def setUp(self):
tasks = [
NwTask.dft_task(mol,
operation="optimize",
xc="b3lyp",
basis_set="6-31++G*"),
NwTask.dft_task(mol,
operation="freq",
xc="b3lyp",
basis_set="6-31++G*"),
NwTask.dft_task(mol,
operation="energy",
xc="b3lyp",
basis_set="6-311++G**"),
NwTask.dft_task(mol,
charge=mol.charge + 1,
operation="energy",
xc="b3lyp",
basis_set="6-311++G**"),
NwTask.dft_task(mol,
charge=mol.charge - 1,
operation="energy",
xc="b3lyp",
basis_set="6-311++G**")
]
self.nwi = NwInput(mol,
tasks,
geometry_options=["units", "angstroms", "noautoz"],
memory_options="total 1000 mb")
self.nwi_symm = NwInput(
mol,
tasks,
geometry_options=["units", "angstroms", "noautoz"],
symmetry_options=["c1"])
def test_from_string_and_file(self):
nwi = NwInput.from_file(os.path.join(test_dir, "ch4.nw"))
self.assertEqual(nwi.tasks[0].theory, "dft")
self.assertEqual(nwi.tasks[0].basis_set["C"], "6-31++G*")
self.assertEqual(nwi.tasks[-1].basis_set["C"], "6-311++G**")
#Try a simplified input.
str_inp = """start H4C1
geometry units angstroms
C 0.0 0.0 0.0
H 0.0 0.0 1.089
H 1.026719 0.0 -0.363
H -0.51336 -0.889165 -0.363
H -0.51336 0.889165 -0.363
end
title "H4C1 dft optimize"
charge 0
basis
H library "6-31++G*"
C library "6-31++G*"
end
dft
xc b3lyp
mult 1
end
task scf optimize
title "H4C1 dft freq"
charge 0
task scf freq
title "H4C1 dft energy"
charge 0
basis
H library "6-311++G**"
C library "6-311++G**"
end
task dft energy
title "H4C1 dft energy"
charge 1
dft
xc b3lyp
mult 2
end
task dft energy
title "H4C1 dft energy"
charge -1
task dft energy
"""
nwi = NwInput.from_string(str_inp)
self.assertEqual(nwi.geometry_options, ['units', 'angstroms'])
self.assertEqual(nwi.tasks[0].theory, "scf")
self.assertEqual(nwi.tasks[0].basis_set["C"], "6-31++G*")
self.assertEqual(nwi.tasks[-1].theory, "dft")
self.assertEqual(nwi.tasks[-1].basis_set["C"], "6-311++G**")
def test_to_from_dict(self):
d = self.nwi.as_dict()
nwi = NwInput.from_dict(d)
self.assertIsInstance(nwi, NwInput)
#Ensure it is json-serializable.
json.dumps(d)
d = self.nwi_symm.as_dict()
nwi_symm = NwInput.from_dict(d)
self.assertIsInstance(nwi_symm, NwInput)
json.dumps(d)
def test_to_from_dict(self):
d = self.nwi.to_dict
nwi = NwInput.from_dict(d)
self.assertIsInstance(nwi, NwInput)
#Ensure it is json-serializable.
json.dumps(d)
d = self.nwi_symm.to_dict
nwi_symm = NwInput.from_dict(d)
self.assertIsInstance(nwi_symm, NwInput)
json.dumps(d)
def correct(self):
backup("*.nw*")
actions = []
nwi = NwInput.from_file(self.input_file)
for e in self.errors:
if e == "autoz error":
action = {"_set": {"geometry_options": ["units",
"angstroms",
"noautoz"]}}
actions.append(action)
elif e == "Bad convergence":
t = nwi.tasks[self.ntasks - 1]
if "cgmin" in t.theory_directives:
nwi.tasks.pop(self.ntasks - 1)
else:
t.theory_directives["cgmin"] = ""
for t in nwi.tasks:
if t.operation.startswith("freq"):
#You cannot calculate hessian with cgmin.
t.theory_directives["nocgmin"] = ""
action = {"_set": {"tasks": [t.as_dict() for t in nwi.tasks]}}
actions.append(action)
else:
# For unimplemented errors, this should just cause the job to
# die.
return {"errors": self.errors, "actions": None}
m = Modder()
for action in actions:
nwi = m.modify_object(action, nwi)
nwi.write_file(self.input_file)
return {"errors": self.errors, "actions": actions}
def setUp(self):
tasks = [
NwTask.dft_task(mol, operation="optimize", xc="b3lyp",
basis_set="6-31++G*"),
NwTask.dft_task(mol, operation="freq", xc="b3lyp",
basis_set="6-31++G*"),
NwTask.dft_task(mol, operation="energy", xc="b3lyp",
basis_set="6-311++G**"),
NwTask.dft_task(mol, charge=mol.charge + 1, operation="energy",
xc="b3lyp", basis_set="6-311++G**"),
NwTask.dft_task(mol, charge=mol.charge - 1, operation="energy",
xc="b3lyp", basis_set="6-311++G**")
]
self.nwi = NwInput(mol, tasks,
geometry_options=["units", "angstroms", "noautoz"],
memory_options="total 1000 mb")
self.nwi_symm = NwInput(mol, tasks,
geometry_options=["units", "angstroms",
"noautoz"],
symmetry_options=["c1"])
def test_from_string_and_file(self):
nwi = NwInput.from_file(os.path.join(test_dir, "ch4.nw"))
self.assertEqual(nwi.tasks[0].theory, "dft")
self.assertEqual(nwi.memory_options, "total 1000 mb stack 400 mb")
self.assertEqual(nwi.tasks[0].basis_set["C"], "6-31++G*")
self.assertEqual(nwi.tasks[-1].basis_set["C"], "6-311++G**")
#Try a simplified input.
str_inp = """start H4C1
geometry units angstroms
C 0.0 0.0 0.0
H 0.0 0.0 1.089
H 1.026719 0.0 -0.363
H -0.51336 -0.889165 -0.363
H -0.51336 0.889165 -0.363
end
title "H4C1 dft optimize"
charge 0
basis
H library "6-31++G*"
C library "6-31++G*"
end
dft
xc b3lyp
mult 1
end
task scf optimize
title "H4C1 dft freq"
charge 0
task scf freq
title "H4C1 dft energy"
charge 0
basis
H library "6-311++G**"
C library "6-311++G**"
end
task dft energy
title "H4C1 dft energy"
charge 1
dft
xc b3lyp
mult 2
end
task dft energy
title "H4C1 dft energy"
charge -1
task dft energy
"""
nwi = NwInput.from_string(str_inp)
self.assertEqual(nwi.geometry_options, ['units', 'angstroms'])
self.assertEqual(nwi.tasks[0].theory, "scf")
self.assertEqual(nwi.tasks[0].basis_set["C"], "6-31++G*")
self.assertEqual(nwi.tasks[-1].theory, "dft")
self.assertEqual(nwi.tasks[-1].basis_set["C"], "6-311++G**")
str_inp_symm = str_inp.replace(
"geometry units angstroms", "geometry units angstroms\n symmetry "
"c1")
nwi_symm = NwInput.from_string(str_inp_symm)
self.assertEqual(nwi_symm.geometry_options, ['units', 'angstroms'])
self.assertEqual(nwi_symm.symmetry_options, ['c1'])
self.assertEqual(nwi_symm.tasks[0].theory, "scf")
self.assertEqual(nwi_symm.tasks[0].basis_set["C"], "6-31++G*")
self.assertEqual(nwi_symm.tasks[-1].theory, "dft")
self.assertEqual(nwi_symm.tasks[-1].basis_set["C"], "6-311++G**")
class NwInputTest(unittest.TestCase):
def setUp(self):
tasks = [
NwTask.dft_task(mol,
operation="optimize",
xc="b3lyp",
basis_set="6-31++G*"),
NwTask.dft_task(mol,
operation="freq",
xc="b3lyp",
basis_set="6-31++G*"),
NwTask.dft_task(mol,
operation="energy",
xc="b3lyp",
basis_set="6-311++G**"),
NwTask.dft_task(mol,
charge=mol.charge + 1,
operation="energy",
xc="b3lyp",
basis_set="6-311++G**"),
NwTask.dft_task(mol,
charge=mol.charge - 1,
operation="energy",
xc="b3lyp",
basis_set="6-311++G**")
]
self.nwi = NwInput(mol,
tasks,
geometry_options=["units", "angstroms", "noautoz"],
memory_options="total 1000 mb")
self.nwi_symm = NwInput(
mol,
tasks,
geometry_options=["units", "angstroms", "noautoz"],
symmetry_options=["c1"])
def test_str(self):
ans = """memory total 1000 mb
geometry units angstroms noautoz
C 0.0 0.0 0.0
H 0.0 0.0 1.089
H 1.026719 0.0 -0.363
H -0.51336 -0.889165 -0.363
H -0.51336 0.889165 -0.363
end
title "H4C1 dft optimize"
charge 0
basis
C library "6-31++G*"
H library "6-31++G*"
end
dft
mult 1
xc b3lyp
end
task dft optimize
title "H4C1 dft freq"
charge 0
basis
C library "6-31++G*"
H library "6-31++G*"
end
dft
mult 1
xc b3lyp
end
task dft freq
title "H4C1 dft energy"
charge 0
basis
C library "6-311++G**"
H library "6-311++G**"
end
dft
mult 1
xc b3lyp
end
task dft energy
title "H4C1 dft energy"
charge 1
basis
C library "6-311++G**"
H library "6-311++G**"
end
dft
mult 2
xc b3lyp
end
task dft energy
title "H4C1 dft energy"
charge -1
basis
C library "6-311++G**"
H library "6-311++G**"
end
dft
mult 2
xc b3lyp
end
task dft energy
"""
self.assertEqual(str(self.nwi), ans)
ans_symm = """geometry units angstroms noautoz
symmetry c1
C 0.0 0.0 0.0
H 0.0 0.0 1.089
H 1.026719 0.0 -0.363
H -0.51336 -0.889165 -0.363
H -0.51336 0.889165 -0.363
end
title "H4C1 dft optimize"
charge 0
basis
C library "6-31++G*"
H library "6-31++G*"
end
dft
mult 1
xc b3lyp
end
task dft optimize
title "H4C1 dft freq"
charge 0
basis
C library "6-31++G*"
H library "6-31++G*"
end
dft
mult 1
xc b3lyp
end
task dft freq
title "H4C1 dft energy"
charge 0
basis
C library "6-311++G**"
H library "6-311++G**"
end
dft
mult 1
xc b3lyp
end
task dft energy
title "H4C1 dft energy"
charge 1
basis
C library "6-311++G**"
H library "6-311++G**"
end
dft
mult 2
xc b3lyp
end
task dft energy
title "H4C1 dft energy"
charge -1
basis
C library "6-311++G**"
H library "6-311++G**"
end
dft
mult 2
xc b3lyp
end
task dft energy
"""
self.assertEqual(str(self.nwi_symm), ans_symm)
def test_to_from_dict(self):
d = self.nwi.as_dict()
nwi = NwInput.from_dict(d)
self.assertIsInstance(nwi, NwInput)
#Ensure it is json-serializable.
json.dumps(d)
d = self.nwi_symm.as_dict()
nwi_symm = NwInput.from_dict(d)
self.assertIsInstance(nwi_symm, NwInput)
json.dumps(d)
def test_from_string_and_file(self):
nwi = NwInput.from_file(os.path.join(test_dir, "ch4.nw"))
self.assertEqual(nwi.tasks[0].theory, "dft")
self.assertEqual(nwi.memory_options, "total 1000 mb stack 400 mb")
self.assertEqual(nwi.tasks[0].basis_set["C"], "6-31++G*")
self.assertEqual(nwi.tasks[-1].basis_set["C"], "6-311++G**")
#Try a simplified input.
str_inp = """start H4C1
geometry units angstroms
C 0.0 0.0 0.0
H 0.0 0.0 1.089
H 1.026719 0.0 -0.363
H -0.51336 -0.889165 -0.363
H -0.51336 0.889165 -0.363
end
title "H4C1 dft optimize"
charge 0
basis
H library "6-31++G*"
C library "6-31++G*"
end
dft
xc b3lyp
mult 1
end
task scf optimize
title "H4C1 dft freq"
charge 0
task scf freq
title "H4C1 dft energy"
charge 0
basis
H library "6-311++G**"
C library "6-311++G**"
end
task dft energy
title "H4C1 dft energy"
charge 1
dft
xc b3lyp
mult 2
end
task dft energy
title "H4C1 dft energy"
charge -1
task dft energy
"""
nwi = NwInput.from_string(str_inp)
self.assertEqual(nwi.geometry_options, ['units', 'angstroms'])
self.assertEqual(nwi.tasks[0].theory, "scf")
self.assertEqual(nwi.tasks[0].basis_set["C"], "6-31++G*")
self.assertEqual(nwi.tasks[-1].theory, "dft")
self.assertEqual(nwi.tasks[-1].basis_set["C"], "6-311++G**")
str_inp_symm = str_inp.replace(
"geometry units angstroms", "geometry units angstroms\n symmetry "
"c1")
nwi_symm = NwInput.from_string(str_inp_symm)
self.assertEqual(nwi_symm.geometry_options, ['units', 'angstroms'])
self.assertEqual(nwi_symm.symmetry_options, ['c1'])
self.assertEqual(nwi_symm.tasks[0].theory, "scf")
self.assertEqual(nwi_symm.tasks[0].basis_set["C"], "6-31++G*")
self.assertEqual(nwi_symm.tasks[-1].theory, "dft")
self.assertEqual(nwi_symm.tasks[-1].basis_set["C"], "6-311++G**")
class NwInputTest(unittest.TestCase):
def setUp(self):
tasks = [
NwTask.dft_task(mol, operation="optimize", xc="b3lyp",
basis_set="6-31++G*"),
NwTask.dft_task(mol, operation="freq", xc="b3lyp",
basis_set="6-31++G*"),
NwTask.dft_task(mol, operation="energy", xc="b3lyp",
basis_set="6-311++G**"),
NwTask.dft_task(mol, charge=mol.charge + 1, operation="energy",
xc="b3lyp", basis_set="6-311++G**"),
NwTask.dft_task(mol, charge=mol.charge - 1, operation="energy",
xc="b3lyp", basis_set="6-311++G**")
]
self.nwi = NwInput(mol, tasks,
geometry_options=["units", "angstroms", "noautoz"],
memory_options="total 1000 mb")
self.nwi_symm = NwInput(mol, tasks,
geometry_options=["units", "angstroms",
"noautoz"],
symmetry_options=["c1"])
def test_str(self):
ans = """memory total 1000 mb
geometry units angstroms noautoz
C 0.0 0.0 0.0
H 0.0 0.0 1.089
H 1.026719 0.0 -0.363
H -0.51336 -0.889165 -0.363
H -0.51336 0.889165 -0.363
end
title "H4C1 dft optimize"
charge 0
basis
C library "6-31++G*"
H library "6-31++G*"
end
dft
mult 1
xc b3lyp
end
task dft optimize
title "H4C1 dft freq"
charge 0
basis
C library "6-31++G*"
H library "6-31++G*"
end
dft
mult 1
xc b3lyp
end
task dft freq
title "H4C1 dft energy"
charge 0
basis
C library "6-311++G**"
H library "6-311++G**"
end
dft
mult 1
xc b3lyp
end
task dft energy
title "H4C1 dft energy"
charge 1
basis
C library "6-311++G**"
H library "6-311++G**"
end
dft
mult 2
xc b3lyp
end
task dft energy
title "H4C1 dft energy"
charge -1
basis
C library "6-311++G**"
H library "6-311++G**"
end
dft
mult 2
xc b3lyp
end
task dft energy
"""
self.assertEqual(str(self.nwi), ans)
ans_symm = """geometry units angstroms noautoz
symmetry c1
C 0.0 0.0 0.0
H 0.0 0.0 1.089
H 1.026719 0.0 -0.363
H -0.51336 -0.889165 -0.363
H -0.51336 0.889165 -0.363
end
title "H4C1 dft optimize"
charge 0
basis
C library "6-31++G*"
H library "6-31++G*"
end
dft
mult 1
xc b3lyp
end
task dft optimize
title "H4C1 dft freq"
charge 0
basis
C library "6-31++G*"
H library "6-31++G*"
end
dft
mult 1
xc b3lyp
end
task dft freq
title "H4C1 dft energy"
charge 0
basis
C library "6-311++G**"
H library "6-311++G**"
end
dft
mult 1
xc b3lyp
end
task dft energy
title "H4C1 dft energy"
charge 1
basis
C library "6-311++G**"
H library "6-311++G**"
end
dft
mult 2
xc b3lyp
end
task dft energy
title "H4C1 dft energy"
charge -1
basis
C library "6-311++G**"
H library "6-311++G**"
end
dft
mult 2
xc b3lyp
end
task dft energy
"""
self.assertEqual(str(self.nwi_symm), ans_symm)
def test_to_from_dict(self):
d = self.nwi.as_dict()
nwi = NwInput.from_dict(d)
self.assertIsInstance(nwi, NwInput)
#Ensure it is json-serializable.
json.dumps(d)
d = self.nwi_symm.as_dict()
nwi_symm = NwInput.from_dict(d)
self.assertIsInstance(nwi_symm, NwInput)
json.dumps(d)
def test_from_string_and_file(self):
nwi = NwInput.from_file(os.path.join(test_dir, "ch4.nw"))
self.assertEqual(nwi.tasks[0].theory, "dft")
self.assertEqual(nwi.memory_options, "total 1000 mb stack 400 mb")
self.assertEqual(nwi.tasks[0].basis_set["C"], "6-31++G*")
self.assertEqual(nwi.tasks[-1].basis_set["C"], "6-311++G**")
#Try a simplified input.
str_inp = """start H4C1
geometry units angstroms
C 0.0 0.0 0.0
H 0.0 0.0 1.089
H 1.026719 0.0 -0.363
H -0.51336 -0.889165 -0.363
H -0.51336 0.889165 -0.363
end
title "H4C1 dft optimize"
charge 0
basis
H library "6-31++G*"
C library "6-31++G*"
end
dft
xc b3lyp
mult 1
end
task scf optimize
title "H4C1 dft freq"
charge 0
task scf freq
title "H4C1 dft energy"
charge 0
basis
H library "6-311++G**"
C library "6-311++G**"
end
task dft energy
title "H4C1 dft energy"
charge 1
dft
xc b3lyp
mult 2
end
task dft energy
title "H4C1 dft energy"
charge -1
task dft energy
"""
nwi = NwInput.from_string(str_inp)
self.assertEqual(nwi.geometry_options, ['units', 'angstroms'])
self.assertEqual(nwi.tasks[0].theory, "scf")
self.assertEqual(nwi.tasks[0].basis_set["C"], "6-31++G*")
self.assertEqual(nwi.tasks[-1].theory, "dft")
self.assertEqual(nwi.tasks[-1].basis_set["C"], "6-311++G**")
str_inp_symm = str_inp.replace("geometry units angstroms",
"geometry units angstroms\n symmetry "
"c1")
nwi_symm = NwInput.from_string(str_inp_symm)
self.assertEqual(nwi_symm.geometry_options, ['units', 'angstroms'])
self.assertEqual(nwi_symm.symmetry_options, ['c1'])
self.assertEqual(nwi_symm.tasks[0].theory, "scf")
self.assertEqual(nwi_symm.tasks[0].basis_set["C"], "6-31++G*")
self.assertEqual(nwi_symm.tasks[-1].theory, "dft")
self.assertEqual(nwi_symm.tasks[-1].basis_set["C"], "6-311++G**")
