def testCorrectEntropy(self):
"""
Tests that correctEntropy effectively makes the isotopomer have the same
thermo as isotopeless with the change in entropy corresponding to the
symmetry difference.
This example compares propane to a asymmetrically labeled propane.
"""
from rmgpy.thermo.nasa import NASA, NASAPolynomial
from copy import deepcopy
from rmgpy import constants
propanei = Species().fromAdjacencyList(
"""
1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S}
2 C u0 p0 c0 {1,S} {3,S} {7,S} {8,S}
3 C u0 p0 c0 i13 {2,S} {9,S} {10,S} {11,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {2,S}
9 H u0 p0 c0 {3,S}
10 H u0 p0 c0 {3,S}
11 H u0 p0 c0 {3,S}
""")
propane = Species().fromAdjacencyList(
"""
1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S}
2 C u0 p0 c0 {1,S} {3,S} {7,S} {8,S}
3 C u0 p0 c0 {2,S} {9,S} {10,S} {11,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {2,S}
9 H u0 p0 c0 {3,S}
10 H u0 p0 c0 {3,S}
11 H u0 p0 c0 {3,S}
""")
# get thermo of propane
original_thermo = NASA(polynomials=[NASAPolynomial(
coeffs=[1.10564,0.0315339,-1.48274e-05,3.39621e-09,-2.97953e-13,-14351.9,18.775],
Tmin=(100,'K'), Tmax=(3370.6,'K')), NASAPolynomial(
coeffs=[-1.45473,0.0241202,-6.87667e-06,9.03634e-10,-4.48389e-14,-6688.59,43.0459],
Tmin=(3370.6,'K'), Tmax=(5000,'K'))], Tmin=(100,'K'), Tmax=(5000,'K'),
comment="""Thermo group additivity estimation: group(Cs-CsCsHH) + gauche(Cs(CsCsRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R)""")
propane.thermo = deepcopy(original_thermo)
propanei.thermo = deepcopy(original_thermo)
correct_entropy(propanei,propane)
self.assertAlmostEqual(propane.getEnthalpy(298),propanei.getEnthalpy(298))
self.assertAlmostEqual(propanei.getEntropy(298)-propane.getEntropy(298),constants.R * np.log(2))
def test_thermo(self):
"""Test that thermodata is loaded correctly from RMG's database"""
spc = Species().fromSMILES(str('O=C=O'))
spc.thermo = self.rmgdb.thermo.getThermoData(spc)
self.assertAlmostEqual(spc.getEnthalpy(298), -393547.040000, 5)
self.assertAlmostEqual(spc.getEntropy(298), 213.71872, 5)
self.assertAlmostEqual(spc.getHeatCapacity(1000), 54.35016, 5)
def test_restart(self):
"""
Test restarting ARC through the ARC class in main.py via the input_dict argument of the API
Rather than through ARC.py. Check that all files are in place and tst file content.
"""
restart_path = os.path.join(arc_path, 'arc', 'testing', 'restart(H,H2O2,N2H3,CH3CO2).yml')
project = 'arc_project_for_testing_delete_after_usage2'
project_directory = os.path.join(arc_path, 'Projects', project)
arc1 = ARC(project=project, ess_settings=dict(),
input_dict=restart_path, project_directory=project_directory)
arc1.execute()
with open(os.path.join(project_directory, 'output', 'thermo.info'), 'r') as f:
thermo_sft_ccsdtf12_bac = False
for line in f.readlines():
if 'thermo_DFT_CCSDTF12_BAC' in line:
thermo_sft_ccsdtf12_bac = True
break
self.assertTrue(thermo_sft_ccsdtf12_bac)
with open(os.path.join(project_directory, 'arc_project_for_testing_delete_after_usage2.info'), 'r') as f:
sts, n2h3, oet, lot, ap = False, False, False, False, False
for line in f.readlines():
if 'Considered the following species and TSs:' in line:
sts = True
elif 'Species N2H3' in line:
n2h3 = True
elif 'Overall time since project initiation:' in line:
oet = True
elif 'Levels of theory used:' in line:
lot = True
elif 'ARC project arc_project_for_testing_delete_after_usage2' in line:
ap = True
self.assertTrue(sts)
self.assertTrue(n2h3)
self.assertTrue(oet)
self.assertTrue(lot)
self.assertTrue(ap)
with open(os.path.join(project_directory, 'arc.log'), 'r') as f:
aei, ver, git, spc, rtm, ldb, therm, src, ter = False, False, False, False, False, False, False, False, False
for line in f.readlines():
if 'ARC execution initiated on' in line:
aei = True
elif '# Version:' in line:
ver = True
elif 'The current git HEAD for ARC is:' in line:
git = True
elif 'Considering species: CH3CO2_rad' in line:
spc = True
elif 'All jobs for species N2H3 successfully converged. Run time: 1:16:03' in line:
rtm = True
elif 'Loading the RMG database...' in line:
ldb = True
elif 'Thermodynamics for H2O2:' in line:
therm = True
elif 'Sources of thermoproperties determined by RMG for the parity plots:' in line:
src = True
elif 'ARC execution terminated on' in line:
ter = True
self.assertTrue(aei)
self.assertTrue(ver)
self.assertTrue(git)
self.assertTrue(spc)
self.assertTrue(rtm)
self.assertTrue(ldb)
self.assertTrue(therm)
self.assertTrue(src)
self.assertTrue(ter)
self.assertTrue(os.path.isfile(os.path.join(project_directory, 'output', 'thermo_parity_plots.pdf')))
with open(os.path.join(project_directory, 'output', 'Species', 'H2O2', 'species_dictionary.txt'), 'r') as f:
lines = f.readlines()
adj_list = str(''.join([line for line in lines if (line and 'H2O2' not in line)]))
mol1 = Molecule().fromAdjacencyList(adj_list)
self.assertEqual(mol1.toSMILES(), str('OO'))
thermo_library_path = os.path.join(project_directory, 'output', 'RMG libraries', 'thermo',
'arc_project_for_testing_delete_after_usage2.py')
new_thermo_library_path = os.path.join(settings['database.directory'], 'thermo', 'libraries',
'arc_project_for_testing_delete_after_usage2.py')
# copy the generated library to RMG-database
shutil.copyfile(thermo_library_path, new_thermo_library_path)
db = RMGDatabase()
db.load(
path=settings['database.directory'],
thermoLibraries=[str('arc_project_for_testing_delete_after_usage2')],
transportLibraries=[],
reactionLibraries=[],
seedMechanisms=[],
kineticsFamilies='none',
kineticsDepositories=[],
statmechLibraries=None,
depository=False,
solvation=False,
testing=True,
)
spc2 = Species().fromSMILES(str('CC([O])=O'))
spc2.generate_resonance_structures()
spc2.thermo = db.thermo.getThermoData(spc2)
self.assertAlmostEqual(spc2.getEnthalpy(298), -178003.44650359568, 1)
self.assertAlmostEqual(spc2.getEntropy(298), 283.5983103176096, 1)
self.assertAlmostEqual(spc2.getHeatCapacity(1000), 118.99753808225603, 1)
self.assertTrue('arc_project_for_testing_delete_after_usage2' in spc2.thermo.comment)
# delete the generated library from RMG-database
os.remove(new_thermo_library_path)
def testCorrectEntropy(self):
"""
Tests that correctEntropy effectively makes the isotopomer have the same
thermo as isotopeless with the change in entropy corresponding to the
symmetry difference.
This example compares propane to a asymmetrically labeled propane.
"""
from rmgpy.thermo.nasa import NASA, NASAPolynomial
from copy import deepcopy
from rmgpy import constants
propanei = Species().fromAdjacencyList("""
1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S}
2 C u0 p0 c0 {1,S} {3,S} {7,S} {8,S}
3 C u0 p0 c0 i13 {2,S} {9,S} {10,S} {11,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {2,S}
9 H u0 p0 c0 {3,S}
10 H u0 p0 c0 {3,S}
11 H u0 p0 c0 {3,S}
""")
propane = Species().fromAdjacencyList("""
1 C u0 p0 c0 {2,S} {4,S} {5,S} {6,S}
2 C u0 p0 c0 {1,S} {3,S} {7,S} {8,S}
3 C u0 p0 c0 {2,S} {9,S} {10,S} {11,S}
4 H u0 p0 c0 {1,S}
5 H u0 p0 c0 {1,S}
6 H u0 p0 c0 {1,S}
7 H u0 p0 c0 {2,S}
8 H u0 p0 c0 {2,S}
9 H u0 p0 c0 {3,S}
10 H u0 p0 c0 {3,S}
11 H u0 p0 c0 {3,S}
""")
# get thermo of propane
original_thermo = NASA(
polynomials=[
NASAPolynomial(coeffs=[
1.10564, 0.0315339, -1.48274e-05, 3.39621e-09,
-2.97953e-13, -14351.9, 18.775
],
Tmin=(100, 'K'),
Tmax=(3370.6, 'K')),
NASAPolynomial(coeffs=[
-1.45473, 0.0241202, -6.87667e-06, 9.03634e-10,
-4.48389e-14, -6688.59, 43.0459
],
Tmin=(3370.6, 'K'),
Tmax=(5000, 'K'))
],
Tmin=(100, 'K'),
Tmax=(5000, 'K'),
comment=
"""Thermo group additivity estimation: group(Cs-CsCsHH) + gauche(Cs(CsCsRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R) + group(Cs-CsHHH) + gauche(Cs(Cs(CsRR)RRR)) + other(R)"""
)
propane.thermo = deepcopy(original_thermo)
propanei.thermo = deepcopy(original_thermo)
correct_entropy(propanei, propane)
self.assertAlmostEqual(propane.getEnthalpy(298),
propanei.getEnthalpy(298))
self.assertAlmostEqual(
propanei.getEntropy(298) - propane.getEntropy(298),
constants.R * np.log(2))
