def test_from_file(self):
filepath = os.path.join(test_dir, 'MethylPyrrolidine_drawn.gjf')
gau = GaussianInput.from_file(filepath)
self.assertEqual(gau.molecule.composition.formula, "H11 C5 N1")
self.assertIn("opt", gau.route_parameters)
self.assertEqual(gau.route_parameters["geom"], "connectivity")
self.assertEqual(gau.functional, "b3lyp")
self.assertEqual(gau.basis_set, "6-311+g(d,p)")
filepath = os.path.join(test_dir, "g305_hb.txt")
with open(filepath) as f:
txt = f.read()
toks = txt.split("--link1--")
for i, t in enumerate(toks):
lines = t.strip().split("\n")
lines = [l.strip() for l in lines]
gau = GaussianInput.from_string("\n".join(lines))
self.assertIsNotNone(gau.molecule)
if i == 0:
mol = gau.molecule
ans = """Molecule Summary (H4 O2)
Reduced Formula: H2O
Sites (6)
1 O 0.000000 0.000000 0.000000
2 O 0.000000 0.000000 2.912902
3 H 0.892596 0.000000 -0.373266
4 H 0.143970 0.000219 0.964351
5 H -0.582554 0.765401 3.042783
6 H -0.580711 -0.766761 3.043012"""
self.assertEqual(str(mol), ans)
def test_from_file(self):
filepath = os.path.join(test_dir, 'MethylPyrrolidine_drawn.gjf')
gau = GaussianInput.from_file(filepath)
self.assertEqual(gau.molecule.composition.formula, "H11 C5 N1")
self.assertIn("opt", gau.route_parameters)
self.assertEqual(gau.route_parameters["geom"], "connectivity")
self.assertEqual(gau.functional, "b3lyp")
self.assertEqual(gau.basis_set, "6-311+g(d,p)")
filepath = os.path.join(test_dir, "g305_hb.txt")
with open(filepath) as f:
txt = f.read()
toks = txt.split("--link1--")
for i, t in enumerate(toks):
lines = t.strip().split("\n")
lines = [l.strip() for l in lines]
gau = GaussianInput.from_string("\n".join(lines))
self.assertIsNotNone(gau.molecule)
if i == 0:
mol = gau.molecule
ans = """Molecule Summary (H4 O2)
Reduced Formula: H2O
Charge = 0, Spin Mult = 1
Sites (6)
1 O 0.000000 0.000000 0.000000
2 O 0.000000 0.000000 2.912902
3 H 0.892596 0.000000 -0.373266
4 H 0.143970 0.000219 0.964351
5 H -0.582554 0.765401 3.042783
6 H -0.580711 -0.766761 3.043012"""
self.assertEqual(str(mol), ans)
def test_init(self):
mol = Molecule(["C", "H", "H", "H", "H"], self.coords)
gau = GaussianInput(mol, charge=1, route_parameters={'SP': "",
"SCF": "Tight"})
self.assertEqual(gau.spin_multiplicity, 2)
mol = Molecule(["C", "H", "H", "H", "H"], self.coords, charge=-1)
gau = GaussianInput(mol, route_parameters={'SP': "", "SCF": "Tight"})
self.assertEqual(gau.spin_multiplicity, 2)
self.assertRaises(ValueError, GaussianInput, mol, spin_multiplicity=1)
def test_str_and_from_string(self):
ans = """#P HF/6-31G(d) SP SCF=Tight Test
H4 C1
0 1
C
H 1 B1
H 1 B2 2 A2
H 1 B3 2 A3 3 D3
H 1 B4 2 A4 4 D4
B1=1.089000
B2=1.089000
A2=109.471221
B3=1.089000
A3=109.471213
D3=120.000017
B4=1.089000
A4=109.471213
D4=119.999966
EPS=12
"""
self.assertEqual(str(self.gau), ans)
gau = GaussianInput.from_string(ans)
self.assertEqual(gau.functional, 'HF')
self.assertEqual(gau.input_parameters['EPS'], 12)
def test_from_string(self):
gau_str = """%mem=5000000
%chk=filename
# mp2/6-31g* scf=direct
SIH4+ H2---SIH2+ CS //MP2(full)/6-31G* MP2=-290.9225259
1,2
Si
X,1,1.
H,1,R1,2,HALF1
H,1,R1,2,HALF1,3,180.,0
X,1,1.,2,90.,3,90.,0
X,1,1.,5,THETA,2,180.,0
H,1,R3,6,HALF3,5,0.,0
H,1,R4,6,HALF3,7,180.,0
R1=1.47014
R3=1.890457
R4=1.83514
HALF1=60.633314
THETA=10.35464
HALF3=11.861807"""
gau = GaussianInput.from_string(gau_str)
self.assertEqual("X3SiH4", gau.molecule.composition.reduced_formula)
def test_str_and_from_string(self):
ans = """#P HF/6-31G(d) SP SCF=Tight Test
H4 C1
0 1
C
H 1 B1
H 1 B2 2 A2
H 1 B3 2 A3 3 D3
H 1 B4 2 A4 4 D4
B1=1.089000
B2=1.089000
A2=109.471221
B3=1.089000
A3=109.471213
D3=120.000017
B4=1.089000
A4=109.471213
D4=119.999966
EPS=12
"""
self.assertEqual(str(self.gau), ans)
gau = GaussianInput.from_string(ans)
self.assertEqual(gau.functional, 'HF')
self.assertEqual(gau.input_parameters['EPS'], 12)
def test_from_string(self):
gau_str = """%mem=5000000
%chk=filename
# mp2/6-31g* scf=direct
SIH4+ H2---SIH2+ CS //MP2(full)/6-31G* MP2=-290.9225259
1,2
Si
X,1,1.
H,1,R1,2,HALF1
H,1,R1,2,HALF1,3,180.,0
X,1,1.,2,90.,3,90.,0
X,1,1.,5,THETA,2,180.,0
H,1,R3,6,HALF3,5,0.,0
H,1,R4,6,HALF3,7,180.,0
R1=1.47014
R3=1.890457
R4=1.83514
HALF1=60.633314
THETA=10.35464
HALF3=11.861807"""
gau = GaussianInput.from_string(gau_str)
self.assertEqual("X3SiH4", gau.molecule.composition.reduced_formula)
def write_mol(mol, filename):
"""
Write a molecule to a file based on file extension. For example, anything
ending in a "xyz" is assumed to be a XYZ file. Supported formats include
xyz, Gaussian input (gjf|g03|g09|com|inp), and pymatgen's JSON serialized
molecules.
Args:
mol (Molecule/IMolecule): Molecule to write
filename (str): A filename to write to.
"""
fname = os.path.basename(filename)
if fnmatch(fname.lower(), "*.xyz*"):
return XYZ(mol).write_file(filename)
elif any([
fnmatch(fname.lower(), "*.{}*".format(r))
for r in ["gjf", "g03", "g09", "com", "inp"]
]):
return GaussianInput(mol).write_file(filename)
elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
with zopen(filename, "w") as f:
return json.dump(mol, f, cls=PMGJSONEncoder)
else:
m = re.search("\.(pdb|mol|mdl|sdf|sd|ml2|sy2|mol2|cml|mrv)",
filename.lower())
if m:
return BabelMolAdaptor(mol).write_file(filename, m.group(1))
raise ValueError("Unrecognized file extension!")
def test_from_file(self):
filepath = os.path.join(test_dir, "MethylPyrrolidine_drawn.gjf")
gau = GaussianInput.from_file(filepath)
self.assertEqual(gau.molecule.composition.formula, "H11 C5 N1")
self.assertIn("opt", gau.route_parameters)
self.assertEqual(gau.route_parameters["geom"], "connectivity")
self.assertEqual(gau.functional, "b3lyp")
self.assertEqual(gau.basis_set, "6-311+g(d,p)")
def setUp(self):
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]]
self.coords = coords
mol = Molecule(["C", "H", "H", "H", "H"], coords)
self.gau = GaussianInput(
mol, route_parameters={'SP': "", "SCF": "Tight"},
input_parameters={"EPS": 12})
def read_mol(filename):
"""
Reads a molecule based on file extension. For example, anything ending in
a "xyz" is assumed to be a XYZ file. Supported formats include xyz,
gaussian input (gjf|g03|g09|com|inp), Gaussian output (.out|and
pymatgen's JSON serialized molecules. Using openbabel,
many more extensions are supported but requires openbabel to be installed.
Args:
filename:
A filename to read from.
Returns:
A Molecule object.
"""
fname = os.path.basename(filename)
if fnmatch(fname.lower(), "*.xyz*"):
return XYZ.from_file(filename).molecule
elif any([
fnmatch(fname.lower(), "*.{}*".format(r))
for r in ["gjf", "g03", "g09", "com", "inp"]
]):
return GaussianInput.from_file(filename).molecule
elif any([
fnmatch(fname.lower(), "*.{}*".format(r))
for r in ["out", "lis", "log"]
]):
return GaussianOutput(filename).final_structure
elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
with zopen(filename) as f:
s = json.load(f, cls=PMGJSONDecoder)
if type(s) != Molecule:
raise IOError("File does not contain a valid serialized "
"molecule")
return s
else:
m = re.search("\.(pdb|mol|mdl|sdf|sd|ml2|sy2|mol2|cml|mrv)",
filename.lower())
if m:
return BabelMolAdaptor.from_file(filename, m.group(1)).pymatgen_mol
raise ValueError("Unrecognized file extension!")
def read_mol(filename):
"""
Reads a molecule based on file extension. For example, anything ending in
a "xyz" is assumed to be a XYZ file. Supported formats include xyz,
gaussian input (gjf|g03|g09|com|inp), Gaussian output (.out|and
pymatgen's JSON serialized molecules. Using openbabel,
many more extensions are supported but requires openbabel to be installed.
Args:
filename:
A filename to read from.
Returns:
A Molecule object.
"""
fname = os.path.basename(filename)
if fnmatch(fname.lower(), "*.xyz*"):
return XYZ.from_file(filename).molecule
elif any([fnmatch(fname.lower(), "*.{}*".format(r))
for r in ["gjf", "g03", "g09", "com", "inp"]]):
return GaussianInput.from_file(filename).molecule
elif any([fnmatch(fname.lower(), "*.{}*".format(r))
for r in ["out", "lis", "log"]]):
return GaussianOutput(filename).final_structure
elif fnmatch(fname, "*.json*") or fnmatch(fname, "*.mson*"):
with zopen(filename) as f:
s = json.load(f, cls=PMGJSONDecoder)
if type(s) != Molecule:
raise IOError("File does not contain a valid serialized "
"molecule")
return s
else:
m = re.search("\.(pdb|mol|mdl|sdf|sd|ml2|sy2|mol2|cml|mrv)",
filename.lower())
if m:
return BabelMolAdaptor.from_file(filename,
m.group(1)).pymatgen_mol
raise ValueError("Unrecognized file extension!")