def clean_species(self):
"""
Custom validation for the species field to ensure that a valid adjacency
list has been provided.
"""
try:
nasa = self.cleaned_data['NASA']
if nasa == '':
return ''
read_thermo_entry(nasa)
except Exception:
import traceback
traceback.print_exc()
raise forms.ValidationError('Invalid NASA Polynomial.')
return nasa
def test_read_thermo_block_5_elem(self):
"""Test that we can read a thermo block with 5 elements"""
species, thermo, formula = read_thermo_entry(self.entry2)
self.assertEqual(species, 'CH3NO2X')
self.assertEqual(formula, {'X': 1, 'C': 1, 'O': 2, 'H': 3, 'N': 1})
self.assertTrue(self.nasa.is_identical_to(thermo))
def test_read_thermo_block(self):
"""Test that we can read a normal thermo block"""
species, thermo, formula = read_thermo_entry(self.entry1)
self.assertEqual(species, 'C2H6')
self.assertEqual(formula, {'H': 6, 'C': 2})
self.assertTrue(self.nasa.is_identical_to(thermo))
def evaluateNASA(request):
"""
Creates webpage form form entering a chemkin format NASA Polynomial and quickly
obtaining it's enthalpy and Cp values.
"""
from rmgpy.chemkin import read_thermo_entry
form = NASAForm()
thermo = None
thermo_data = None
if request.method == 'POST':
posted = NASAForm(request.POST, error_class=DivErrorList)
initial = request.POST.copy()
if posted.is_valid():
nasa = posted.cleaned_data['nasa']
if nasa != '':
species, thermo, formula = read_thermo_entry(nasa)
try:
thermo_data = thermo.to_thermo_data()
except:
# if we cannot convert the thermo to thermo data, we will not be able to display the
# H298, S298, and Cp values, but that's ok.
pass
form = NASAForm(initial, error_class=DivErrorList)
return render(request, 'NASA.html', {'form': form, 'thermo': thermo, 'thermoData': thermo_data})
def test_read_thermo_entry_bad_element_count(self, mock_logging):
"""
Test that invalid element count logs the appropriate warning.
This test uses the `mock` module in order to test calls to logging.
The `mock.patch` decorator replaces the logging module instance in
rmgpy.chemkin with a mock instance that can be accessed by this
unit test. By using the mock instance, it is possible to assert that
the expected logging statements are being created.
"""
entry = """C2H6 H XC X L 100.000 5000.000 827.28 1
2.44813916E+00 1.83377834E-02-7.25714119E-06 1.35300042E-09-9.60327447E-14 2
-1.19655244E+04 8.07917520E+00 3.50507145E+00-3.65219841E-03 6.32200490E-05 3
-8.01049582E-08 3.19734088E-11-1.15627878E+04 6.67152939E+00 4
"""
with self.assertRaises(ValueError):
read_thermo_entry(entry)
mock_logging.info.assert_called_with(
"Trouble reading line 'C2H6 H XC X L 100.000 5000.000 827.28 1' element segment 'H X'")
def test_read_thermo_entry_no_temperature_range(self):
"""Test that missing temperature range can be handled for thermo entry."""
entry = """C2H6 H 6C 2 G 1
2.44813916E+00 1.83377834E-02-7.25714119E-06 1.35300042E-09-9.60327447E-14 2
-1.19655244E+04 8.07917520E+00 3.50507145E+00-3.65219841E-03 6.32200490E-05 3
-8.01049582E-08 3.19734088E-11-1.15627878E+04 6.67152939E+00 4
"""
species, thermo, formula = read_thermo_entry(entry, Tmin=100.0, Tint=827.28, Tmax=5000.0)
self.assertEqual(species, 'C2H6')
self.assertEqual(formula, {'H': 6, 'C': 2})
self.assertTrue(isinstance(thermo, NASA))
def test_read_thermo_entry_not_float(self, mock_logging):
"""
Test that non-float parameters log the appropriate warning.
This test uses the `mock` module in order to test calls to logging.
The `mock.patch` decorator replaces the logging module instance in
rmgpy.chemkin with a mock instance that can be accessed by this
unit test. By using the mock instance, it is possible to assert that
the expected logging statements are being created.
"""
entry = """C2H6 H 6C 2 G 100.000 5000.000 827.28 1
X.44813916E+00 1.83377834E-02-7.25714119E-06 1.35300042E-09-9.60327447E-14 2
-1.19655244E+04 8.07917520E+00 3.50507145E+00-3.65219841E-03 6.32200490E-05 3
-8.01049582E-08 3.19734088E-11-1.15627878E+04 6.67152939E+00 4
"""
species, thermo, formula = read_thermo_entry(entry)
mock_logging.warning.assert_called_with("could not convert string to float: 'X.44813916E+00'")
self.assertEqual(species, 'C2H6')
self.assertIsNone(formula)
self.assertIsNone(thermo)
