If species object list is supplied
Prod_stoic : list of reaction stoichiometries for Products
Raises
------
FileNotFoundError
If the surf.inp or gas.inp file isn't found.
NameError
If the species file does not exist
AttributeError
If the species list is incorrect format
"""
if species is not None:
species_dict = pMuTT_list_to_dict(species)
rxns = []
with open(filename, 'r') as lines:
for line in lines:
if re.findall(r'(^[^\!].+)( *<*(?<![0-9][eE])[=\-]>* *)', line):
rxns.append(line.strip())
RHS = []
LHS = []
for rxn in rxns:
LHS.append(re.split(r' *<*(?<![0-9][eE])[=\-]>* *', rxn)[0])
RHS.append(re.split(r' *<*(?<![0-9][eE])[=\-]>* *', rxn)[1])
Reactants = []
Products = []
React_obj = []
Prod_obj = []
React_stoic = []
Prod_stoic = []
for Reacs, Prods in zip(LHS, RHS):
Reactants.append(re.split(r' *\+ *| +', Reacs))
Products.append(re.split(r' *\+ *| +', Prods)[0:-3])
R = []
RS = []
Rx = []
for RR in Reactants[-1]:
stoic = re.findall(r'^[0-9]*', RR)[0]
if stoic == '':
stoic = 1
else:
RR = RR.replace(stoic, "")
stoic = int(stoic)
Rx.append(RR)
RS.append(stoic)
if species is not None:
R.append(species_dict[RR])
Reactants[-1] = Rx
React_stoic.append(RS)
P = []
PS = []
Px = []
for PP in Products[-1]:
stoic = re.findall(r'^[0-9]*', PP)[0]
if stoic == '':
stoic = 1
else:
PP = PP.replace(stoic, "")
stoic = int(stoic)
Px.append(PP)
PS.append(stoic)
if species is not None:
P.append(species_dict[PP])
Products[-1] = Px
Prod_stoic.append(PS)
React_obj.append(R)
Prod_obj.append(P)
Reactions = []
for rxn, Prods in zip(rxns, Products):
Reactions.append(rxn[0:rxn.rindex(Prods[-1]) + len(Prods[-1])])
if species is not None:
return (Reactions, Reactants, React_obj, React_stoic, Products,
Prod_obj, Prod_stoic)
else:
return (Reactions, Reactants, React_stoic, Products, Prod_stoic)
import os
import numpy as np
from matplotlib import pyplot as plt
from pMuTT.io_.thermdat import read_thermdat
from pMuTT import pMuTT_list_to_dict
from pMuTT import reaction as rxn
'''
Read the thermdat
'''
base_path = os.path.dirname(__file__)
nasa_list = read_thermdat(os.path.join(base_path, 'thermdat'))
nasa_dict = pMuTT_list_to_dict(nasa_list, key='name')
'''
Create the reaction object
'''
reaction_str = 'H2+0.5O2=H2O'
rxn_nasa = rxn.Reaction.from_string(reaction_str=reaction_str,
species=nasa_dict)
'''
Check that the equation is balanced
'''
rxn_nasa.check_element_balance()
'''
Get thermodynamics from Reaction
'''
T = np.linspace(200., 3500.)
HoRT_rxn = rxn_nasa.get_delta_HoRT(T=T)
# [0]: https://vlachosgroup.github.io/pMuTT/io.html#pMuTT.io_.thermdat.read_thermdat
# ## Reactions
# 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