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 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 setUp(self):
self.task = NwTask(0, 1, basis_set={"H": "6-31g"}, theory="dft",
theory_directives={"xc": "b3lyp"})
self.task_cosmo = NwTask(0, 1, basis_set={"H": "6-31g"}, theory="dft",
theory_directives={"xc": "b3lyp"},
alternate_directives={'cosmo': "cosmo"})
self.task_esp = NwTask(0, 1, basis_set={"H": "6-31g"}, theory="esp")
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_dft_cosmo_task(self):
task = NwTask.dft_task(
mol,
charge=mol.charge,
operation="energy",
xc="b3lyp",
basis_set="6-311++G**",
alternate_directives={"cosmo": {
"dielec": 78.0
}},
)
ans = """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
cosmo
dielec 78.0
end
task dft energy"""
self.assertEqual(str(task), ans)
def setUp(self):
self.task = NwTask(0, 1, basis_set={"H": "6-31g"}, theory="dft",
theory_directives={"xc": "b3lyp"})
self.task_cosmo = NwTask(0, 1, basis_set={"H": "6-31g"}, theory="dft",
theory_directives={"xc": "b3lyp"},
alternate_directives={'cosmo': "cosmo"})
self.task_esp = NwTask(0, 1, basis_set={"H": "6-31g"}, theory="esp")
def test_esp_task(self):
task = NwTask.esp_task(mol, charge=mol.charge, operation="", basis_set="6-311++G**")
ans = """title "H4C1 esp "
charge 0
basis cartesian
C library "6-311++G**"
H library "6-311++G**"
end
task esp """
self.assertEqual(str(task), ans)
def test_esp_task(self):
task = NwTask.esp_task(mol, charge=mol.charge, operation="",
basis_set="6-311++G**")
ans = """title "H4C1 esp "
charge 0
basis cartesian
C library "6-311++G**"
H library "6-311++G**"
end
task esp """
self.assertEqual(str(task), ans)
def test_dft_task(self):
task = NwTask.dft_task(mol, charge=1, operation="energy")
ans = """title "H4C1 dft energy"
charge 1
basis
C library "6-31g"
H library "6-31g"
end
dft
mult 2
xc b3lyp
end
task dft energy"""
self.assertEqual(str(task), ans)
def test_dft_task(self):
task = NwTask.dft_task(mol, charge=1, operation="energy")
ans = """title "H4C1 dft energy"
charge 1
basis cartesian
C library "6-31g"
H library "6-31g"
end
dft
mult 2
xc b3lyp
end
task dft energy"""
self.assertEqual(str(task), ans)
def test_multi_bset(self):
t = NwTask.from_molecule(
mol, theory="dft", basis_set={"C": "6-311++G**", "H": "6-31++G**"}, theory_directives={"xc": "b3lyp"}
)
ans = """title "H4C1 dft optimize"
charge 0
basis cartesian
C library "6-311++G**"
H library "6-31++G**"
end
dft
xc b3lyp
end
task dft optimize"""
self.assertEqual(str(t), ans)
def test_multi_bset(self):
t = NwTask.from_molecule(
mol, theory="dft", basis_set={"C": "6-311++G**",
"H": "6-31++G**"},
theory_directives={"xc": "b3lyp"})
ans = """title "H4C1 dft optimize"
charge 0
basis cartesian
C library "6-311++G**"
H library "6-31++G**"
end
dft
xc b3lyp
end
task dft optimize"""
self.assertEqual(str(t), ans)
def test_dft_cosmo_task(self):
task = NwTask.dft_task(
mol, charge=mol.charge, operation="energy",
xc="b3lyp", basis_set="6-311++G**",
alternate_directives={'cosmo': {"dielec": 78.0}})
ans = """title "H4C1 dft energy"
charge 0
basis
C library "6-311++G**"
H library "6-311++G**"
end
dft
mult 1
xc b3lyp
end
cosmo
dielec 78.0
end
task dft energy"""
self.assertEqual(str(task), ans)
class NwTaskTest(unittest.TestCase):
def setUp(self):
self.task = NwTask(
0,
1,
basis_set={"H": "6-31g"},
theory="dft",
theory_directives={"xc": "b3lyp"},
)
self.task_cosmo = NwTask(
0,
1,
basis_set={"H": "6-31g"},
theory="dft",
theory_directives={"xc": "b3lyp"},
alternate_directives={"cosmo": "cosmo"},
)
self.task_esp = NwTask(0, 1, basis_set={"H": "6-31g"}, theory="esp")
def test_multi_bset(self):
t = NwTask.from_molecule(
mol,
theory="dft",
basis_set={
"C": "6-311++G**",
"H": "6-31++G**"
},
theory_directives={"xc": "b3lyp"},
)
ans = """title "H4C1 dft optimize"
charge 0
basis cartesian
C library "6-311++G**"
H library "6-31++G**"
end
dft
xc b3lyp
end
task dft optimize"""
self.assertEqual(str(t), ans)
def test_str_and_from_string(self):
ans = """title "dft optimize"
charge 0
basis cartesian
H library "6-31g"
end
dft
xc b3lyp
end
task dft optimize"""
self.assertEqual(str(self.task), ans)
def test_to_from_dict(self):
d = self.task.as_dict()
t = NwTask.from_dict(d)
self.assertIsInstance(t, NwTask)
def test_init(self):
self.assertRaises(NwInputError,
NwTask,
0,
1, {"H": "6-31g"},
theory="bad")
self.assertRaises(NwInputError,
NwTask,
0,
1, {"H": "6-31g"},
operation="bad")
def test_dft_task(self):
task = NwTask.dft_task(mol, charge=1, operation="energy")
ans = """title "H4C1 dft energy"
charge 1
basis cartesian
C library "6-31g"
H library "6-31g"
end
dft
mult 2
xc b3lyp
end
task dft energy"""
self.assertEqual(str(task), ans)
def test_dft_cosmo_task(self):
task = NwTask.dft_task(
mol,
charge=mol.charge,
operation="energy",
xc="b3lyp",
basis_set="6-311++G**",
alternate_directives={"cosmo": {
"dielec": 78.0
}},
)
ans = """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
cosmo
dielec 78.0
end
task dft energy"""
self.assertEqual(str(task), ans)
def test_esp_task(self):
task = NwTask.esp_task(mol,
charge=mol.charge,
operation="",
basis_set="6-311++G**")
ans = """title "H4C1 esp "
charge 0
basis cartesian
C library "6-311++G**"
H library "6-311++G**"
end
task esp """
self.assertEqual(str(task), ans)
def test_to_from_dict(self):
d = self.task.as_dict()
t = NwTask.from_dict(d)
self.assertIsInstance(t, NwTask)
def test_to_from_dict(self):
d = self.task.as_dict()
t = NwTask.from_dict(d)
self.assertIsInstance(t, NwTask)
class NwTaskTest(unittest.TestCase):
def setUp(self):
self.task = NwTask(0, 1, basis_set={"H": "6-31g"}, theory="dft",
theory_directives={"xc": "b3lyp"})
self.task_cosmo = NwTask(0, 1, basis_set={"H": "6-31g"}, theory="dft",
theory_directives={"xc": "b3lyp"},
alternate_directives={'cosmo': "cosmo"})
self.task_esp = NwTask(0, 1, basis_set={"H": "6-31g"}, theory="esp")
def test_multi_bset(self):
t = NwTask.from_molecule(
mol, theory="dft", basis_set={"C": "6-311++G**",
"H": "6-31++G**"},
theory_directives={"xc": "b3lyp"})
ans = """title "H4C1 dft optimize"
charge 0
basis
C library "6-311++G**"
H library "6-31++G**"
end
dft
xc b3lyp
end
task dft optimize"""
self.assertEqual(str(t), ans)
def test_str_and_from_string(self):
ans = """title "dft optimize"
charge 0
basis
H library "6-31g"
end
dft
xc b3lyp
end
task dft optimize"""
self.assertEqual(str(self.task), ans)
def test_to_from_dict(self):
d = self.task.as_dict()
t = NwTask.from_dict(d)
self.assertIsInstance(t, NwTask)
def test_init(self):
self.assertRaises(NwInputError, NwTask, 0, 1, {"H": "6-31g"},
theory="bad")
self.assertRaises(NwInputError, NwTask, 0, 1, {"H": "6-31g"},
operation="bad")
def test_dft_task(self):
task = NwTask.dft_task(mol, charge=1, operation="energy")
ans = """title "H4C1 dft energy"
charge 1
basis
C library "6-31g"
H library "6-31g"
end
dft
mult 2
xc b3lyp
end
task dft energy"""
self.assertEqual(str(task), ans)
def test_dft_cosmo_task(self):
task = NwTask.dft_task(
mol, charge=mol.charge, operation="energy",
xc="b3lyp", basis_set="6-311++G**",
alternate_directives={'cosmo': {"dielec": 78.0}})
ans = """title "H4C1 dft energy"
charge 0
basis
C library "6-311++G**"
H library "6-311++G**"
end
dft
mult 1
xc b3lyp
end
cosmo
dielec 78.0
end
task dft energy"""
self.assertEqual(str(task), ans)
def test_esp_task(self):
task = NwTask.esp_task(mol, charge=mol.charge, operation="",
basis_set="6-311++G**")
ans = """title "H4C1 esp "
charge 0
basis
C library "6-311++G**"
H library "6-311++G**"
end
task esp """
self.assertEqual(str(task), ans)
#!/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)
