def test__polynomial():
""" test pac99_io.reader.__
"""
pac99_poly = pac99_io.reader.nasa_polynomial(OUT_STR)
assert pac99_poly == read_text_file(['data'], 'pac99_poly.dat')
name = 'mol'
atom_dct = {'C': 2, 'H': 4, 'N': 2, 'O': 6}
ckin_poly = pac99_io.pac2ckin_poly(name, atom_dct, pac99_poly)
assert ckin_poly == read_text_file(['data'], 'ckin_poly.dat')
def test__convert():
""" test pac99_io._convert.pac2ckin_poly
"""
ckin_poly = pac2ckin_poly(name, atom_dict, comment_str, pac_poly_str):
ref_ckin_poly = """
"""
assert ckin_poly == ref_ckin_poly
def test__polynomial():
""" test pac99_io.reader.nasa_polynomial
test pac99_io._convert.pac3ckin_poly
"""
# Read and Convert C2H4N2O6
out_str = pathtools.read_file(DAT_PATH, 'C2H4N2O6.c97')
pac99_poly = pac99_io.reader.nasa_polynomial(out_str)
assert pac99_poly == (pathtools.read_file(DAT_PATH,
'C2H4N2O6.paccpoly').rstrip())
name = 'C2H4N2O6'
atom_dct = {'C': 2, 'H': 4, 'N': 2, 'O': 6}
ckin_poly = pac99_io.pac2ckin_poly(name, atom_dct, pac99_poly)
assert ckin_poly == pathtools.read_file(DAT_PATH, 'C2H4N2O6.ckinpoly')
# Read and Convert CO
out_str = pathtools.read_file(DAT_PATH, 'CO.c97')
pac99_poly = pac99_io.reader.nasa_polynomial(out_str)
assert pac99_poly == (pathtools.read_file(DAT_PATH,
'CO.paccpoly')).rstrip()
name = 'CO'
atom_dct = {'C': 1, 'O': 1}
ckin_poly = pac99_io.pac2ckin_poly(name, atom_dct, pac99_poly)
assert ckin_poly == pathtools.read_file(DAT_PATH, 'CO.ckinpoly')
# Read and Convert H2
out_str = pathtools.read_file(DAT_PATH, 'H2.c97')
pac99_poly = pac99_io.reader.nasa_polynomial(out_str)
assert pac99_poly == (pathtools.read_file(DAT_PATH,
'H2.paccpoly')).rstrip()
name = 'H2'
atom_dct = {'H': 2}
ckin_poly = pac99_io.pac2ckin_poly(name, atom_dct, pac99_poly)
assert ckin_poly == pathtools.read_file(DAT_PATH, 'H2.ckinpoly')
def build_polynomial(spc_name, spc_dct, temps,
pf_path, nasa_path, starting_path):
""" Build a nasa polynomial
"""
print('Generating NASA polynomials at path: {}'.format(nasa_path))
# Generate forumula
spc_dct_i = spc_dct[spc_name]
formula = automol.inchi.formula_string(spc_dct_i['inchi'])
formula_dct = automol.inchi.formula(spc_dct_i['inchi'])
hform0 = spc_dct_i['Hfs'][0]
# Go to NASA path
if not os.path.exists(nasa_path):
os.makedirs(nasa_path)
pathtools.go_to(nasa_path)
# Write and run ThermP to get the Hf298K and coefficients
write_thermp_inp(formula, hform0, temps)
pfrunner.run_thermp(pf_path, nasa_path)
thermp_out_str = pathtools.read_file(nasa_path, 'thermp.out')
hform298 = thermp_io.reader.hf298k(thermp_out_str)
# Run PAC99 to get a NASA polynomial string in its format
pfrunner.run_pac(formula, nasa_path)
c97_file = pathtools.prepare_path(nasa_path, formula + '.c97')
with open(c97_file, 'r') as file_obj:
pac99_out_str = file_obj.read()
# pac99_out_str = pathtools.read_file(o97_file)
pac99_poly_str = pac99_io.reader.nasa_polynomial(pac99_out_str)
# Obtain CHEMKIN string using PAC99 polynomial
ckin_poly_str = pac99_io.pac2ckin_poly(
spc_name, formula_dct, pac99_poly_str)
# Write the full CHEMKIN strings
header_str = '\n'
nasa_str = writer.ckin.nasa_polynomial(hform0, hform298, ckin_poly_str)
full_ckin_str = header_str + nasa_str
print('\nCHEMKIN Polynomial:')
print(full_ckin_str)
# Go back to starting path
pathtools.go_to(starting_path)
return full_ckin_str