def resp_charges(smile, bset="hf/6-31g"):
# https://github.com/Mishima-syk/psikit
pk = Psikit.read_from_smiles(smiles_str=smile)
pk.energy()
pk.optimize(basis_sets=bset)
return pk.cal_resp_charges()
def calc_FOE(smi, idx):
pk = Psikit()
pk.read_from_smiles(smi)
pk.optimize()
print(f'H**O: {pk.H**O}, LUMO: {pk.LUMO}')
with open(f'./psikitout/{idx}.txt', 'w') as outf:
outf.write(f'{smi}\t{pk.H**O}\t{pk.LUMO}\n')
return (pk.H**O, pk.LUMO)
def test_mul1_energy():
pk = Psikit()
pk.read_from_smiles("CO")
energy = pk.energy(multiplicity=1)
assert pytest.approx(-115.0421871159, 0.000000005) == energy
def test_mul3_energy():
pk = Psikit()
pk.read_from_smiles("CO")
energy = pk.energy(multiplicity=4)
assert pytest.approx(-40.19996313, 0.000000005) == energy
def test_read_from_smiles():
pk = Psikit()
pk.read_from_smiles("C")
assert type(pk.mol) is rdkit.Chem.rdchem.Mol
def test_optimize():
pk = Psikit()
pk.read_from_smiles("C")
energy = pk.optimize()
assert pytest.approx(-40.20171733, 0.000000005) == energy
def test_energy_sto3g():
pk = Psikit()
pk.read_from_smiles("C")
energy = pk.energy(basis_sets="scf/sto-3g")
assert pytest.approx(-39.724747932, 0.000000005) == energy
def test_energy():
pk = Psikit()
pk.read_from_smiles("C")
energy = pk.energy()
assert pytest.approx(-40.19996313, 0.000000005) == energy
def test_read_from_molfiles():
pk = Psikit()
pk.read_from_molfile("tests/test.mol")
assert type(pk.mol) is rdkit.Chem.rdchem.Mol
def makeinput(self):
from psikit import Psikit
pk = Psikit()
pk.read_from_molfile(self.molfile)
self.molname = 'mol'
self.geom = pk.mol2xyz()
self.basis = prompt("""Select Basis
1: SCF-3G
2: 6-31G*
3: 6-31G**
4: cc-pDZ
: """)
self.scf_type = prompt("""Select scf_type
1: pk
2: df
: """)
self.pcm_scf_type = prompt("""Select pcm_scf_type
1: total
2: separate
: """)
self.unit = prompt("""Select Unit 1: Angstrom, 2:AU
: """)
self.SolverType = prompt("""select SolverType 1: IEFPCM, 2: CPCM
: """)
self.Solvent = prompt("""select Solvent listed below
1:'Water',
2:'Propylene Carbonate',
3:'Dimethylsulfoxide',
4:'Nitromethane',
5:'Acetonitrile',
6:'Methanol',
7:'Ethanol',
8:'Acetone',
9:'1,2-Dichloroethane',
10:'Methylenechloride',
11:'Tetrahydrofurane',
12:'Aniline',
13:'Chlorobenzene',
14:'Chloroform',
15:'Toluene',
16:'1,4-Dioxane',
17:'Benzene',
18:'Carbon Tetrachloride',
19:'Cyclohexane',
20:'N-heptane',
21:'Explicit'
: """)
#self.calc_type = prompt("""Select type 1:GePol, 2: Restart
#: """)
self.calc_type = '1'
self.scaling = prompt("""Scaling ? bool 1:True 2:False
: """)
self.area = prompt("""Inpt area default 0.3
: """)
self.mode = prompt("""select mode 1:Implicit, 2:Atom, 3:Explicit
: """)
data = {
"name": self.molname,
"geom": self.geom,
"basis": BASIS[self.basis],
"scf_type": SCF_TYPE[self.scf_type],
"pcm_scf_type": PCM_SCF_TYPE[self.pcm_scf_type],
"unit": UNITS[self.unit],
"SolverType": SOLVER_TYPE[self.SolverType],
"Solvent": SOLVENT[self.Solvent],
"Type": TYPE[self.calc_type],
"Scaling": 'true' if self.scaling == '1' else 'false',
"Area": self.area,
"Mode": MODE[self.mode]
}
env = Environment(loader=FileSystemLoader(self.filepath))
temp = env.get_template(os.path.join(self.filepath, 'input.tpl'))
outdata = temp.render(**data)
with open("input.dat", "w") as output:
output.write(outdata)
print("done")
print("you can run pcm solver with psi4 just type")
print('psi4 input.dat')