def read_xyzwv(cls, filename_full, gf_type=None):
npoints_re = re.compile(r'' + "^\s*(\d+)\s*$" + '', re.IGNORECASE)
xyzwv_re = re.compile(r'' + "^\s*(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)" + '', re.IGNORECASE)
i = 0
with open(filename_full) as f:
for line in f:
if npoints_re.match(line):
npoints = numpy.int(npoints_re.match(line).group(1))
v = numpy.zeros((npoints,))
xyz = numpy.zeros((npoints, 3))
w = numpy.zeros((npoints,))
if xyzwv_re.match(line):
xyz[i, :] = [xyzwv_re.match(line).group(1),
xyzwv_re.match(line).group(2),
xyzwv_re.match(line).group(3)]
w[i] = xyzwv_re.match(line).group(4)
v[i] = xyzwv_re.match(line).group(5)
i = i + 1
grid = Grids.customgrid(None, xyz, w)
import hashlib
m = hashlib.md5()
m.update("Gridfunction read from file:")
m.update(os.path.abspath(filename_full))
gf = GridFunctionFactory.newGridFunction(grid, v, checksum=m.digest(), gf_type=gf_type)
return gf
def read_xyzw(filename_full):
npoints_re = re.compile(r"^\s*(\d+)\s*$", re.IGNORECASE)
xyzw_re = re.compile(
r"^\s*(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)" +
r"\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)", re.IGNORECASE)
i = 0
with open(filename_full) as f:
for line in f:
if npoints_re.match(line):
npoints = numpy.int(npoints_re.match(line).group(1))
v = numpy.zeros((npoints, ))
xyz = numpy.zeros((npoints, 3))
w = numpy.zeros((npoints, ))
if xyzw_re.match(line):
xyz[i, :] = [
xyzw_re.match(line).group(1),
xyzw_re.match(line).group(2),
xyzw_re.match(line).group(3)
]
w[i] = xyzw_re.match(line).group(4)
i = i + 1
grid = Grids.customgrid(None, xyz, w)
return grid
def _make_gfs_from_numpy(filename_full, grid_xyzw, elpot, nucpot, rho,
rhod, rhodd):
grid = Grids.customgrid(None, numpy.ascontiguousarray(grid_xyzw[:,
0:3]),
numpy.ascontiguousarray(grid_xyzw[:, 3]))
import hashlib
m = hashlib.md5()
m.update("Electrostatic potential read from file:")
m.update(os.path.abspath(filename_full))
pot_gf = GridFunctionFactory.newGridFunction(grid,
elpot,
checksum=m.digest(),
gf_type="potential")
if nucpot is not None:
m = hashlib.md5()
m.update("Nuclear potential read from file:")
m.update(os.path.abspath(filename_full))
nucpot_gf = GridFunctionFactory.newGridFunction(
grid, nucpot, checksum=m.digest(), gf_type="potential")
else:
nucpot_gf = None
m = hashlib.md5()
m.update("Density read from file:")
m.update(filename_full)
dens_gf = GridFunctionFactory.newGridFunction(grid,
rho,
checksum=m.digest(),
gf_type="density")
m = hashlib.md5()
m.update("Density gradient read from file:")
m.update(filename_full)
densgrad = GridFunctionFactory.newGridFunction(grid,
rhod,
checksum=m.digest())
m = hashlib.md5()
m.update("Density Hessian read from file:")
m.update(filename_full)
denshess = GridFunctionFactory.newGridFunction(grid,
rhodd,
checksum=m.digest())
rho_gf = GridFunctionContainer([dens_gf, densgrad, denshess])
return grid, pot_gf, nucpot_gf, rho_gf
def read_density_elpot_xyzwv(cls, filename_full):
"""
FIXME: This needs a docstring explaining the file format!
"""
npoints_re = re.compile(r'' + "^\s*(\d+)\s+\d" + '', re.IGNORECASE)
density_re = re.compile(r'' + "^\s*(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)" + '', re.IGNORECASE)
ngngnn_re = re.compile(r'' + "^\s*(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)\s+(-?[0-9a-zA-Z+-.]+)" + '', re.IGNORECASE)
i = 0
with open(filename_full) as f:
for line in f:
if npoints_re.match(line):
npoints = numpy.int(npoints_re.match(line).group(1))
rho = numpy.zeros((npoints, 10))
elpot = numpy.zeros((npoints))
grid_xyzw = numpy.zeros((npoints, 4))
if density_re.match(line):
# leaving space for the hessian of the density, force zeros for those
rho[i, :] = [density_re.match(line).group(7),
density_re.match(line).group(8),
density_re.match(line).group(9),
density_re.match(line).group(10),
0, 0, 0, 0, 0, 0]
elpot[i] = density_re.match(line).group(5)
elpot[i] += float(density_re.match(line).group(6))
grid_xyzw[i, :] = [density_re.match(line).group(1),
density_re.match(line).group(2),
density_re.match(line).group(3),
density_re.match(line).group(4)]
i = i + 1
elif ngngnn_re.match(line):
rho[i, :] = [density_re.match(line).group(7),
density_re.match(line).group(8),
density_re.match(line).group(9),
density_re.match(line).group(10),
density_re.match(line).group(11),
density_re.match(line).group(12),
density_re.match(line).group(13),
density_re.match(line).group(14),
density_re.match(line).group(15),
density_re.match(line).group(16)]
elpot[i] = density_re.match(line).group(5)
elpot[i] += float(density_re.match(line).group(6))
grid_xyzw[i, :] = [density_re.match(line).group(1),
density_re.match(line).group(2),
density_re.match(line).group(3),
density_re.match(line).group(4)]
i = i + 1
grid = Grids.customgrid(None, numpy.ascontiguousarray(grid_xyzw[:, 0:3]),
numpy.ascontiguousarray(grid_xyzw[:, 3]))
import hashlib
m = hashlib.md5()
m.update("Electrostatic potential read from file:")
m.update(os.path.abspath(filename_full))
pot_gf = GridFunctionFactory.newGridFunction(grid, elpot, checksum=m.digest(),
gf_type="potential")
m = hashlib.md5()
m.update("Density read from file:")
m.update(filename_full)
dens_gf = GridFunctionFactory.newGridFunction(grid, numpy.ascontiguousarray(rho[:, 0]),
checksum=m.digest(), gf_type="density")
m = hashlib.md5()
m.update("Density gradient read from file:")
m.update(filename_full)
densgrad = GridFunctionFactory.newGridFunction(grid, numpy.ascontiguousarray(rho[:, 1:4]),
checksum=m.digest())
m = hashlib.md5()
m.update("Density Hessian read from file:")
m.update(filename_full)
denshess = GridFunctionFactory.newGridFunction(grid, numpy.ascontiguousarray(rho[:, 4:10]),
checksum=m.digest())
rho_gf = GridFunctionContainer([dens_gf, densgrad, denshess])
return grid, pot_gf, rho_gf
def read_xml(filename_full):
xyzw = read_xmldataset_to_numpy(filename_full, ['gridpoints'])
grid = Grids.customgrid(None, xyzw[:, 0:3], xyzw[:, 3])
return grid
