def test_mep(self):
ftmp = tempfile.NamedTemporaryFile()
mep = cubegen.mep(mol, ftmp.name, mf.make_rdm1(), nx=10, ny=10, nz=10)
self.assertEqual(mep.shape, (10, 10, 10))
self.assertAlmostEqual(lib.finger(mep), -0.3198103636180436, 9)
mep = cubegen.mep(mol,
ftmp.name,
mf.make_rdm1(),
nx=10,
ny=10,
nz=10,
resolution=0.5)
self.assertEqual(mep.shape, (12, 18, 15))
self.assertAlmostEqual(lib.finger(mep), -4.653995909548524, 9)
def parse_nx(data):
d = data.split()
return int(d[0]), numpy.array([float(x) for x in d[1:]])
self.nx, self.xs = parse_nx(f.readline())
self.ny, self.ys = parse_nx(f.readline())
self.nz, self.zs = parse_nx(f.readline())
atoms = []
for ia in range(natm):
d = f.readline().split()
atoms.append([int(d[0]), [float(x) for x in d[2:]]])
self.mol = gto.M(atom=atoms, unit='Bohr')
data = f.read()
cube_data = numpy.array([float(x) for x in data.split()])
return cube_data.reshape([self.nx, self.ny, self.nz])
if __name__ == '__main__':
from pyscf import gto, scf
from pyscf.tools import cubegen
mol = gto.M(atom='''O 0.00000000, 0.000000, 0.000000
H 0.761561, 0.478993, 0.00000000
H -0.761561, 0.478993, 0.00000000''',
basis='6-31g*')
mf = scf.RHF(mol).run()
cubegen.density(mol, 'h2o_den.cube', mf.make_rdm1()) #makes total density
cubegen.mep(mol, 'h2o_pot.cube', mf.make_rdm1())
cubegen.orbital(mol, 'h2o_mo1.cube', mf.mo_coeff[:, 0])
def get_esp_cube(mol, mf, cube_fn="esp.cub"):
cubegen.mep(mol, cube_fn, mf.make_rdm1())
def test_cubegen(self): """ Compute the density and store into a cube file """ cubegen.density(mol, 'h2o_den.cube', mf.make_rdm1(), nx=20, ny=20, nz=20) cubegen.mep(mol, 'h2o_pot.cube', mf.make_rdm1(), nx=20, ny=20, nz=20) #slow
Write orbitals, electron density, molecular electrostatic potential in
Gaussian cube file format.
'''
from pyscf import gto, scf
from pyscf.tools import cubegen
mol = gto.M(atom='''
O 0.0000000, 0.000000, 0.00000000
H 0.761561 , 0.478993, 0.00000000
H -0.761561, 0.478993, 0.00000000''', basis='6-31g*')
mf = scf.RHF(mol).run()
# electron density
cubegen.density(mol, 'h2o_den.cube', mf.make_rdm1())
# electron density slice
cubegen.density(mol, 'h2o_den_slice.cube', mf.make_rdm1(), nx=1, ny=1, nz=80)
# molecular electrostatic potential
cubegen.mep(mol, 'h2o_pot.cube', mf.make_rdm1())
# molecular electrostatic potential slice
cubegen.mep(mol, 'h2o_pot_slice.cube', mf.make_rdm1(), nx=1, ny=1, nz=80)
# 1st MO
cubegen.orbital(mol, 'h2o_mo1.cube', mf.mo_coeff[:,0])
# 1st MO orbital slice
cubegen.orbital(mol, 'h2o_mo1_slice.cube', mf.mo_coeff[:,0], nx=1, ny=1, nz=80)
f.write('%12.6f%12.6f%12.6f\n' % tuple(self.boxorig.tolist()))
f.write('%5d%12.6f%12.6f%12.6f\n' % (self.nx, self.xs[1], 0, 0))
f.write('%5d%12.6f%12.6f%12.6f\n' % (self.ny, 0, self.ys[1], 0))
f.write('%5d%12.6f%12.6f%12.6f\n' % (self.nz, 0, 0, self.zs[1]))
for ia in range(mol.natm):
chg = mol.atom_charge(ia)
f.write('%5d%12.6f'% (chg, chg))
f.write('%12.6f%12.6f%12.6f\n' % tuple(coord[ia]))
for ix in range(self.nx):
for iy in range(self.ny):
for iz0, iz1 in lib.prange(0, self.nz, 6):
fmt = '%13.5E' * (iz1-iz0) + '\n'
f.write(fmt % tuple(field[ix,iy,iz0:iz1].tolist()))
def read(self, cube_file):
raise NotImplementedError
if __name__ == '__main__':
from pyscf import gto, scf
from pyscf.tools import cubegen
mol = gto.M(atom='''O 0.00000000, 0.000000, 0.000000
H 0.761561, 0.478993, 0.00000000
H -0.761561, 0.478993, 0.00000000''', basis='6-31g*')
mf = scf.RHF(mol).run()
cubegen.density(mol, 'h2o_den.cube', mf.make_rdm1()) #makes total density
cubegen.mep(mol, 'h2o_pot.cube', mf.make_rdm1())
cubegen.orbital(mol, 'h2o_mo1.cube', mf.mo_coeff[:,0])