def test_write_thermo_block(self):
"""Test that we can write a normal thermo block"""
species = Species(smiles='CC')
species.thermo = self.nasa
result = write_thermo_entry(species, verbose=False)
self.assertEqual(result, self.entry1)
def test_write_thermo_block_5_elem(self):
"""Test that we can write a thermo block for a species with 5 elements"""
species = Species().from_adjacency_list("""
1 O u0 p3 c-1 {3,S}
2 O u0 p2 c0 {3,D}
3 N u0 p0 c+1 {1,S} {2,D} {4,S}
4 C u0 p0 c0 {3,S} {5,S} {6,S} {7,S}
5 H u0 p0 c0 {4,S}
6 H u0 p0 c0 {4,S}
7 H u0 p0 c0 {4,S}
8 X u0 p0 c0
""")
species.thermo = self.nasa
result = write_thermo_entry(species, verbose=False)
self.assertEqual(result, self.entry2)
def write_chemkin(self, output_directory):
"""
Appends the thermo block to `chem.inp` and species name to
`species_dictionary.txt` within the `outut_directory` specified
"""
species = self.species
with open(os.path.join(output_directory, 'chem.inp'), 'a') as f:
if isinstance(species, Species):
if species.molecule and isinstance(species.molecule[0],
Molecule):
element_counts = get_element_count(species.molecule[0])
else:
try:
element_counts = species.props['element_counts']
except KeyError:
element_counts = self.element_count_from_conformer()
else:
element_counts = {'C': 0, 'H': 0}
chemkin_thermo_string = write_thermo_entry(
species, element_counts=element_counts, verbose=True)
f.write('{0}\n'.format(chemkin_thermo_string))
# write species dictionary
if isinstance(species, Species):
if species.molecule and isinstance(species.molecule[0], Molecule):
spec_dict_path = os.path.join(output_directory,
'species_dictionary.txt')
is_species_in_dict = False
if os.path.isfile(spec_dict_path):
with open(spec_dict_path, 'r') as f:
# check whether the species dictionary contains this species, in which case do not re-append
for line in f.readlines():
if species.label == line.strip():
is_species_in_dict = True
break
if not is_species_in_dict:
with open(spec_dict_path, 'a') as f:
f.write(species.molecule[0].to_adjacency_list(
remove_h=False, label=species.label))
f.write('\n')
return chemkin_thermo_string