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_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.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 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 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 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 get_nwinput(self, mol):
functional = "b3lyp"
geom_opt_bset = {}
scf_bset = {}
for el in mol.composition.elements:
geom_opt_bset[el.symbol] = "6-31+g*"
scf_bset[el.symbol] = "6-31++g**" if el.Z <= 18 else "6-31+g*"
if len(mol) > 1:
# Insert opt and freq job for molecules with more than one atom.
tasks = [
NwTask.dft_task(mol, operation="optimize", xc=functional,
basis_set=geom_opt_bset),
NwTask.dft_task(mol, operation="freq", xc=functional,
basis_set=geom_opt_bset)
]
else:
tasks = []
tasks.extend([
NwTask.dft_task(mol, operation="energy", xc=functional,
basis_set=scf_bset),
NwTask.dft_task(mol, charge=mol.charge + 1, operation="energy",
xc=functional, basis_set=scf_bset),
NwTask.dft_task(mol, charge=mol.charge - 1, operation="energy",
xc=functional, basis_set=scf_bset)
])
return NwInput(mol, tasks)
def _prepare_pymatgen_dict(parameters,struct=None):
from pymatgen.io.nwchem import NwInput
import copy
par = copy.deepcopy(parameters)
add_cell = par.pop('add_cell',False)
if struct:
if add_cell:
par['geometry_options'].append(
'\n system crystal\n'
' lat_a {}\n lat_b {}\n lat_c {}\n'
' alpha {}\n beta {}\n gamma {}\n'
' end'.format(*(struct.cell_lengths+struct.cell_angles)))
if 'mol' not in par:
par['mol'] = {}
if 'sites' not in par['mol']:
par['mol']['sites'] = []
atoms = struct.get_ase()
for i,atom_type in enumerate(atoms.get_chemical_symbols()):
xyz = []
if add_cell:
xyz = atoms.get_scaled_positions()[i]
else:
xyz = atoms.get_positions()[i]
par['mol']['sites'].append({
'species': [ { 'element': atom_type, 'occu': 1 } ],
'xyz': xyz
})
return str(NwInput.from_dict(par))
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 cartesian
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 cartesian
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 cartesian
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 cartesian
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 cartesian
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 cartesian
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 cartesian
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 cartesian
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 cartesian
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 cartesian
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 cartesian
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 cartesian
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 cartesian
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 cartesian
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**")
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**")
#!/usr/bin/env python
# coding: utf-8
from __future__ import division, print_function, unicode_literals, \
absolute_import
from pymatgen import Molecule
from pymatgen.io.nwchem import NwInput, NwTask
coords = [[0.000000, 0.000000, 0.000000], [0.000000, 0.000000, 1.089000],
[1.026719, 0.000000, -0.363000], [-0.513360, -0.889165, -0.363000],
[-0.513360, 0.889165, -0.363000]]
mol = Molecule(["C", "H", "H", "H", "H"], coords)
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*")
]
nwi = NwInput(mol, tasks)
print(nwi)
