def test_read_negative(self):
str_molecule = """$molecule
-1 1
S -1.1516880000 0.8568110000 -0.0787470000
S 1.1527500000 -0.8580450000 -0.0786430000
O -1.6523520000 1.8607750000 -1.0252100000
O -0.9052880000 1.2448490000 1.3156410000
O 0.9072410000 -1.2461780000 1.3158760000
O 1.6543670000 -1.8616640000 -1.0249090000
C -2.5841130000 -0.3746500000 0.0297340000
C 2.5833220000 0.3755850000 0.0296900000
F -3.6480730000 0.2204040000 0.6112110000
F -2.2609850000 -1.4531020000 0.7616580000
F -2.9656640000 -0.7966010000 -1.1900330000
F 3.6467050000 -0.2152590000 0.6163310000
F 2.2560700000 1.4560310000 0.7568190000
F 2.9672080000 0.7933560000 -1.1908790000
N -0.0001900000 -0.0016540000 -0.8250640000
$end
$rem
job_type = opt
basis = 6-311++g*
max_scf_cycles = 200
gen_scfman = true
scf_algorithm = diis
method = wb97xd
geom_opt_max_cycles = 200
$end
"""
qcinp = QCInput.from_string(str_molecule)
self.assertEqual(str_molecule, str(qcinp))
def test_read_negative(self):
str_molecule = """$molecule
-1 1
S -1.1516880000 0.8568110000 -0.0787470000
S 1.1527500000 -0.8580450000 -0.0786430000
O -1.6523520000 1.8607750000 -1.0252100000
O -0.9052880000 1.2448490000 1.3156410000
O 0.9072410000 -1.2461780000 1.3158760000
O 1.6543670000 -1.8616640000 -1.0249090000
C -2.5841130000 -0.3746500000 0.0297340000
C 2.5833220000 0.3755850000 0.0296900000
F -3.6480730000 0.2204040000 0.6112110000
F -2.2609850000 -1.4531020000 0.7616580000
F -2.9656640000 -0.7966010000 -1.1900330000
F 3.6467050000 -0.2152590000 0.6163310000
F 2.2560700000 1.4560310000 0.7568190000
F 2.9672080000 0.7933560000 -1.1908790000
N -0.0001900000 -0.0016540000 -0.8250640000
$end
$rem
job_type = opt
basis = 6-311++g*
max_scf_cycles = 200
gen_scfman = true
scf_algorithm = diis
method = wb97xd
geom_opt_max_cycles = 200
$end
"""
qcinp = QCInput.from_string(str_molecule)
self.assertEqual(str_molecule,str(qcinp))
def test_read_plots(self):
str_molecule = """$molecule
0 2
O 1.6159947668 0.3522275191 0.3343192028
O -0.5921658045 1.4368355787 1.2632324885
C 0.4160355545 -0.4617433561 0.2180766834
C -0.7655230468 0.4776728409 0.1826587618
C 2.8437090411 -0.3853724291 0.0935770045
C -1.7918488579 2.2003569978 1.5593659974
H 0.4649228147 -1.0347597878 -0.7097270414
H 3.6714833661 0.3051154983 0.2509025369
H 2.8395611019 -0.7401009356 -0.9372741555
H -2.1017802975 2.7482577804 0.6678359687
H -1.5445030956 2.8894960726 2.3658396091
Mg 1.2856817013 1.9249743897 1.4285694502
$end
$rem
job_type = sp
basis = def2-tzvppd
max_scf_cycles = 200
gen_scfman = true
xc_grid = 3
scf_algorithm = gdm
resp_charges = true
symmetry = false
sym_ignore = true
method = wb97xv
solvent_method = smd
ideriv = 1
thresh = 14
scf_guess_always = true
plots = true
make_cube_files = true
$end
$smx
solvent thf
$end
$plots
grid_spacing 0.05
total_density 0
$end
"""
qcinp = QCInput.from_string(str_molecule)
self.assertEqual(str_molecule, str(qcinp))
def test_from_string(self):
string = """$molecule
0 1
S -0.00250959 -0.05817469 -0.02921636
C 1.70755408 -0.03033788 -0.01382912
H 2.24317221 -0.05215019 0.92026728
C 2.21976393 0.01718014 -1.27293235
H 3.27786220 0.04082146 -1.48539646
C 1.20867399 0.04478540 -2.27007793
H 1.40292257 0.10591684 -3.33110912
C -0.05341046 0.01577217 -1.74839343
C -1.32843436 0.03545064 -2.45531187
C -1.55195156 0.08743920 -3.80184635
H -0.75245172 0.10267657 -4.52817967
C -2.93293778 0.08408786 -4.13352169
H -3.31125108 0.11340328 -5.14405819
C -3.73173288 0.02741365 -3.03412864
H -4.80776535 0.00535688 -2.99564645
S -2.81590978 -0.00516172 -1.58990580
$end
$rem
jobtype = opt
method = wb97m-v
basis = def2-tzvppd
gen_scfman = true
geom_opt_max_cycles = 75
max_scf_cycles = 300
scf_algorithm = diis
scf_guess = sad
sym_ignore = true
symmetry = false
thresh = 14
$end
$opt
CONSTRAINT
tors 6 8 9 10 0.0
ENDCONSTRAINT
$end
"""
qcinput_test = QCInput.from_string(string)
species = [
"S",
"C",
"H",
"C",
"H",
"C",
"H",
"C",
"C",
"C",
"H",
"C",
"H",
"C",
"H",
"S",
]
coords = [
[-0.00250959, -0.05817469, -0.02921636],
[1.70755408, -0.03033788, -0.01382912],
[2.24317221, -0.05215019, 0.92026728],
[2.21976393, 0.01718014, -1.27293235],
[3.27786220, 0.04082146, -1.48539646],
[1.20867399, 0.04478540, -2.27007793],
[1.40292257, 0.10591684, -3.33110912],
[-0.05341046, 0.01577217, -1.74839343],
[-1.32843436, 0.03545064, -2.45531187],
[-1.55195156, 0.08743920, -3.80184635],
[-0.75245172, 0.10267657, -4.52817967],
[-2.93293778, 0.08408786, -4.13352169],
[-3.31125108, 0.11340328, -5.14405819],
[-3.73173288, 0.02741365, -3.03412864],
[-4.80776535, 0.00535688, -2.99564645],
[-2.81590978, -0.00516172, -1.58990580],
]
molecule_actual = Molecule(species, coords)
self.assertEqual(molecule_actual, qcinput_test.molecule)
rem_actual = {
"job_type": "opt",
"method": "wb97m-v",
"basis": "def2-tzvppd",
"gen_scfman": "true",
"geom_opt_max_cycles": "75",
"max_scf_cycles": "300",
"scf_algorithm": "diis",
"scf_guess": "sad",
"sym_ignore": "true",
"symmetry": "false",
"thresh": "14",
}
self.assertDictEqual(rem_actual, qcinput_test.rem)
opt_actual = {"CONSTRAINT": ["tors 6 8 9 10 0.0"]}
self.assertDictEqual(opt_actual, qcinput_test.opt)
def test_read_nbo(self):
str_molecule = """$molecule
0 2
C -2.0338520000 0.0865500000 -1.4158570000
C -1.2819580000 0.3850830000 -0.1564990000
C -2.0067300000 1.1271820000 0.9225950000
C 0.1219120000 -0.0366190000 0.0148810000
C 0.6767790000 -1.0507090000 -0.7802400000
C 2.0072450000 -1.4517610000 -0.6185380000
C 2.8079970000 -0.8434840000 0.3427930000
C 2.2778880000 0.1645690000 1.1416530000
C 0.9468200000 0.5630060000 0.9784410000
H -1.3919850000 0.1591240000 -2.2995570000
H -2.4671570000 -0.9174600000 -1.3722490000
H -2.8505080000 0.8017250000 -1.5613060000
H -3.0889210000 0.9823990000 0.8362370000
H -1.7216740000 0.7761670000 1.9194500000
H -1.8021560000 2.1999010000 0.8510710000
H 0.0793240000 -1.5592640000 -1.5324310000
H 2.4136820000 -2.2421190000 -1.2440900000
H 3.8415290000 -1.1539430000 0.4689660000
H 2.8984450000 0.6464300000 1.8925800000
H 0.5733200000 1.3632210000 1.6120990000
$end
$rem
job_type = sp
max_scf_cycles = 200
gen_scfman = true
xc_grid = 3
scf_algorithm = diis
method = wb97xv
basis = def2-tzvp
symmetry = false
sym_ignore = true
nbo = true
$end
$nbo
$end
"""
qcinp = QCInput.from_string(str_molecule)
self.assertEqual(str_molecule, str(qcinp))
str_molecule = """$molecule
0 2
C -2.0338520000 0.0865500000 -1.4158570000
C -1.2819580000 0.3850830000 -0.1564990000
C -2.0067300000 1.1271820000 0.9225950000
C 0.1219120000 -0.0366190000 0.0148810000
C 0.6767790000 -1.0507090000 -0.7802400000
C 2.0072450000 -1.4517610000 -0.6185380000
C 2.8079970000 -0.8434840000 0.3427930000
C 2.2778880000 0.1645690000 1.1416530000
C 0.9468200000 0.5630060000 0.9784410000
H -1.3919850000 0.1591240000 -2.2995570000
H -2.4671570000 -0.9174600000 -1.3722490000
H -2.8505080000 0.8017250000 -1.5613060000
H -3.0889210000 0.9823990000 0.8362370000
H -1.7216740000 0.7761670000 1.9194500000
H -1.8021560000 2.1999010000 0.8510710000
H 0.0793240000 -1.5592640000 -1.5324310000
H 2.4136820000 -2.2421190000 -1.2440900000
H 3.8415290000 -1.1539430000 0.4689660000
H 2.8984450000 0.6464300000 1.8925800000
H 0.5733200000 1.3632210000 1.6120990000
$end
$rem
job_type = sp
max_scf_cycles = 200
gen_scfman = true
xc_grid = 3
scf_algorithm = diis
method = wb97xv
basis = def2-tzvp
symmetry = false
sym_ignore = true
nbo = true
$end
$nbo
print = 1
$end
"""
qcinp = QCInput.from_string(str_molecule)
self.assertEqual(str_molecule, str(qcinp))
def test_from_string(self):
string = """$molecule
0 1
S -0.00250959 -0.05817469 -0.02921636
C 1.70755408 -0.03033788 -0.01382912
H 2.24317221 -0.05215019 0.92026728
C 2.21976393 0.01718014 -1.27293235
H 3.27786220 0.04082146 -1.48539646
C 1.20867399 0.04478540 -2.27007793
H 1.40292257 0.10591684 -3.33110912
C -0.05341046 0.01577217 -1.74839343
C -1.32843436 0.03545064 -2.45531187
C -1.55195156 0.08743920 -3.80184635
H -0.75245172 0.10267657 -4.52817967
C -2.93293778 0.08408786 -4.13352169
H -3.31125108 0.11340328 -5.14405819
C -3.73173288 0.02741365 -3.03412864
H -4.80776535 0.00535688 -2.99564645
S -2.81590978 -0.00516172 -1.58990580
$end
$rem
jobtype = opt
method = wb97m-v
basis = def2-tzvppd
gen_scfman = true
geom_opt_max_cycles = 75
max_scf_cycles = 300
scf_algorithm = diis
scf_guess = sad
sym_ignore = true
symmetry = false
thresh = 14
$end
$opt
CONSTRAINT
tors 6 8 9 10 0.0
ENDCONSTRAINT
$end
"""
qcinput_test = QCInput.from_string(string)
species = ["S", "C", "H", "C", "H", "C", "H",
"C", "C", "C", "H", "C", "H", "C", "H", "S"]
coords = [[-0.00250959, -0.05817469, -0.02921636],
[1.70755408, -0.03033788, -0.01382912],
[2.24317221, -0.05215019, 0.92026728],
[2.21976393, 0.01718014, -1.27293235],
[3.27786220, 0.04082146, -1.48539646],
[1.20867399, 0.04478540, -2.27007793],
[1.40292257, 0.10591684, -3.33110912],
[-0.05341046, 0.01577217, -1.74839343],
[-1.32843436, 0.03545064, -2.45531187],
[-1.55195156, 0.08743920, -3.80184635],
[-0.75245172, 0.10267657, -4.52817967],
[-2.93293778, 0.08408786, -4.13352169],
[-3.31125108, 0.11340328, -5.14405819],
[-3.73173288, 0.02741365, -3.03412864],
[-4.80776535, 0.00535688, -2.99564645],
[-2.81590978, -0.00516172, -1.58990580]]
molecule_actual = Molecule(species, coords)
self.assertEqual(molecule_actual, qcinput_test.molecule)
rem_actual = {
"job_type": "opt",
"method": "wb97m-v",
"basis": "def2-tzvppd",
"gen_scfman": "true",
"geom_opt_max_cycles": "75",
"max_scf_cycles": "300",
"scf_algorithm": "diis",
"scf_guess": "sad",
"sym_ignore": "true",
"symmetry": "false",
"thresh": "14"
}
self.assertDictEqual(rem_actual, qcinput_test.rem)
opt_actual = {"CONSTRAINT": ["tors 6 8 9 10 0.0"]}
self.assertDictEqual(opt_actual, qcinput_test.opt)
