def test_orb(self):
ftmp = tempfile.NamedTemporaryFile()
orb = cubegen.orbital(mol,
ftmp.name,
mf.mo_coeff[:, 0],
nx=10,
ny=10,
nz=10)
self.assertEqual(orb.shape, (10, 10, 10))
self.assertAlmostEqual(lib.finger(orb), -0.11804191128016768, 9)
orb = cubegen.orbital(mol,
ftmp.name,
mf.mo_coeff[:, 0],
nx=10,
ny=10,
nz=10,
resolution=0.5)
self.assertEqual(orb.shape, (12, 18, 15))
self.assertAlmostEqual(lib.finger(orb), -0.8591778390706646, 9)
orb = cubegen.orbital(mol,
ftmp.name,
mf.mo_coeff[:, 0],
nx=10,
ny=1,
nz=1)
self.assertEqual(orb.shape, (10, 1, 1))
self.assertAlmostEqual(lib.finger(orb), 6.921008881822988e-09, 9)
def write_cube(mf, p):
''' write the localized orbitals as cube files '''
l_cube = [] # list of all cube file names
for s in range(p.nspin):
s_cube = []
occ = len(mf.mo_coeff[s][mf.mo_occ[s] == 1])
for i in range(occ):
f_cube = '{}_orb_{}_spin{}.cube'.format(p.pycom_loc, i, s)
s_cube.append(f_cube)
orbital(mf.mol,
f_cube,
p.pycom_orb[s][:, i],
nx=p.nx,
ny=p.ny,
nz=p.nz)
l_cube.append(s_cube)
p.l_cube = l_cube
return p
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])
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])
ptss_list.append(ptss)
fmt = "{0:2d} {1:12.8g} {2:9.3g} [{3:9.3g}, {4:9.3g}, {5:9.3g}]"
fmt += " [{6:9.3g}, {7:9.3g}, {8:9.3g}]"
fmt += " {9:12.8g} {10:12.8g}"
print(
state.kind[0],
fmt.format(i, val, state.oscillator_strengths[i],
*state.transition_dipole_moments[i],
*state.state_dipole_moments[i], ptss, ptlr),
)
# Dump LUNTO and HONTO
u, s, v = np.linalg.svd(ρ_tdm_tot)
# LUNTOs
cubegen.orbital(mol=mol,
coeff=u.T[0],
outfile="nto_{}_LUNTO.cube".format(i))
# HONTOs
cubegen.orbital(mol=mol, coeff=v[0], outfile="nto_{}_HONTO.cube".format(i))
# Print timings summary:
print()
print(state.timer.describe())
print("Number of orbitals:", state.reference_state.n_orbs)
results = {
"excitation_energies": state.excitation_energies.tolist(),
"oscillator_strengths": state.oscillator_strengths.tolist(),
"ptss": ptss_list,
"ptlr": ptlr_list,
}
Test pyscf dft calculations
@author: Bing Gu
"""
from pyscf import gto, dft
from pyscf.tools import cubegen
import numpy as np
from pprint import pprint
#p 6-31g(d) 5d ub3lyp tda(nstates=60,full,alltransitiondensities)
mol = gto.M(atom='''
H 0 0 0.00000000
H 0.00000000 -0.00000000 0.74
''',
basis='321g',
charge=0,
spin=0)
mf = dft.RKS(mol)
mf.xc = 'B3LYP'
mf.kernel()
# save mo coeffcients
np.save('mo_coeff', mf.mo_coeff)
j = 1
cubegen.orbital(mol, 'mo' + str(j) + '.cube', mf.mo_coeff[:, j])
from pyscf.tools import cubegen
from pyscf.data.nist import BOHR
import numpy as np
ang2bohr = 1.0 / BOHR
mol = gto.M(atom='''
O 0.0000000000000000 0.0000000000000000 0.000
H -0.26312631683261728 0.92177640310981912 0.000
H 0.9645910938303689 4.0006988432649347E-002 0.000
''',
basis='aug-cc-pVDZ')
mm_crd = np.array(
[[2.9125407227330018, 0.0000000000000000, 0.000],
[3.3354011353264896, -0.41314678971687741, -0.75710308103585677],
[3.3354011558614673, -0.41314667699843621, 0.75710313896414105]])
mm_crd *= ang2bohr
mm_chgs = np.array([-0.68, 0.34, 0.34])
mf = qmmm.mm_charge(scf.RHF(mol), mm_crd, mm_chgs).run()
# electron density
cubegen.density(mol, 'h2o_den_qmmm.cube', mf.make_rdm1())
# molecular electrostatic potential
cubegen.mep(mol, 'h2o_pot_qmmm.cube', mf.make_rdm1())
# 1st MO
nhomo = mf.mol.nelec[0]
cubegen.orbital(mol, 'h2o_homo_qmmm.cube', mf.mo_coeff[:, nhomo - 1])