def test_aos_libnao(self): """ Computing of the atomic orbitals """ sv = mf(label='water', cd=os.path.dirname(os.path.abspath(__file__))) cc = Cube(sv, nx=20, ny=20, nz=20) aos = sv.comp_aos_den(cc.get_coords()) self.assertEqual(aos.shape[0], cc.nx*cc.ny*cc.nz) self.assertEqual(aos.shape[1], sv.norbs)
def test_aos_libnao(self):
""" Computing of the atomic orbitals """
sv = mf(label='water', cd=os.path.dirname(os.path.abspath(__file__)))
cc = Cube(sv, nx=20, ny=20, nz=20)
aos = sv.comp_aos_den(cc.get_coords())
self.assertEqual(aos.shape[0], cc.nx * cc.ny * cc.nz)
self.assertEqual(aos.shape[1], sv.norbs)
def test_mo_cube_libnao(self): """ Computing of the atomic orbitals """ sv = mf(label='water', cd=os.path.dirname(os.path.abspath(__file__))) cc = Cube(sv, nx=40, ny=40, nz=40) co2val = sv.comp_aos_den(cc.get_coords()) nocc_0t = int(sv.nelectron / 2) c2orb = np.dot(co2val, sv.wfsx.x[0,0,nocc_0t,:,0]).reshape((cc.nx, cc.ny, cc.nz)) cc.write(c2orb, "water_mo.cube", comment='H**O')
def MO(mol,
C,
orbital,
outfile='orbital',
nx=80,
ny=80,
nz=80,
resolution=None,
save=True):
"""Calculates electron density and write out in cube format.
Args:
mol : Mole
Molecule to calculate the electron density for.
outfile : str
Name of Cube file to be written.
dm : ndarray
Density matrix of molecule.
Kwargs:
nx : int
Number of grid point divisions in x direction.
Note this is function of the molecule's size; a larger molecule
will have a coarser representation than a smaller one for the
same value. Conflicts to keyword resolution.
ny : int
Number of grid point divisions in y direction.
nz : int
Number of grid point divisions in z direction.
resolution: float
Resolution of the mesh grid in the cube box. If resolution is
given in the input, the input nx/ny/nz have no effects. The value
of nx/ny/nz will be determined by the resolution and the cube box
size.
"""
cc = Cube(mol, nx, ny, nz, resolution)
# Compute density on the .cube grid
coords = cc.get_coords()
ngrids = cc.get_ngrids()
#blksize = min(8000, ngrids)
blksize = ngrids
rho = np.empty(ngrids)
for ip0, ip1 in lib.prange(0, ngrids, blksize):
ao = numint.eval_ao(mol, coords[ip0:ip1])
MO = np.array([i @ C[:, orbital] for i in ao])
MO = MO.reshape((nx, ny, nz))
if save:
cc.write(MO,
outfile,
comment='Orbital ' + str(orbital) +
' in real space (e/Bohr^3)')
x = (coords[:, 0].min(), coords[:, 0].max(), nx)
y = (coords[:, 1].min(), coords[:, 1].max(), ny)
z = (coords[:, 2].min(), coords[:, 2].max(), nz)
return MO, np.array([y, x, z])
def test_mo_cube_libnao(self):
""" Computing of the atomic orbitals """
sv = mf(label='water', cd=os.path.dirname(os.path.abspath(__file__)))
cc = Cube(sv, nx=40, ny=40, nz=40)
co2val = sv.comp_aos_den(cc.get_coords())
nocc_0t = int(sv.nelectron / 2)
c2orb = np.dot(co2val, sv.wfsx.x[0, 0, nocc_0t, :, 0]).reshape(
(cc.nx, cc.ny, cc.nz))
cc.write(c2orb, "water_mo.cube", comment='H**O')
def test_mo_cube_libnao(self): """ Computing of the atomic orbitals """ from pyscf.nao import system_vars_c from pyscf.tools.cubegen import Cube sv = system_vars_c().init_siesta_xml(label='water', cd=os.path.dirname(os.path.abspath(__file__))) cc = Cube(sv, nx=40, ny=40, nz=40) co2val = sv.comp_aos_den(cc.get_coords()) nocc_0t = int(sv.nelectron / 2) c2orb = np.dot(co2val, sv.wfsx.x[0,0,nocc_0t,:,0]).reshape((cc.nx, cc.ny, cc.nz)) cc.write(c2orb, "water_mo.cube", comment='H**O')
def test_aos_libnao(self):
""" Computing of the atomic orbitals """
from pyscf.nao import system_vars_c
from pyscf.tools.cubegen import Cube
sv = system_vars_c().init_siesta_xml(label='water',
cd=os.path.dirname(
os.path.abspath(__file__)))
cc = Cube(sv, nx=20, ny=20, nz=20)
aos = sv.comp_aos_den(cc.get_coords())
self.assertEqual(aos.shape[0], cc.nx * cc.ny * cc.nz)
self.assertEqual(aos.shape[1], sv.norbs)
def test_cube_sv(self):
""" Compute the density and store into a cube file """
from pyscf.tools.cubegen import Cube
sv = nao_mf(label='water', cd=os.path.dirname(os.path.abspath(__file__)))
cc = Cube(sv, nx=50, ny=50, nz=50)
dens = sv.dens_elec(cc.get_coords(), sv.make_rdm1())
dens = dens[:,0].reshape(cc.nx,cc.ny,cc.nz)
cc.write(dens, "water.cube", comment='Valence electron density in real space (e/Bohr^3)')
self.assertEqual(len(cc.xs), cc.nx)
self.assertEqual(len(cc.ys), cc.ny)
self.assertEqual(len(cc.zs), cc.nz)
self.assertAlmostEqual(dens.sum()*cc.get_volume_element(), 8.0, 1)
def AO(mol,
C,
outfile='AO_dir/AOs',
nx=80,
ny=80,
nz=80,
resolution=None,
save=True):
counter = 1
if not os.path.exists(outfile):
os.makedirs(outfile)
else:
exists = True
while exists:
cache = outfile + '_' + str(counter)
exists = os.path.exists(cache)
counter += 1
outfile = cache
os.makedirs(cache)
cc = Cube(mol, nx, ny, nz, resolution)
# Compute density on the .cube grid
coords = cc.get_coords()
ngrids = cc.get_ngrids()
#blksize = min(8000, ngrids)
blksize = ngrids
rho = np.empty(ngrids)
for ip0, ip1 in lib.prange(0, ngrids, blksize):
ao = numint.eval_ao(mol, coords[ip0:ip1])
x = (coords[:, 0].min(), coords[:, 0].max(), nx)
y = (coords[:, 1].min(), coords[:, 1].max(), ny)
z = (coords[:, 2].min(), coords[:, 2].max(), nz)
if save:
np.savetxt(outfile + '/AOs', ao)
np.savetxt(outfile + '/C', C)
np.savetxt(outfile + '/coords', np.array([y, x, z]))
f = open(outfile + '/geom_basis', 'w')
f.write(str(mol.atom) + '_')
f.write(str(mol.basis))
f.close()
#cc.write(np.array([]),outfile + '_geom',comment = 'Geometry')
return ao, np.array([y, x, z])
def test_cube_c(self):
""" Compute the density and store into a cube file """
# Initialize the class cube_c
cc = Cube(mol, nx=20, ny=20, nz=20)
# Compute density on the .cube grid
coords = cc.get_coords()
ngrids = cc.get_ngrids()
blksize = min(8000, ngrids)
rho = np.empty(ngrids)
ao = None
dm = mf.make_rdm1()
for ip0, ip1 in gen_grid.prange(0, ngrids, blksize):
ao = numint.eval_ao(mol, coords[ip0:ip1], out=ao)
rho[ip0:ip1] = numint.eval_rho(mol, ao, dm)
rho = rho.reshape(cc.nx,cc.ny,cc.nz)
# Write out density to the .cube file
cc.write(rho, "h2o_den_cube_c.cube", comment='Electron density in real space (e/Bohr^3)')