def read_geometry(self, velocity=False, species_Z=False):
""" Returns a `Geometry` object from the XV file
Parameters
----------
species_Z : bool, optional
if ``True`` the atomic numbers are the species indices (useful when
reading the ChemicalSpeciesLabel block simultaneously).
velocity : bool, optional
also return the velocities in the file
Returns
-------
Geometry
velocity : only if `velocity` is true.
"""
sc = self.read_supercell()
# Read number of atoms
na = int(self.readline())
xyz = np.empty([na, 3], np.float64)
vel = np.empty([na, 3], np.float64)
atms = [None] * na
sp = np.empty([na], np.int32)
for ia in range(na):
line = list(map(float, self.readline().split()[:8]))
sp[ia] = int(line[0])
if species_Z:
atms[ia] = Atom(sp[ia])
else:
atms[ia] = Atom(int(line[1]))
xyz[ia, :] = line[2:5]
vel[ia, :] = line[5:8]
xyz *= Bohr2Ang
vel *= Bohr2Ang
# Ensure correct sorting
max_s = sp.max()
sp -= 1
# Ensure we can remove the atom after having aligned them
atms2 = Atoms(AtomUnknown(1000), na=na)
for i in range(max_s):
idx = (sp[:] == i).nonzero()[0]
if len(idx) == 0:
# Always ensure we have "something" for the unoccupied places
atms2[idx] = AtomUnknown(1000 + i)
else:
atms2[idx] = atms[idx[0]]
geom = Geometry(xyz, atms2.reduce(), sc=sc)
if velocity:
return geom, vel
return geom
def write_grid(self, *args, **kwargs):
""" Store grid(s) data to an XSF file
Examples
--------
>>> g1 = Grid(0.1, sc=2.)
>>> g2 = Grid(0.1, sc=2.)
>>> get_sile('output.xsf', 'w').write_grid(g1, g2)
Parameters
----------
*args : Grid
a list of data-grids to be written to the XSF file.
Each argument gets the field name ``?grid_<>`` where <> starts
with the integer 0, and *?* is ``real_``/``imag_`` for complex
valued grids.
geometry : Geometry, optional
the geometry stored in the file, defaults to ``args[0].geometry``
fmt : str, optional
floating point format for data (.5e)
buffersize : int, optional
size of the buffer while writing the data, (6144)
"""
sile_raise_write(self)
geom = kwargs.get('geometry', args[0].geometry)
if geom is None:
geom = Geometry([0, 0, 0], AtomUnknown(999), sc=args[0].sc)
self.write_geometry(geom)
# Buffer size for writing
buffersize = kwargs.get('buffersize', min(6144, args[0].grid.size))
# Format for precision
fmt = kwargs.get('fmt', '.5e')
self._write('BEGIN_BLOCK_DATAGRID_3D\n')
name = kwargs.get('name', 'sisl_grid_{}'.format(len(args)))
# Transfer all spaces to underscores (no spaces allowed)
self._write(' ' + name.replace(' ', '_') + '\n')
_v3 = (('{:' + fmt + '} ') * 3).strip() + '\n'
def write_cell(grid):
# Now write the grid
self._write(' {} {} {}\n'.format(*grid.shape))
self._write(' ' + _v3.format(*grid.origo))
self._write(' ' + _v3.format(*grid.cell[0, :]))
self._write(' ' + _v3.format(*grid.cell[1, :]))
self._write(' ' + _v3.format(*grid.cell[2, :]))
for i, grid in enumerate(args):
is_complex = np.iscomplexobj(grid.grid)
name = kwargs.get('grid' + str(i), str(i))
if is_complex:
self._write(f' BEGIN_DATAGRID_3D_real_{name}\n')
else:
self._write(f' BEGIN_DATAGRID_3D_{name}\n')
write_cell(grid)
# for z
# for y
# for x
# write...
_fmt = '{:' + fmt + '}\n'
for x in np.nditer(np.asarray(grid.grid.real.T,
order='C').reshape(-1),
flags=['external_loop', 'buffered'],
op_flags=[['readonly']],
order='C',
buffersize=buffersize):
self._write((_fmt * x.shape[0]).format(*x.tolist()))
self._write(' END_DATAGRID_3D\n')
# Skip if not complex
if not is_complex:
continue
self._write(f' BEGIN_DATAGRID_3D_imag_{name}\n')
write_cell(grid)
for x in np.nditer(np.asarray(grid.grid.imag.T,
order='C').reshape(-1),
flags=['external_loop', 'buffered'],
op_flags=[['readonly']],
order='C',
buffersize=buffersize):
self._write((_fmt * x.shape[0]).format(*x.tolist()))
self._write(' END_DATAGRID_3D\n')
self._write('END_BLOCK_DATAGRID_3D\n')