def density(mol, outfile, dm, nx=80, ny=80, nz=80):
coord = mol.atom_coords()
box = numpy.max(coord, axis=0) - numpy.min(coord, axis=0) + 4
boxorig = numpy.min(coord, axis=0) - 2
xs = numpy.arange(nx) * (box[0] / nx)
ys = numpy.arange(ny) * (box[1] / ny)
zs = numpy.arange(nz) * (box[2] / nz)
coords = lib.cartesian_prod([xs, ys, zs])
coords = numpy.asarray(coords, order="C") - (-boxorig)
nao = mol.nao_nr()
ngrids = nx * ny * nz
blksize = min(200, ngrids)
rho = numpy.empty(ngrids)
for ip0, ip1 in gen_grid.prange(0, ngrids, blksize):
ao = numint.eval_ao(mol, coords[ip0:ip1])
rho[ip0:ip1] = numint.eval_rho(mol, ao, dm)
rho = rho.reshape(nx, ny, nz)
with open(outfile, "w") as f:
f.write("Density in real space\n")
f.write("Comment line\n")
f.write("%5d" % mol.natm)
f.write(" %14.8f %14.8f %14.8f\n" % tuple(boxorig.tolist()))
f.write("%5d %14.8f %14.8f %14.8f\n" % (nx, xs[1], 0, 0))
f.write("%5d %14.8f %14.8f %14.8f\n" % (ny, 0, ys[1], 0))
f.write("%5d %14.8f %14.8f %14.8f\n" % (nz, 0, 0, zs[1]))
for ia in range(mol.natm):
chg = mol.atom_charge(ia)
f.write("%5d %f" % (chg, chg))
f.write(" %14.8f %14.8f %14.8f\n" % tuple(coord[ia]))
fmt = " %14.8e" * nz + "\n"
for ix in range(nx):
for iy in range(ny):
f.write(fmt % tuple(rho[ix, iy].tolist()))
def density_cut(mol, dm, nx=80, ny=80, z_value=0):
from scipy.constants import physical_constants
from pyscf import lib
from pyscf.dft import gen_grid, numint
nz = 1
coord = mol.atom_coords()
box = np.max(coord,axis=0) - np.min(coord,axis=0) + 6
boxorig = np.min(coord,axis=0) - 3
xs = np.arange(nx) * (box[0]/nx)
ys = np.arange(ny) * (box[1]/ny)
zs = np.array([z_value])
#zs = np.arange(nz) * (box[2]/nz)
coords = lib.cartesian_prod([xs,ys,zs])
coords = np.asarray(coords, order='C') - (-boxorig)
ngrids = nx * ny * nz
blksize = min(8000, ngrids)
rho = np.empty(ngrids)
ao = None
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(nx,ny)
# needed for conversion as x,y are in bohr for some reason
a0 = physical_constants["Bohr radius"][0]
return rho.T, (xs + boxorig[0]) * a0, (ys + boxorig[1]) * a0
def density(mol, outfile, dm, nx=80, ny=80, nz=80):
coord = [mol.atom_coord(ia) for ia in range(mol.natm)]
box = numpy.max(coord,axis=0) - numpy.min(coord,axis=0) + 4
boxorig = numpy.min(coord,axis=0) - 2
xs = numpy.arange(nx) * (box[0]/nx)
ys = numpy.arange(ny) * (box[1]/ny)
zs = numpy.arange(nz) * (box[2]/nz)
coords = numpy.vstack(numpy.meshgrid(xs,ys,zs)).reshape(3,-1).T
coords = numpy.asarray(coords, order='C') - (-boxorig)
nao = mol.nao_nr()
ngrids = nx * ny * nz
blksize = min(200, ngrids)
rho = numpy.empty(ngrids)
for ip0, ip1 in gen_grid.prange(0, ngrids, blksize):
ao = numint.eval_ao(mol, coords[ip0:ip1])
rho[ip0:ip1] = numint.eval_rho(mol, ao, dm)
rho = rho.reshape(nx,ny,nz)
with open(outfile, 'w') as f:
f.write('Density in real space\n')
f.write('Comment line\n')
f.write('%5d' % mol.natm)
f.write(' %14.8f %14.8f %14.8f\n' % tuple(boxorig.tolist()))
f.write('%5d %14.8f %14.8f %14.8f\n' % (nx, xs[1], 0, 0))
f.write('%5d %14.8f %14.8f %14.8f\n' % (ny, 0, ys[1], 0))
f.write('%5d %14.8f %14.8f %14.8f\n' % (nz, 0, 0, zs[1]))
for ia in range(mol.natm):
chg = mol.atom_charge(ia)
f.write('%5d %f' % (chg, chg))
f.write(' %14.8f %14.8f %14.8f\n' % tuple(mol.atom_coord(ia).tolist()))
fmt = ' %14.8e' * nz + '\n'
for ix in range(nx):
for iy in range(ny):
f.write(fmt % tuple(rho[ix,iy].tolist()))
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)')
def density(mol, outfile, dm, nx=80, ny=80, nz=80, pad=4.0, gridspacing=None):
"""Calculates electron density.
Args:
mol (Mole): Molecule to calculate the electron density for.
outfile (str): Name of Cube file to be written.
dm (str): Density matrix of molecule.
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.
ny (int): Number of grid point divisions in y direction.
nz (int): Number of grid point divisions in z direction.
pad (float): Amount of padding (in Angstrom) in all dimensions that will
be applied in the automatic construction of the rectangular
grid volume based on the geometry of the system.
gridspacing (float): Distance, in Angstroms, between points in the grid,
in all dimensions. This will override the nx,ny,nz
the parameters. Note the following values:
value/Angstroms points/Bohr Gaussian grid term
0.1763 3 Coarse
0.0882 6 Medium
0.0441 12 Fine
"""
grid = grid_utils.Grid(mol, nx, ny, nz, pad, gridspacing)
ngrids = grid.coords.shape[0]
blksize = min(8000, ngrids)
rho = numpy.empty(ngrids)
ao = None
for ip0, ip1 in gen_grid.prange(0, ngrids, blksize):
ao = numint.eval_ao(mol, grid.coords[ip0:ip1], out=ao)
rho[ip0:ip1] = numint.eval_rho(mol, ao, dm)
rho = rho.reshape(grid.nx, grid.ny, grid.nz)
grid_utils.write_formatted_cube_file(
outfile, 'Electron density in real space (e/Bohr^3)', grid, rho)
def density(mol, outfile, dm, nx=80, ny=80, nz=80):
coord = mol.atom_coords()
box = numpy.max(coord, axis=0) - numpy.min(coord, axis=0) + 6
boxorig = numpy.min(coord, axis=0) - 3
xs = numpy.arange(nx) * (box[0] / nx)
ys = numpy.arange(ny) * (box[1] / ny)
zs = numpy.arange(nz) * (box[2] / nz)
coords = lib.cartesian_prod([xs, ys, zs])
coords = numpy.asarray(coords, order='C') - (-boxorig)
nao = mol.nao_nr()
ngrids = nx * ny * nz
blksize = min(200, ngrids)
rho = numpy.empty(ngrids)
for ip0, ip1 in gen_grid.prange(0, ngrids, blksize):
ao = numint.eval_ao(mol, coords[ip0:ip1])
rho[ip0:ip1] = numint.eval_rho(mol, ao, dm)
rho = rho.reshape(nx, ny, nz)
with open(outfile, 'w') as f:
f.write('Electron density in real space (e/Bohr^3)\n')
f.write('PySCF Version: %s Date: %s\n' %
(pyscf.__version__, time.ctime()))
f.write('%5d' % mol.natm)
f.write(' %14.8f %14.8f %14.8f\n' % tuple(boxorig.tolist()))
f.write('%5d %14.8f %14.8f %14.8f\n' % (nx, xs[1], 0, 0))
f.write('%5d %14.8f %14.8f %14.8f\n' % (ny, 0, ys[1], 0))
f.write('%5d %14.8f %14.8f %14.8f\n' % (nz, 0, 0, zs[1]))
for ia in range(mol.natm):
chg = mol.atom_charge(ia)
f.write('%5d %f' % (chg, chg))
f.write(' %14.8f %14.8f %14.8f\n' % tuple(coord[ia]))
fmt = ' %14.8e' * nz + '\n'
for ix in range(nx):
for iy in range(ny):
f.write(fmt % tuple(rho[ix, iy].tolist()))
def isomep(mol,
outfile,
dm,
electronic_iso=0.002,
iso_tol=0.00003,
nx=80,
ny=80,
nz=80,
pad=4.0,
gridspacing=None):
"""Calculates MEP on a specific electron density surface.
Args:
mol (Mole): Molecule to calculate the electron density for.
outfile (str): Name of Cube file to be written.
dm (str): Density matrix of molecule.
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.
ny (int): Number of grid point divisions in y direction.
nz (int): Number of grid point divisions in z direction.
pad (float): Amount of padding (in Angstrom) in all dimensions that will
be applied in the automatic construction of the rectangular
grid volume based on the geometry of the system.
gridspacing (float): Distance, in Angstroms, between points in the grid,
in all dimensions. This will override the nx,ny,nz
the parameters. Note the following values:
value/Angstroms points/Bohr Gaussian grid term
0.1763 3 Coarse
0.0882 6 Medium
0.0441 12 Fine
"""
grid = grid_utils.Grid(mol, nx, ny, nz, pad, gridspacing)
LOGGER.debug("grid coords shape: %s", grid.coords.shape)
LOGGER.debug("grid coords first element shape: %s", grid.coords[0].shape)
ngrids = grid.coords.shape[0]
blksize = min(8000, ngrids)
rho = numpy.empty(ngrids)
ao = None
for ip0, ip1 in gen_grid.prange(0, ngrids, blksize):
ao = numint.eval_ao(mol, grid.coords[ip0:ip1], out=ao)
rho[ip0:ip1] = numint.eval_rho(mol, ao, dm)
LOGGER.note("Total number of density voxels: %d", len(rho))
is_surface_voxel = numpy.logical_and(rho > (electronic_iso - iso_tol),
rho < (electronic_iso + iso_tol))
LOGGER.debug("Surface voxel count from logical_and: %d",
numpy.count_nonzero(is_surface_voxel))
surface_voxel_grid_indices = numpy.nonzero(is_surface_voxel)[0]
LOGGER.debug2("Surface voxel indices: %s", surface_voxel_grid_indices)
LOGGER.debug2("Surface voxel indices shape: %s",
surface_voxel_grid_indices.shape)
# Number of voxels at the defined electronic_iso surface
# Used for area
# Voxels at surface
#(num > (ISO - TOL) ) && (num < (ISO + TOL) )
surface_voxel_count = surface_voxel_grid_indices.shape[0]
surface_voxel_coords = grid.coords[surface_voxel_grid_indices[0]]
for i in range(1, surface_voxel_grid_indices.shape[0]):
surface_voxel_coord = grid.coords[surface_voxel_grid_indices[i]]
LOGGER.debug4("surface voxel coord shape: %s",
surface_voxel_coord.shape)
surface_voxel_coords = numpy.append(surface_voxel_coords,
surface_voxel_coord,
axis=0)
LOGGER.debug("surface_voxel_coords shape: %s", surface_voxel_coords.shape)
surface_voxel_coords = surface_voxel_coords.reshape(
(surface_voxel_grid_indices.shape[0], 3))
LOGGER.debug("surface_voxel_coords shape: %s", surface_voxel_coords.shape)
LOGGER.debug3("First coord from grid: %s",
grid.coords[surface_voxel_grid_indices[0]])
LOGGER.debug3("First coord from surf voxel array: %s",
surface_voxel_coords[0])
is_in_surface = numpy.greater(rho, electronic_iso)
LOGGER.debug("Voxel count from numpy.greater: %d",
numpy.count_nonzero(is_in_surface))
# Number of voxels *within* the defined electronic_iso surface
# Used for volume
inner_voxel_count = numpy.count_nonzero(is_in_surface)
# This time, actually change
LOGGER.debug("rho shape: %s", rho.shape)
rho = rho.reshape(grid.nx, grid.ny, grid.nz)
LOGGER.debug("rho shape: %s", rho.shape)
LOGGER.note("surface voxels_found: %d", surface_voxel_count)
voxel_area = gridspacing * gridspacing
LOGGER.info("Each voxel area / A^2: %f", voxel_area)
LOGGER.info("inner surface area / A^2: %f",
surface_voxel_count * voxel_area)
LOGGER.info("inner voxel count: %d", inner_voxel_count)
voxel_volume = gridspacing * gridspacing * gridspacing
LOGGER.info("Each voxel volume / A^3: %f", voxel_volume)
inner_volume = inner_voxel_count * voxel_volume
LOGGER.info("Total inner volume / A^3: %f", inner_volume)
mep_values = mep_for_coords(mol, dm, surface_voxel_coords)
LOGGER.debug("MEP values shape: %s", mep_values.shape)
mep_values = mep_values.reshape((mep_values.shape[0], 1))
LOGGER.debug("MEP values shape: %s", mep_values.shape)
#Add the potentials to the coordinates: each row describes one point.
coords_with_mep_values = numpy.append(surface_voxel_coords,
mep_values,
axis=1)
cube_information = "Molecular electrostatic potential in real space on {:.5f} isodensity surface. Volume: {:.6f}".format(
electronic_iso, inner_volume)
grid_utils.write_unformatted_cube_file(outfile, cube_information, grid,
coords_with_mep_values)
def density(mol, outfile, dm, nx=80, ny=80, nz=80):
"""Calculates electron density.
Args:
mol (Mole): Molecule to calculate the electron density for.
outfile (str): Name of Cube file to be written.
dm (str): Density matrix of molecule.
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.
ny (int): Number of grid point divisions in y direction.
nz (int): Number of grid point divisions in z direction.
"""
coord = mol.atom_coords()
box = numpy.max(coord, axis=0) - numpy.min(coord, axis=0) + 6
boxorig = numpy.min(coord, axis=0) - 3
xs = numpy.arange(nx) * (box[0] / nx)
ys = numpy.arange(ny) * (box[1] / ny)
zs = numpy.arange(nz) * (box[2] / nz)
coords = lib.cartesian_prod([xs, ys, zs])
coords = numpy.asarray(coords, order='C') - (-boxorig)
ngrids = nx * ny * nz
blksize = min(8000, ngrids)
rho = numpy.empty(ngrids)
ao = None
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(nx, ny, nz)
with open(outfile, 'w') as f:
f.write('Electron density in real space (e/Bohr^3)\n')
f.write('PySCF Version: %s Date: %s\n' %
(pyscf.__version__, time.ctime()))
f.write('%5d' % mol.natm)
f.write('%12.6f%12.6f%12.6f\n' % tuple(boxorig.tolist()))
f.write('%5d%12.6f%12.6f%12.6f\n' % (nx, xs[1], 0, 0))
f.write('%5d%12.6f%12.6f%12.6f\n' % (ny, 0, ys[1], 0))
f.write('%5d%12.6f%12.6f%12.6f\n' % (nz, 0, 0, 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(nx):
for iy in range(ny):
for iz in range(0, nz, 6):
remainder = (nz - iz)
if (remainder > 6):
fmt = '%13.5E' * 6 + '\n'
f.write(fmt % tuple(rho[ix, iy, iz:iz + 6].tolist()))
else:
fmt = '%13.5E' * remainder + '\n'
f.write(fmt %
tuple(rho[ix, iy, iz:iz + remainder].tolist()))
break