def read_grid(self, name='gridfunc', idx=0, *args, **kwargs):
""" Reads a grid in the current SIESTA.grid.nc file
Enables the reading and processing of the grids created by SIESTA
"""
# Swap as we swap back in the end
sc = self.read_sc().swapaxes(0, 2)
# Create the grid
nx = len(self._dimension('n1'))
ny = len(self._dimension('n2'))
nz = len(self._dimension('n3'))
if name is None:
v = self._variable('gridfunc')
else:
v = self._variable(name)
# Create the grid, SIESTA uses periodic, always
grid = Grid([nz, ny, nx], bc=Grid.Periodic, sc=sc,
dtype=v.dtype)
if len(v[:].shape) == 3:
grid.grid = v[:, :, :]
else:
grid.grid = v[idx, :, :, :]
# Read the grid, we want the z-axis to be the fastest
# looping direction, hence x,y,z == 0,1,2
return grid.swapaxes(0, 2)
def test_default(sisl_tmp):
f = sisl_tmp('GRID.xsf', _dir)
print(f)
grid = Grid(0.2)
grid.grid = np.random.rand(*grid.shape)
grid.write(f)
assert grid.geometry is None
def test_imaginary(sisl_tmp):
f = sisl_tmp('GRID.xsf', _dir)
geom = Geometry(np.random.rand(10, 3), np.random.randint(1, 70, 10), sc=[10, 10, 10, 45, 60, 90])
grid = Grid(0.2, geometry=geom, dtype=np.complex128)
grid.grid = np.random.rand(*grid.shape) + 1j*np.random.rand(*grid.shape)
grid.write(f)
assert not grid.geometry is None
def read_grid(self, spin=0, *args, **kwargs):
""" Read grid contained in the Grid file
Parameters
----------
spin : int or array_like, optional
the spin-index for retrieving one of the components. If a vector
is passed it refers to the fraction per indexed component. I.e.
``[0.5, 0.5]`` will return sum of half the first two components.
Default to the first component.
"""
# Read the sizes
nspin, mesh = _siesta.read_grid_sizes(self.file)
# Read the cell and grid
cell = _siesta.read_grid_cell(self.file)
grid = _siesta.read_grid(self.file, nspin, mesh[0], mesh[1], mesh[2])
if isinstance(spin, Integral):
grid = grid[:, :, :, spin]
else:
if len(spin) > grid.shape[0]:
raise ValueError(self.__class__.__name__ + '.read_grid requires spin to be an integer or '
'an array of length equal to the number of spin components.')
g = grid[:, :, :, 0] * spin[0]
for i, scale in enumerate(spin[1:]):
g += grid[:, :, :, 1+i] * scale
grid = g
cell = np.array(cell.T, np.float64)
cell.shape = (3, 3)
g = Grid(mesh, sc=SuperCell(cell), dtype=np.float32)
g.grid = np.array(grid.swapaxes(0, 2), np.float32) * self.grid_unit
return g
def read_grid(self):
""" Returns `Grid` object from the CUBE file """
geom = self.read_geom()
# Now seek behind to read grid sizes
self.fh.seek(0)
# Skip headers and origo
self.readline()
self.readline()
na = int(self.readline().split()[0])
ngrid = [0] * 3
for i in [0, 1, 2]:
tmp = self.readline().split()
ngrid[i] = int(tmp[0])
# Read past the atoms
for i in range(na):
self.readline()
grid = Grid(ngrid, dtype=np.float32, geom=geom)
grid.grid = np.loadtxt(self.fh, dtype=grid.dtype)
grid.grid.shape = ngrid
return grid
def read_grid(self):
""" Returns `Grid` object from the CUBE file """
geom = self.read_geom()
# Now seek behind to read grid sizes
self.fh.seek(0)
# Skip headers and origo
self.readline()
self.readline()
na = int(self.readline().split()[0])
ngrid = [0] * 3
for i in [0, 1, 2]:
tmp = self.readline().split()
ngrid[i] = int(tmp[0])
# Read past the atoms
for i in range(na):
self.readline()
grid = Grid(ngrid, dtype=np.float32, geom=geom)
grid.grid = np.loadtxt(self.fh, dtype=grid.dtype)
grid.grid.shape = ngrid
return grid
def test_default_size(sisl_tmp):
f = sisl_tmp('GRID.cube', _dir)
grid = Grid(0.2, sc=2.0)
grid.grid = np.random.rand(*grid.shape)
grid.write(f)
read = grid.read(f)
assert np.allclose(grid.grid, read.grid)
assert grid.geometry is None
assert len(read.geometry) == 1
def read_grid(self, name, idx=0):
""" Reads a grid in the current SIESTA.nc file
Enables the reading and processing of the grids created by SIESTA
"""
# Swap as we swap back in the end
geom = self.read_geom().swapaxes(0, 2)
# Shorthand
g = self.groups['GRID']
# Create the grid
nx = len(g.dimensions['nx'])
ny = len(g.dimensions['ny'])
nz = len(g.dimensions['nz'])
# Shorthand variable name
v = g.variables[name]
# Create the grid, SIESTA uses periodic, always
grid = Grid([nz, ny, nx], bc=Grid.Periodic, dtype=v.dtype)
if len(v[:].shape) == 3:
grid.grid = v[:, :, :]
else:
grid.grid = v[idx, :, :, :]
try:
u = v.unit
if u == 'Ry':
# Convert to ev
grid *= Ry2eV
except:
# Simply, we have no units
pass
# Read the grid, we want the z-axis to be the fastest
# looping direction, hence x,y,z == 0,1,2
grid = grid.swapaxes(0, 2)
grid.set_geom(geom)
return grid
def read_grid(self, name, idx=0):
""" Reads a grid in the current SIESTA.nc file
Enables the reading and processing of the grids created by SIESTA
"""
# Swap as we swap back in the end
geom = self.read_geom().swapaxes(0, 2)
# Shorthand
g = self.groups['GRID']
# Create the grid
nx = len(g.dimensions['nx'])
ny = len(g.dimensions['ny'])
nz = len(g.dimensions['nz'])
# Shorthand variable name
v = g.variables[name]
# Create the grid, SIESTA uses periodic, always
grid = Grid([nz, ny, nx], bc=Grid.Periodic, dtype=v.dtype)
if len(v[:].shape) == 3:
grid.grid = v[:, :, :]
else:
grid.grid = v[idx, :, :, :]
try:
u = v.unit
if u == 'Ry':
# Convert to ev
grid *= Ry2eV
except:
# Simply, we have no units
pass
# Read the grid, we want the z-axis to be the fastest
# looping direction, hence x,y,z == 0,1,2
grid = grid.swapaxes(0, 2)
grid.set_geom(geom)
return grid
def test_geometry(sisl_tmp):
f = sisl_tmp('GRID.cube', _dir)
geom = Geometry(np.random.rand(10, 3), np.random.randint(1, 70, 10), sc=[10, 10, 10, 45, 60, 90])
grid = Grid(0.2, geometry=geom)
grid.grid = np.random.rand(*grid.shape)
grid.write(f)
read = grid.read(f)
assert np.allclose(grid.grid, read.grid)
assert not grid.geometry is None
assert not read.geometry is None
assert grid.geometry == read.geometry
def test_imaginary_fail_geometry(sisl_tmp):
fr = sisl_tmp('GRID_real.cube', _dir)
fi = sisl_tmp('GRID_imag.cube', _dir)
geom = Geometry(np.random.rand(10, 3), np.random.randint(1, 70, 10), sc=[10, 10, 10, 45, 60, 90])
grid = Grid(0.2, geometry=geom, dtype=np.complex128)
grid.grid = np.random.rand(*grid.shape) + 1j*np.random.rand(*grid.shape)
grid.write(fr)
# Assert it fails on geometry
grid2 = Grid(0.3, dtype=np.complex128)
grid2.write(fi, imag=True)
grid.read(fr, imag=fi)
def read_grid(self, index=0, dtype=np.float64, *args, **kwargs):
""" Read grid contained in the Grid file
Parameters
----------
index : int or array_like, optional
the spin-index for retrieving one of the components. If a vector
is passed it refers to the fraction per indexed component. I.e.
``[0.5, 0.5]`` will return sum of half the first two components.
Default to the first component.
dtype : numpy.float64, optional
default data-type precision
"""
index = kwargs.get('spin', index)
# Read the sizes and cell
nspin, mesh = self.read_grid_size()
cell = _siesta.read_grid_cell(self.file)
_bin_check(self, 'read_grid', 'could not read grid cell.')
grid = _siesta.read_grid(self.file, nspin, mesh[0], mesh[1], mesh[2])
_bin_check(self, 'read_grid', 'could not read grid.')
if isinstance(index, Integral):
grid = grid[:, :, :, index]
else:
if len(index) > grid.shape[0]:
raise ValueError(
self.__class__.__name__ +
'.read_grid requires spin to be an integer or '
'an array of length equal to the number of spin components.'
)
# It is F-contiguous, hence the last index
g = grid[:, :, :, 0] * index[0]
for i, scale in enumerate(index[1:]):
g += grid[:, :, :, 1 + i] * scale
grid = g
cell = np.array(cell.T, np.float64)
cell.shape = (3, 3)
# Simply create the grid (with no information)
# We will overwrite the actual grid
g = Grid([1, 1, 1], sc=SuperCell(cell))
# NOTE: there is no need to swap-axes since the returned array is in F ordering
# and thus the first axis is the fast (x, y, z) is retained
g.grid = (grid * self.grid_unit).astype(dtype=dtype,
order='C',
copy=False)
return g
def test_isosurface_non_orthogonal(self, setup):
pytest.importorskip("skimage", reason="scikit-image not available")
# If the grid is non-orthogonal, there should be 20 unique values
# (10 for each (HERE), see test_isosurface_orthogonal)
grid = Grid(0.1, sc=[[1, 0, 0], [0, 1, 0], [0, 2, 1]])
grid.grid = np.tile([1, 2, 3, 4, 5, 4, 3, 2, 1, 0],
100).reshape(10, 10, 10)
verts, *returns = grid.isosurface(2.5)
# we have twice as many since the 3rd lattice vector has components in y
assert np.unique(verts[:, 1]).shape == (20, )
assert np.unique(verts[:, 2]).shape == (2, )
def test_isosurface_orthogonal(self, setup):
pytest.importorskip("skimage", reason="scikit-image not available")
# Build an empty grid
grid = Grid(0.1, sc=[[1, 0, 0], [0, 1, 0], [0, 0, 1]])
# Fill it with some values that have a clear isosurface
grid.grid = np.tile([1, 2, 3, 4, 5, 4, 3, 2, 1, 0],
100).reshape(10, 10, 10)
# Calculate the isosurface for the value of 2.5
verts, *returns = grid.isosurface(2.5)
# The third dimension should contain only two coordinates
# [1, 2, (HERE) 3, 4, 5, 4, 3, (HERE) 2, 1, 0]
assert np.unique(verts[:, 1]).shape == (10, )
assert np.unique(verts[:, 2]).shape == (2, )
def read_grid(self, index=0, dtype=np.float64):
""" Reads the charge density from the file and returns with a grid (plus geometry)
Parameters
----------
index : int, optional
the index of the grid to read. For a spin-polarized VASP calculation 0 and 1 are
allowed, UP/DOWN. For non-collinear 0, 1, 2 or 3 is allowed which equals,
TOTAL, x, y, z charge density with the Cartesian directions equal to the charge
magnetization.
dtype : numpy.dtype, optional
grid stored dtype
Returns
-------
Grid : charge density grid with associated geometry
"""
geom = self.read_geometry()
V = geom.sc.volume
# Now we are past the cell and geometry
# We can now read the size of CHGCAR
self.readline()
nx, ny, nz = list(map(int, self.readline().split()))
n = nx * ny * nz
i = 0
vals = []
while i < n * (index + 1):
dat = [float(l) for l in self.readline().split()]
vals.append(dat)
i += len(dat)
vals = np.swapaxes(np.array(vals).reshape(nz, ny, nx), 0, 2)
vals = vals[index * n:(index + 1) * n] / V
# Create the grid with data
# Since we populate the grid data afterwards there
# is no need to create a bigger grid than necessary.
grid = Grid([1, 1, 1], dtype=dtype, geometry=geom)
grid.grid = vals
return grid
def test_imaginary(sisl_tmp):
fr = sisl_tmp('GRID_real.cube', _dir)
fi = sisl_tmp('GRID_imag.cube', _dir)
geom = Geometry(np.random.rand(10, 3), np.random.randint(1, 70, 10), sc=[10, 10, 10, 45, 60, 90])
grid = Grid(0.2, geometry=geom, dtype=np.complex128)
grid.grid = np.random.rand(*grid.shape) + 1j*np.random.rand(*grid.shape)
grid.write(fr)
grid.write(fi, imag=True)
read = grid.read(fr)
read_i = grid.read(fi)
read.grid = read.grid + 1j*read_i.grid
assert np.allclose(grid.grid, read.grid)
assert not grid.geometry is None
assert not read.geometry is None
assert grid.geometry == read.geometry
read = grid.read(fr, imag=fi)
assert np.allclose(grid.grid, read.grid)
read = grid.read(fr, imag=read_i)
assert np.allclose(grid.grid, read.grid)
def read_grid(self, name, spin=0, **kwargs):
""" Reads a grid in the current Siesta.nc file
Enables the reading and processing of the grids created by Siesta
Parameters
----------
name : str
name of the grid variable to read
spin : int or array_like, optional
the spin-index for retrieving one of the components. If a vector
is passed it refers to the fraction per indexed component. I.e.
``[0.5, 0.5]`` will return sum of half the first two components.
Default to the first component.
"""
spin = kwargs.get('index', spin)
geom = self.read_geometry()
# Shorthand
g = self.groups['GRID']
# Create the grid
nx = len(g.dimensions['nx'])
ny = len(g.dimensions['ny'])
nz = len(g.dimensions['nz'])
# Shorthand variable name
v = g.variables[name]
# Create the grid, Siesta uses periodic, always
grid = Grid([nz, ny, nx],
bc=Grid.PERIODIC,
geometry=geom,
dtype=v.dtype)
# Unit-conversion
BohrC2AngC = Bohr2Ang**3
unit = {
'Rho': 1. / BohrC2AngC,
'RhoInit': 1. / BohrC2AngC,
'RhoTot': 1. / BohrC2AngC,
'RhoDelta': 1. / BohrC2AngC,
'RhoXC': 1. / BohrC2AngC,
'RhoBader': 1. / BohrC2AngC,
'Chlocal': 1. / BohrC2AngC,
}.get(name, 1.)
if len(v[:].shape) == 3:
grid.grid = v[:, :, :] * unit
elif isinstance(spin, Integral):
grid.grid = v[spin, :, :, :] * unit
else:
if len(spin) > v.shape[0]:
raise SileError(
self.__class__.__name__ +
'.read_grid requires spin to be an integer or '
'an array of length equal to the number of spin components.'
)
grid.grid[:, :, :] = v[0, :, :, :] * (spin[0] * unit)
for i, scale in enumerate(spin[1:]):
grid.grid[:, :, :] += v[1 + i, :, :, :] * (scale * unit)
try:
if v.unit == 'Ry':
# Convert to ev
grid *= Ry2eV
except:
# Allowed pass due to pythonic reading
pass
# Read the grid, we want the z-axis to be the fastest
# looping direction, hence x,y,z == 0,1,2
grid.grid = np.copy(np.swapaxes(grid.grid, 0, 2), order='C')
return grid
def read_grid(self, index=0, dtype=np.float64):
""" Reads the potential (in eV) from the file and returns with a grid (plus geometry)
Parameters
----------
index : int or array_like, optional
the index of the potential to read. For a spin-polarized VASP calculation 0 and 1 are
allowed, UP/DOWN. For non-collinear 0, 1, 2 or 3 is allowed which equals,
TOTAL, x, y, z total potential with the Cartesian directions equal to the potential
for the magnetization directions. For array-like they refer to the fractional
contributions for each corresponding index.
dtype : numpy.dtype, optional
grid stored dtype
Returns
-------
Grid : potential with associated geometry
"""
geom = self.read_geometry()
V = geom.sc.volume
# Now we are past the cell and geometry
# We can now read the size of LOCPOT
self.readline()
nx, ny, nz = list(map(int, self.readline().split()))
n = nx * ny * nz
is_index = True
if isinstance(index, Integral):
max_index = index + 1
else:
is_index = False
max_index = len(index)
rl = self.readline
vals = []
vapp = vals.append
i = 0
while i < n * max_index:
dat = [l for l in rl().split()]
vapp(dat)
i += len(dat)
if i % n == 0 and i < n * max_index:
# Each time a new spin-index is present, we need to read the coordinates
j = 0
while j < geom.na:
j += len(rl().split())
# one line of nx, ny, nz
rl()
# Cut size before proceeding (otherwise it *may* fail)
vals = np.array(vals).astype(dtype).ravel()
if is_index:
val = vals[n * index:n * (index + 1)].reshape(nz, ny, nx)
else:
vals = vals[:n * max_index].reshape(-1, nz, ny, nx)
val = vals[0] * index[0]
for i, scale in enumerate(index[1:]):
val += vals[i + 1] * scale
del vals
# Make it C-ordered with nx, ny, nz
val = np.swapaxes(val, 0, 2) / V
# Create the grid with data
# Since we populate the grid data afterwards there
# is no need to create a bigger grid than necessary.
grid = Grid([1, 1, 1], dtype=dtype, geometry=geom)
grid.grid = val
return grid
def test_default_size(sisl_tmp):
f = sisl_tmp('GRID.xsf', _dir)
grid = Grid(0.2, sc=2.0)
grid.grid = np.random.rand(*grid.shape)
grid.write(f)
assert grid.geometry is None
def read_grid(self, imag=None):
""" Returns `Grid` object from the CUBE file
Parameters
----------
imag : str or Sile or Grid
the imaginary part of the grid. If the geometries does not match
an error will be raised.
"""
if not imag is None:
if not isinstance(imag, Grid):
imag = Grid.read(imag)
geom = self.read_geometry()
if geom is None:
self.fh.seek(0)
sc = self.read_supercell()
else:
sc = geom.sc
# Now seek behind to read grid sizes
self.fh.seek(0)
# Skip headers and origin
self.readline()
self.readline()
na = int(self.readline().split()[0])
ngrid = [0] * 3
for i in [0, 1, 2]:
tmp = self.readline().split()
ngrid[i] = int(tmp[0])
# Read past the atoms
for i in range(na):
self.readline()
if geom is None:
grid = Grid(ngrid, dtype=np.float64, sc=sc)
else:
grid = Grid(ngrid, dtype=np.float64, geometry=geom)
grid.grid.shape = (-1, )
# TODO check performance of this
# We are currently doing this to enable reading
# 1-column data and 6-column data.
lines = [
item for sublist in self.fh.readlines()
for item in sublist.split()
]
grid.grid[:] = np.array(lines).astype(grid.dtype)
grid.grid.shape = ngrid
if imag is None:
return grid
# We are expecting an imaginary part
if not grid.geometry.equal(imag.geometry):
raise SislError(
str(self) + ' and its imaginary part does not have the same '
'geometry. Hence a combined complex Grid cannot be formed.')
if grid != imag:
raise SislError(
str(self) + ' and its imaginary part does not have the same '
'shape. Hence a combined complex Grid cannot be formed.')
# Now we have a complex grid
grid.grid = grid.grid + 1j * imag.grid
return grid