def test_opt_gamess():
"""
Test Optimization in Gamess using methanol in water.
"""
methanol = Molecule('test/test_files/ion_methanol.xyz')
methanol.properties['symmetry'] = 'Cs'
s = Settings()
s.specific.gamess.contrl.nzvar = 12
s.specific.gamess.system.timlim = 2
s.specific.gamess.system.mwords = 2
s.specific.gamess.pcm.solvnt = 'water'
s.specific.gamess.basis.gbasis = 'sto'
s.specific.gamess.basis.ngauss = 3
s.specific.gamess.guess.guess = 'huckel'
s.specific.gamess.stapt.optol = '1d-5'
s.specific.gamess.zmat["izmat(1)"] = "1,1,2, 1,2,3, 1,3,4, 1,3,5, 1,3,6, \n"\
"2,1,2,3, 2,2,3,4, 2,2,3,5, 2,2,3,6, \n"\
"3,1,2,3,4, 3,1,2,3,5, 3,1,2,3,6"
inp = templates.geometry.overlay(s)
methanol_geometry = gamess(inp, methanol, work_dir='/tmp')
mol_opt = run(methanol_geometry.molecule)
coords = concat([a.coords for a in mol_opt.atoms])
expected_coords = [
-0.9956983464, 0.9204754677, -0.0002616586, -0.72585581, -0.0802380791,
2.18166e-05, 0.741292161, 0.0371204735, -1.69738e-05, 1.1448441964,
0.5632291664, -0.9026112278, 1.1448447102, 0.562978981, 0.9027182521,
1.1454516521, -0.9993402516, 1.04943e-05
]
assert abs(sum(zipWith(operator.sub)(coords)(expected_coords))) < 1e-7
def test_opt_orca():
"""
Test Orca input generation and run functions.
"""
h2o = Molecule('test/test_files/h2o.xyz', 'xyz', charge=0, multiplicity=1)
h2o_geometry = dftb(templates.geometry, h2o)
s = Settings()
# generic keyword "basis" must be present in the generic dictionary
s.basis = "sto_dzp"
# "specific" allows the user to apply specific keywords for a
# package that are not in a generic dictionary
# s.specific.adf.basis.core = "large"
r = templates.singlepoint.overlay(s)
h2o_singlepoint = orca(r, h2o_geometry.molecule)
dipole = h2o_singlepoint.dipole
final_result = run(dipole, n_processes=1)
expected_dipole = [0.82409, 0.1933, -0.08316]
diff = sqrt(sum((x - y) ** 2 for x, y in zip(final_result,
expected_dipole)))
print("Expected dipole computed with Orca 3.0.3 is:", expected_dipole)
print("Actual dipole is:", final_result)
assert diff < 1e-2
def test_opt_orca():
"""Test Orca input generation and run functions."""
h2o = Molecule(PATH_MOLECULES / "h2o.xyz", 'xyz', charge=0, multiplicity=1)
h2o_geometry = dftb(templates.geometry, h2o)
s = Settings()
# generic keyword "basis" must be present in the generic dictionary
s.basis = "sto_dzp"
# s.specific.adf.basis.core = "large"
r = templates.singlepoint.overlay(s)
h2o_singlepoint = orca(r, h2o_geometry.molecule)
dipole = h2o_singlepoint.dipole
final_result = run(dipole, n_processes=1)
expected_dipole = [0.82409, 0.1933, -0.08316]
diff = sqrt(sum((x - y)**2 for x, y in zip(final_result, expected_dipole)))
logger.info(
f"Expected dipole computed with Orca 3.0.3 is: {expected_dipole}")
logger.info(f"Actual dipole is: {final_result}")
assertion.lt(diff, 1e-2)
def test_opt_orca():
"""
Test Orca input generation and run functions.
"""
h2o = Molecule('test/test_files/h2o.xyz', 'xyz', charge=0, multiplicity=1)
h2o_geometry = dftb(templates.geometry, h2o)
s = Settings()
# generic keyword "basis" must be present in the generic dictionary
s.basis = "sto_dzp"
# "specific" allows the user to apply specific keywords for a
# package that are not in a generic dictionary
# s.specific.adf.basis.core = "large"
r = templates.singlepoint.overlay(s)
h2o_singlepoint = orca(r, h2o_geometry.molecule)
dipole = h2o_singlepoint.dipole
final_result = run(dipole, n_processes=1)
expected_dipole = [0.82409, 0.1933, -0.08316]
diff = sqrt(sum((x - y)**2 for x, y in zip(final_result, expected_dipole)))
print("Expected dipole computed with Orca 3.0.3 is:", expected_dipole)
print("Actual dipole is:", final_result)
assert diff < 1e-2
def test_opt_gamess():
"""
Test Optimization in Gamess using methanol in water.
"""
methanol = Molecule('test/test_files/ion_methanol.xyz')
methanol.properties['symmetry'] = 'Cs'
s = Settings()
s.specific.gamess.contrl.nzvar = 12
s.specific.gamess.system.timlim = 2
s.specific.gamess.system.mwords = 2
s.specific.gamess.pcm.solvnt = 'water'
s.specific.gamess.basis.gbasis = 'sto'
s.specific.gamess.basis.ngauss = 3
s.specific.gamess.guess.guess = 'huckel'
s.specific.gamess.stapt.optol = '1d-5'
s.specific.gamess.zmat["izmat(1)"] = "1,1,2, 1,2,3, 1,3,4, 1,3,5, 1,3,6, \n"\
"2,1,2,3, 2,2,3,4, 2,2,3,5, 2,2,3,6, \n"\
"3,1,2,3,4, 3,1,2,3,5, 3,1,2,3,6"
inp = templates.geometry.overlay(s)
methanol_geometry = gamess(inp, methanol, work_dir='/tmp')
mol_opt = run(methanol_geometry.molecule)
coords = concat([a.coords for a in mol_opt.atoms])
expected_coords = [-0.9956983464, 0.9204754677, -0.0002616586, -0.72585581,
-0.0802380791, 2.18166e-05, 0.741292161, 0.0371204735,
-1.69738e-05, 1.1448441964, 0.5632291664, -0.9026112278,
1.1448447102, 0.562978981, 0.9027182521,
1.1454516521, -0.9993402516, 1.04943e-05]
assert abs(sum(zipWith(operator.sub)(coords)(expected_coords))) < 1e-7
def test_methanol_opt_orca():
"""Run a methanol optimization and retrieve the optimized geom."""
methanol = Molecule(PATH_MOLECULES / "methanol.xyz")
s = Settings()
s.specific.orca.main = "RKS B3LYP SVP Opt NumFreq TightSCF SmallPrint"
s.specific.orca.scf = " print[p_mos] 1"
opt = orca(s, methanol)
# extract coordinates
mol_opt = run(opt.molecule)
coords = collapse([a.coords for a in mol_opt.atoms])
logger.info(coords)
def test_hessian_transfer():
"""Test DFTB -> Orca hessian transfer."""
h2o = molkit.from_smiles('O')
h2o.properties.symmetry = 'C1'
h2o_freq = dftb(templates.freq, h2o, job_name="freq").hessian
s = Settings()
s.inithess = h2o_freq
h2o_opt = orca(templates.geometry.overlay(s), h2o, job_name="opt")
energy = h2o_opt.energy
dipole = h2o_opt.dipole
wf = gather(energy, dipole)
logger.info(run(wf))
def test_hessian_transfer():
"""
Test DFTB -> Orca hessian transfer
"""
h2o = molkit.from_smiles('O')
h2o.properties.symmetry = 'C1'
h2o_freq = dftb(templates.freq, h2o, job_name="freq").hessian
s = Settings()
s.inithess = h2o_freq
h2o_opt = orca(templates.geometry.overlay(s), h2o, job_name="opt")
energy = h2o_opt.energy
dipole = h2o_opt.dipole
wf = gather(energy, dipole)
print(run(wf))
def test_methanol_opt_orca():
"""
Run a methanol optimization and retrieve the optimized geom.
"""
methanol = Molecule('test/test_files/methanol.xyz')
s = Settings()
s.specific.orca.main = "RKS B3LYP SVP Opt TightSCF SmallPrint"
opt = orca(s, methanol)
mol_opt = run(opt.molecule)
expected_coords = [-1.311116, -0.051535, -0.000062, 0.097548, 0.033890,
-0.000077, -1.683393, -1.092152, -0.000066,
-1.734877, 0.448868, 0.891460, -1.734894, 0.448881,
-0.891567, 0.460481, -0.857621, -0.000038]
coords = concat([a.coords for a in mol_opt.atoms])
assert abs(sum(zipWith(operator.sub)(coords)(expected_coords))) < 1e-7
def test_methanol_opt_orca():
"""
Run a methanol optimization and retrieve the optimized geom.
"""
methanol = Molecule('test/test_files/methanol.xyz')
s = Settings()
s.specific.orca.main = "RKS B3LYP SVP Opt TightSCF SmallPrint"
opt = orca(s, methanol)
mol_opt = run(opt.molecule)
expected_coords = [
-1.311116, -0.051535, -0.000062, 0.097548, 0.033890, -0.000077,
-1.683393, -1.092152, -0.000066, -1.734877, 0.448868, 0.891460,
-1.734894, 0.448881, -0.891567, 0.460481, -0.857621, -0.000038
]
coords = concat([a.coords for a in mol_opt.atoms])
assert abs(sum(zipWith(operator.sub)(coords)(expected_coords))) < 1e-7