def test__thermo():
""" test
"""
ref_hform298 = -0.028389069688367432
formula_str = automol.formula.string(FORMULA)
thermp_script_str = autorun.SCRIPT_DCT['thermp']
pac99_script_str = autorun.SCRIPT_DCT['pac99'].format(formula_str)
with tempfile.TemporaryDirectory(dir=PATH) as run_dir:
hform298, nasa_poly = autorun.thermo(thermp_script_str,
pac99_script_str,
run_dir,
PF_STR,
NAME,
FORMULA,
HFORM0,
enthalpyt=ENTHALPYT,
breakt=BREAKT,
convert=True)
assert numpy.isclose(hform298, ref_hform298)
assert nasa_poly == read_text_file(['data'], 'ch4nasa.ckin', path=PATH)
def build_polynomial(spc_name, spc_dct, pf_path, nasa_path):
""" Build a nasa polynomial
"""
# Read the temperatures from the pf.dat file, check if viable
temps = pfrunner.read_messpf_temps(pf_path)
ioprinter.nasa('fit', temps=temps)
ioprinter.generating('NASA polynomials', nasa_path)
# Generate forumula
spc_dct_i = spc_dct[spc_name]
formula_str = automol.inchi.formula_string(spc_dct_i['inchi'])
formula_dct = automol.inchi.formula(spc_dct_i['inchi'])
hform0 = spc_dct_i['Hfs'][0]
thermp_script_str = autorun.SCRIPT_DCT['thermp']
pac99_script_str = autorun.SCRIPT_DCT['pac99'].format(formula_str)
# Copy MESSPF output file to THERMP run dir and rename to pf.dat
pf_str = ioformat.pathtools.read_file(pf_path, 'pf.dat')
print('pf_path test:', pf_path)
print('pf_str test:', pf_str)
hform298, poly_str = autorun.thermo(
thermp_script_str, pac99_script_str, nasa_path,
pf_str, spc_name, formula_dct, hform0,
enthalpyt=0.0, breakt=1000.0, convert=True)
# Write the full CHEMKIN strings
ckin_str = writer.ckin.nasa_polynomial(hform0, hform298, poly_str)
full_ckin_str = '\n' + ckin_str
# Print thermo
return full_ckin_str
def _run_autorun(name, fml, hform0, pf_str, run_dir):
""" Generate a NASA polynomial for a given species by calling
ThermP+PAC99
"""
print(f' - Running ThermP+PAC99 at {run_dir}')
fml_str = automol.formula.string(fml)
thermp_script_str = autorun.SCRIPT_DCT['thermp']
pac99_script_str = autorun.SCRIPT_DCT['pac99'].format(fml_str)
hform298, nasa_poly = autorun.thermo(thermp_script_str,
pac99_script_str,
run_dir,
pf_str,
name,
fml,
hform0,
enthalpyt=ENTHALPYT,
breakt=BREAKT,
convert=True)
return hform298, nasa_poly
def build_polynomial(spc_name,
spc_dct,
pf_path,
nasa_path,
spc_locs_idx=None,
spc_mod=None):
""" For a given species: obtain partition function data read from a
MESSPF output file currently existing in the RUN filesystem as well as
the previously computed 0 K heat-of-formation from the species
dictionary. Then use this to run ThermP and PAC99 in the RUN filesystem
to generate a ChemKin-formatted 7-coefficient NASA polynomial.
:param spc_name: mechanism name of species to write MESSPF input for
:type spc_name: str
:param spc_dct:
:type spc_dct:
:param pf_path: path to existing MESSPF file in RUN filesystem
:type pf_path: str
:param nasa_path: path to run ThermP+PAC99 in RUN filesystem
:type nasa_path: str
:rtype: str
"""
# Read the temperatures from the pf.dat file, check if viable
ioprinter.nasa('fit', path=pf_path)
ioprinter.generating('NASA polynomials', nasa_path)
# Generate forumula
spc_dct_i = spc_dct[spc_name]
formula_str = automol.inchi.formula_string(spc_dct_i['inchi'])
formula_dct = automol.inchi.formula(spc_dct_i['inchi'])
if spc_locs_idx == 'final':
hform0 = spc_dct_i['Hfs']['final'][0]
spc_label = spc_name
elif spc_locs_idx is not None:
hform0 = spc_dct_i['Hfs'][spc_locs_idx][spc_mod][0]
spc_label = spc_name # + '_{:g}'.format(spc_locs_idx)
# spc_label = spc_name + '_' + spc_locs[1][:5]
else:
hform0 = spc_dct_i['Hfs'][0]
spc_label = spc_name
thermp_script_str = autorun.SCRIPT_DCT['thermp']
pac99_script_str = autorun.SCRIPT_DCT['pac99'].format(formula_str)
# Copy MESSPF output file to THERMP run dir and rename to pf.dat
pf_str = ioformat.pathtools.read_file(pf_path, 'pf.dat')
hform298, poly_str = autorun.thermo(thermp_script_str,
pac99_script_str,
nasa_path,
pf_str,
spc_label,
formula_dct,
hform0,
enthalpyt=0.0,
breakt=1000.0,
convert=True)
# Write the full CHEMKIN strings
ckin_str = '\n' + writer.ckin.nasa_polynomial(hform0, hform298, poly_str)
return ckin_str