def test_disable_symmetry(self):
ans = '''$comments
Test Methane
$end
$molecule
0 1
C 0.00000000 0.00000000 0.00000000
H 0.00000000 0.00000000 1.08900000
H 1.02671900 0.00000000 -0.36300000
H -0.51336000 -0.88916500 -0.36300000
Cl -0.51336000 0.88916500 -0.36300000
$end
$rem
jobtype = sp
exchange = b3lyp
basis = 6-31+g*
sym_ignore = True
symmetry = False
$end
'''
qctask = QcTask(mol, title="Test Methane", exchange="B3LYP",
jobtype="SP",
basis_set="6-31+G*")
qctask.disable_symmetry()
self.assertEqual(str(qctask), ans)
self.elementary_io_verify(ans, qctask)
def test_use_cosmo(self):
ans = '''$comments
Test Methane
$end
$molecule
0 1
C 0.00000000 0.00000000 0.00000000
H 0.00000000 0.00000000 1.08900000
H 1.02671900 0.00000000 -0.36300000
H -0.51336000 -0.88916500 -0.36300000
Cl -0.51336000 0.88916500 -0.36300000
$end
$rem
jobtype = sp
exchange = b3lyp
basis = 6-31+g*
solvent_dielectric = 35.0
solvent_method = cosmo
$end
'''
qctask = QcTask(mol, title="Test Methane", exchange="B3LYP",
jobtype="SP",
basis_set="6-31+G*")
qctask.use_cosmo(dielectric_constant=35.0)
self.assertEqual(str(qctask), ans)
self.elementary_io_verify(ans, qctask)
def test_scale_geom_opt_threshold(self):
ans = '''$comments
Test Methane
$end
$molecule
0 1
C 0.00000000 0.00000000 0.00000000
H 0.00000000 0.00000000 1.08900000
H 1.02671900 0.00000000 -0.36300000
H -0.51336000 -0.88916500 -0.36300000
Cl -0.51336000 0.88916500 -0.36300000
$end
$rem
jobtype = sp
exchange = b3lyp
basis = 6-31+g*
geom_opt_tol_displacement = 120
geom_opt_tol_energy = 10
geom_opt_tol_gradient = 30
$end
'''
qctask = QcTask(mol, title="Test Methane", exchange="B3LYP",
jobtype="SP",
basis_set="6-31+G*")
qctask.scale_geom_opt_threshold(gradient=0.1, displacement=0.1,
energy=0.1)
self.assertEqual(str(qctask), ans)
self.elementary_io_verify(ans, qctask)
def test_set_geom_opt_use_gdiis(self):
ans = '''$comments
Test Methane
$end
$molecule
0 1
C 0.00000000 0.00000000 0.00000000
H 0.00000000 0.00000000 1.08900000
H 1.02671900 0.00000000 -0.36300000
H -0.51336000 -0.88916500 -0.36300000
Cl -0.51336000 0.88916500 -0.36300000
$end
$rem
jobtype = sp
exchange = b3lyp
basis = 6-31+g*
geom_opt_max_diis = -1
$end
'''
qctask = QcTask(mol, title="Test Methane", exchange="B3LYP",
jobtype="SP",
basis_set="6-31+G*")
qctask.set_geom_opt_use_gdiis()
self.assertEqual(str(qctask), ans)
self.elementary_io_verify(ans, qctask)
def test_set_dft_grid(self):
ans = '''$comments
Test Methane
$end
$molecule
0 1
C 0.00000000 0.00000000 0.00000000
H 0.00000000 0.00000000 1.08900000
H 1.02671900 0.00000000 -0.36300000
H -0.51336000 -0.88916500 -0.36300000
Cl -0.51336000 0.88916500 -0.36300000
$end
$rem
jobtype = sp
exchange = b3lyp
basis = 6-31+g*
xc_grid = 000110000590
$end
'''
qctask = QcTask(mol, title="Test Methane", exchange="B3LYP",
jobtype="SP",
basis_set="6-31+G*")
qctask.set_dft_grid(radical_points=110, angular_points=590)
self.assertEqual(str(qctask), ans)
self.elementary_io_verify(ans, qctask)
def test_geom_opt_max_cycles(self):
ans = '''$comments
Test Methane
$end
$molecule
1 2
C 0.00000000 0.00000000 0.00000000
H 0.00000000 0.00000000 1.08900000
H 1.02671900 0.00000000 -0.36300000
H -0.51336000 -0.88916500 -0.36300000
Cl -0.51336000 0.88916500 -0.36300000
$end
$rem
jobtype = sp
exchange = b3lyp
basis = 6-31+g*
geom_opt_max_cycles = 100
$end
'''
qctask = QcTask(mol, title="Test Methane", exchange="B3LYP",
jobtype="SP", charge=1, spin_multiplicity=2,
basis_set="6-31+G*")
qctask.set_geom_max_iterations(100)
self.assertEqual(str(qctask), ans)
self.elementary_io_verify(ans, qctask)
def test_set_scf_initial_guess(self):
ans = '''$comments
Test Methane
$end
$molecule
0 1
C 0.00000000 0.00000000 0.00000000
H 0.00000000 0.00000000 1.08900000
H 1.02671900 0.00000000 -0.36300000
H -0.51336000 -0.88916500 -0.36300000
Cl -0.51336000 0.88916500 -0.36300000
$end
$rem
jobtype = sp
exchange = b3lyp
basis = 6-31+g*
scf_guess = gwh
$end
'''
qctask = QcTask(mol, title="Test Methane", exchange="B3LYP",
jobtype="SP",
basis_set="6-31+G*")
qctask.set_scf_initial_guess("GWH")
self.assertEqual(str(qctask), ans)
self.elementary_io_verify(ans, qctask)
def test_set_max_scf_iterations(self):
ans = '''$comments
Test Methane
$end
$molecule
0 1
C 0.00000000 0.00000000 0.00000000
H 0.00000000 0.00000000 1.08900000
H 1.02671900 0.00000000 -0.36300000
H -0.51336000 -0.88916500 -0.36300000
Cl -0.51336000 0.88916500 -0.36300000
$end
$rem
jobtype = sp
exchange = b3lyp
basis = 6-31+g*
max_scf_cycles = 100
scf_algorithm = diis_gdm
$end
'''
qctask = QcTask(mol, title="Test Methane", exchange="B3LYP",
jobtype="SP",
basis_set="6-31+G*")
qctask.set_scf_algorithm_and_iterations(algorithm="diis_gdm",
iterations=100)
self.assertEqual(str(qctask), ans)
self.elementary_io_verify(ans, qctask)
def test_set_memory(self):
ans = '''$comments
Test Methane
$end
$molecule
0 1
C 0.00000000 0.00000000 0.00000000
H 0.00000000 0.00000000 1.08900000
H 1.02671900 0.00000000 -0.36300000
H -0.51336000 -0.88916500 -0.36300000
Cl -0.51336000 0.88916500 -0.36300000
$end
$rem
jobtype = sp
exchange = b3lyp
basis = 6-31+g*
mem_static = 500
mem_total = 18000
$end
'''
qctask = QcTask(mol, title="Test Methane", exchange="B3LYP",
jobtype="SP",
basis_set="6-31+G*")
qctask.set_memory(total=18000, static=500)
self.assertEqual(str(qctask), ans)
self.elementary_io_verify(ans, qctask)
def test_set_integral_threshold(self):
ans = '''$comment
Test Methane
$end
$molecule
0 1
C 0.00000000 0.00000000 0.00000000
H 0.00000000 0.00000000 1.08900000
H 1.02671900 0.00000000 -0.36300000
H -0.51336000 -0.88916500 -0.36300000
Cl -0.51336000 0.88916500 -0.36300000
$end
$rem
jobtype = sp
exchange = b3lyp
basis = 6-31+g*
thresh = 14
$end
'''
qctask = QcTask(mol, title="Test Methane", exchange="B3LYP",
jobtype="SP",
basis_set="6-31+G*")
qctask.set_integral_threshold(thresh=14)
self.assertEqual(str(qctask), ans)
self.elementary_io_verify(ans, qctask)
def test_set_max_num_of_scratch_files(self):
ans = '''$comment
Test Methane
$end
$molecule
0 1
C 0.00000000 0.00000000 0.00000000
H 0.00000000 0.00000000 1.08900000
H 1.02671900 0.00000000 -0.36300000
H -0.51336000 -0.88916500 -0.36300000
Cl -0.51336000 0.88916500 -0.36300000
$end
$rem
jobtype = sp
exchange = b3lyp
basis = 6-31+g*
max_sub_file_num = 500
$end
'''
qctask = QcTask(mol, title="Test Methane", exchange="B3LYP",
jobtype="SP",
basis_set="6-31+G*")
qctask.set_max_num_of_scratch_files(500)
self.assertEqual(str(qctask), ans)
self.elementary_io_verify(ans, qctask)
def to_and_from_dict_verify(self, qctask):
"""
Helper function. This function should be called in each specific test.
"""
d1 = qctask.to_dict
qc2 = QcTask.from_dict(d1)
d2 = qc2.to_dict
self.assertEqual(d1, d2)
def from_dict(cls, d):
h = QChemErrorHandler(input_file=d["input_file"],
output_file=d["output_file"],
ex_backup_list=d["ex_backup_list"],
rca_gdm_thresh=d["rca_gdm_thresh"],
scf_max_cycles=d["scf_max_cycles"],
geom_max_cycles=d["geom_max_cycles"])
h.outdata = d["outdata"]
h.qcinp = QcInput.from_dict(d["qcinp"]) if d["qcinp"] else None
h.error_step_id = d["error_step_id"]
h.errors = d["errors"]
h.fix_step = QcTask.from_dict(d["fix_step"]) if d["fix_step"] else None
return h
def test_use_pcm(self):
ans = '''$comments
Test Methane
$end
$molecule
0 1
C 0.00000000 0.00000000 0.00000000
H 0.00000000 0.00000000 1.08900000
H 1.02671900 0.00000000 -0.36300000
H -0.51336000 -0.88916500 -0.36300000
Cl -0.51336000 0.88916500 -0.36300000
$end
$rem
jobtype = sp
exchange = b3lyp
basis = 6-31+g*
solvent_method = pcm
$end
$pcm
radii uff
theory ssvpe
vdwscale 1.1
$end
$pcm_solvent
dielectric 78.3553
$end
'''
qctask = QcTask(mol, title="Test Methane", exchange="B3LYP",
jobtype="SP",
basis_set="6-31+G*")
qctask.use_pcm()
self.assertEqual(str(qctask), ans)
self.elementary_io_verify(ans, qctask)
qctask = QcTask(mol, title="Test Methane", exchange="B3LYP",
jobtype="SP",
basis_set="6-31+G*")
qctask.use_pcm(pcm_params={"Radii": "FF",
"Theory": "CPCM",
"SASrad": 1.5,
"HPoints": 1202},
solvent_params={"Dielectric": 20.0,
"Temperature": 300.75,
"NSolventAtoms": 2,
"SolventAtom": [[8, 1, 186, 1.30],
[1, 2, 187, 1.01]]},
radii_force_field="OPLSAA")
ans = '''$comments
Test Methane
$end
$molecule
0 1
C 0.00000000 0.00000000 0.00000000
H 0.00000000 0.00000000 1.08900000
H 1.02671900 0.00000000 -0.36300000
H -0.51336000 -0.88916500 -0.36300000
Cl -0.51336000 0.88916500 -0.36300000
$end
$rem
jobtype = sp
exchange = b3lyp
basis = 6-31+g*
force_fied = oplsaa
solvent_method = pcm
$end
$pcm
hpoints 1202
radii bondi
sasrad 1.5
theory cpcm
vdwscale 1.1
$end
$pcm_solvent
dielectric 20.0
nsolventatoms 2
solventatom 8 1 186 1.30
solventatom 1 2 187 1.01
temperature 300.75
$end
'''
self.assertEqual(str(qctask), ans)
self.elementary_io_verify(ans, qctask)
def test_read_zmatrix(self):
contents = '''$moLEcule
1 2
S
C 1 1.726563
H 2 1.085845 1 119.580615
C 2 1.423404 1 114.230851 3 -180.000000 0
H 4 1.084884 2 122.286346 1 -180.000000 0
C 4 1.381259 2 112.717365 1 0.000000 0
H 6 1.084731 4 127.143779 2 -180.000000 0
C 6 1.415867 4 110.076147 2 0.000000 0
F 8 1.292591 6 124.884374 4 -180.000000 0
$end
$reM
BASIS = 6-31+G*
EXCHANGE = B3LYP
jobtype = freq
$end
'''
qctask = QcTask.from_string(contents)
ans = '''$molecule
1 2
S 0.00000000 0.00000000 0.00000000
C 0.00000000 0.00000000 1.72656300
H -0.94431813 0.00000000 2.26258784
C 1.29800105 -0.00000002 2.31074808
H 1.45002821 -0.00000002 3.38492732
C 2.30733813 -0.00000003 1.36781908
H 3.37622632 -0.00000005 1.55253338
C 1.75466906 -0.00000003 0.06427152
F 2.44231414 -0.00000004 -1.03023099
$end
$rem
jobtype = freq
exchange = b3lyp
basis = 6-31+g*
$end
'''
ans_tokens = ans.split('\n')
ans_text_part = ans_tokens[:2] + ans_tokens[11:]
ans_coords_part = ans_tokens[2:11]
converted_tokens = str(qctask).split('\n')
converted_text_part = converted_tokens[:2] + converted_tokens[11:]
converted_coords_part = converted_tokens[2:11]
self.assertEqual(ans_text_part, converted_text_part)
for ans_coords, converted_coords in zip(ans_coords_part,
converted_coords_part):
ans_coords_tokens = ans_coords.split()
converted_coords_tokens = converted_coords.split()
self.assertEqual(ans_coords_tokens[0], converted_coords_tokens[0])
xyz1 = ans_coords_tokens[1:]
xyz2 = converted_coords_tokens[1:]
for t1, t2 in zip(xyz1, xyz2):
self.assertTrue(abs(float(t1)-float(t2)) < 0.0001)
def from_string_verify(self, contents, ref_dict):
qctask = QcTask.from_string(contents)
d2 = qctask.to_dict
self.assertEqual(ref_dict, d2)
