def test_str_and_from_string(self):
ans = """#P HF/6-31G(d) SCF=Tight SP
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_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 = """Full Formula (H4 O2)
Reduced Formula: H2O
Charge = 0, Spin Mult = 1
Sites (6)
0 O 0.000000 0.000000 0.000000
1 O 0.000000 0.000000 2.912902
2 H 0.892596 0.000000 -0.373266
3 H 0.143970 0.000219 0.964351
4 H -0.582554 0.765401 3.042783
5 H -0.580711 -0.766761 3.043012"""
self.assertEqual(str(mol), ans)
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_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 = """Full Formula (H4 O2)
Reduced Formula: H2O
Charge = 0, Spin Mult = 1
Sites (6)
0 O 0.000000 0.000000 0.000000
1 O 0.000000 0.000000 2.912902
2 H 0.892596 0.000000 -0.373266
3 H 0.143970 0.000219 0.964351
4 H -0.582554 0.765401 3.042783
5 H -0.580711 -0.766761 3.043012"""
self.assertEqual(str(mol), ans)
def test_str_and_from_string(self):
ans = """#P HF/6-31G(d) SCF=Tight SP
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 parse_file(filename):
with open(filename) as f:
txt = f.read()
toks = txt.split("--link1--")
for t in toks:
try:
lines = t.strip().split("\n")
lines = [l.strip() for l in lines]
gau = GaussianInput.from_string("\n".join(lines))
yield (gau.molecule, gau.charge, gau.spin_multiplicity)
except:
print("error in {}".format(t))
