def __init__(self, nspinor, nsppol, nspden, datar, structure, iorder="c"):
"""
Args:
nspinor: Number of spinorial components.
nsppol: Number of spins.
nspden: Number of spin density components.
datar: [nspden, nx, ny, nz] array with the scalar field in real space.
See also ``read_denpot``.
structure: |Structure| object describing the crystalline structure.
iorder: Order of the array. "c" for C ordering, "f" for Fortran ordering.
"""
self.nspinor, self.nsppol, self.nspden = nspinor, nsppol, nspden
# Convert to Abipy Structure.
self._structure = Structure.as_structure(structure)
iorder = iorder.lower()
assert iorder in ["f", "c"]
if iorder == "f":
# (z,x,y) --> (x,y,z)
datar = transpose_last3dims(datar)
# Init Mesh3D
mesh_shape = datar.shape[-3:]
self._mesh = Mesh3D(mesh_shape, structure.lattice.matrix)
# Make sure we have the correct shape.
self._datar = np.reshape(datar, (nspden,) + self.mesh.shape)
def __init__(self, nspinor, nsppol, nspden, datar, structure, iorder="c"):
"""
Args:
nspinor:
Number of spinorial components.
nsppol:
Number of spins.
nspden:
Number of spin density components.
datar:
numpy array with the scalar field in real space.
structure:
pymatgen structure
iorder:
Order of the array. "c" for C ordering, "f" for Fortran ordering.
"""
self.nspinor = nspinor
self.nsppol = nsppol
self.nspden = nspden
self.structure = structure
self.datar = datar
if iorder.lower() == "f": # (z,x,y) --> (x,y,z)
self.datar = transpose_last3dims(self.datar)
# Init Mesh3D
mesh_shape = self.datar.shape[-3:]
self.mesh = Mesh3D(mesh_shape, structure.lattice_vectors(), pbc=True)
# Make sure we have the correct shape.
self.datar = np.reshape(self.datar, (nspden,) + self.mesh.shape)
# FFT R --> G.
self.datag = self.mesh.fft_r2g(self.datar)
def __init__(self, nspinor, nsppol, nspden, datar, structure, iorder="c"):
"""
Args:
nspinor: Number of spinorial components.
nsppol: Number of spins.
nspden: Number of spin density components.
datar: numpy array with the scalar field in real space. shape [..., nx, ny, nz]
structure: :class:`Structure` object describing the crystalline structure.
iorder: Order of the array. "c" for C ordering, "f" for Fortran ordering.
"""
self.nspinor, self.nsppol, self.nspden = nspinor, nsppol, nspden
self._structure = structure
iorder = iorder.lower()
assert iorder in ["f", "c"]
if iorder == "f":
# (z,x,y) --> (x,y,z)
datar = transpose_last3dims(datar)
# Init Mesh3D
mesh_shape = datar.shape[-3:]
self._mesh = Mesh3D(mesh_shape, structure.lattice_vectors())
# Make sure we have the correct shape.
self._datar = np.reshape(datar, (nspden,) + self.mesh.shape)
def __init__(self, nspinor, nsppol, nspden, datar, structure, iorder="c"):
"""
Args:
nspinor: Number of spinorial components.
nsppol: Number of spins.
nspden: Number of spin density components.
datar: numpy array with the scalar field in real space. shape [..., nx, ny, nz]
structure: :class:`Structure` object describing the crystalline structure.
iorder: Order of the array. "c" for C ordering, "f" for Fortran ordering.
"""
self.nspinor, self.nsppol, self.nspden = nspinor, nsppol, nspden
self._structure = structure
iorder = iorder.lower()
assert iorder in ["f", "c"]
if iorder == "f":
# (z,x,y) --> (x,y,z)
datar = transpose_last3dims(datar)
# Init Mesh3D
mesh_shape = datar.shape[-3:]
self._mesh = Mesh3D(mesh_shape, structure.lattice_vectors())
# Make sure we have the correct shape.
self._datar = np.reshape(datar, (nspden,) + self.mesh.shape)
def xsf_write_data(file, structure, data, add_replicas=True, cplx_mode=None):
"""
Write data in the Xcrysden format (XSF)
Args:
file: file-like object.
structure: :class:`Structure` object.
data: array-like object in C-order, i.e data[nx,ny,nz]
add_replicas: If True, data is padded with redundant data points.
in order to have a periodic 3D array of shape=(nx+1,ny+1,nz+1).
cplx_mode: string defining the data to print when data is a complex array.
Possible choices are (case-insensitive):
- "re" for real part.
- "im" for imaginary part.
- "abs" for the absolute value
"""
fwrite = file.write
# Check this one
if add_replicas:
data = add_periodic_replicas(data)
if np.iscomplexobj(data):
if cplx_mode is None:
raise TypeError(
"cplx_mode must be specified when data is a complex array.")
cplx_mode = cplx_mode.lower()
if cplx_mode == "re":
data = data.real
elif cplx_mode == "im":
data = data.imag
elif cplx_mode == "abs":
data = np.abs(data)
else:
raise ValueError("Wrong value for cplx_mode: %s" % cplx_mode)
shape = data.shape
ndim = data.ndim
if ndim == 3:
ngrids = 1
data = np.asarray([data])
elif ndim == 4:
ngrids = shape[0]
else:
raise ValueError("ndim %d is not supported" % ndim)
# Xcrysden uses Fortran-order.
# Transpose (...,x,y,z) --> (...,z,y,x) to speed up the write below.
fdata = transpose_last3dims(data)
fgrid = fdata.shape[-3:]
cell = structure.lattice_vectors(space="r")
origin = np.zeros(3)
fwrite('BEGIN_BLOCK_DATAGRID_3D\n')
fwrite(' data\n')
for dg in range(ngrids):
fwrite(" BEGIN_DATAGRID_3Dgrid#" + str(dg + 1) + "\n")
fwrite('%d %d %d\n' % shape[-3:])
fwrite('%f %f %f\n' % tuple(origin))
for i in range(3):
fwrite('%f %f %f\n' % tuple(cell[i]))
for z in range(fgrid[0]):
for y in range(fgrid[1]):
slice_x = fdata[dg, z, y]
fwrite(' '.join(['%f' % d for d in slice_x]))
fwrite('\n')
fwrite('\n')
fwrite(' END_DATAGRID_3D\n')
fwrite('END_BLOCK_DATAGRID_3D\n')
def xsf_write_data(file, structure, data, add_replicas=True, cplx_mode=None):
"""
Write data in the Xcrysden format (XSF)
Args:
file: file-like object.
structure: :class:`Structure` object.
data: array-like object in C-order, i.e data[nx,ny,nz]
add_replicas: If True, data is padded with redundant data points.
in order to have a periodic 3D array of shape=(nx+1,ny+1,nz+1).
cplx_mode: string defining the data to print when data is a complex array.
Possible choices are (case-insensitive):
- "re" for real part.
- "im" for imaginary part.
- "abs" for the absolute value
"""
fwrite = file.write
# Check this one
if add_replicas:
data = add_periodic_replicas(data)
if np.iscomplexobj(data):
if cplx_mode is None:
raise TypeError("cplx_mode must be specified when data is a complex array.")
cplx_mode = cplx_mode.lower()
if cplx_mode == "re":
data = data.real
elif cplx_mode == "im":
data = data.imag
elif cplx_mode == "abs":
data = np.abs(data)
else:
raise ValueError("Wrong value for cplx_mode: %s" % cplx_mode)
shape = data.shape
ndim = data.ndim
if ndim == 3:
ngrids = 1
data = np.asarray([data])
elif ndim == 4:
ngrids = shape[0]
else:
raise ValueError("ndim %d is not supported" % ndim)
# Xcrysden uses Fortran-order.
# Transpose (...,x,y,z) --> (...,z,y,x) to speed up the write below.
fdata = transpose_last3dims(data)
fgrid = fdata.shape[-3:]
cell = structure.lattice_vectors(space="r")
origin = np.zeros(3)
fwrite('BEGIN_BLOCK_DATAGRID_3D\n')
fwrite(' data\n')
for dg in range(ngrids):
fwrite(" BEGIN_DATAGRID_3Dgrid#" + str(dg+1) + "\n")
fwrite('%d %d %d\n' % shape[-3:])
fwrite('%f %f %f\n' % tuple(origin))
for i in range(3):
fwrite('%f %f %f\n' % tuple(cell[i]))
for z in range(fgrid[0]):
for y in range(fgrid[1]):
slice_x = fdata[dg,z,y]
fwrite(' '.join(['%f' % d for d in slice_x]) )
fwrite('\n')
fwrite('\n')
fwrite(' END_DATAGRID_3D\n')
fwrite('END_BLOCK_DATAGRID_3D\n')
def xsf_write_data(file, structure, cdata, add_replicas):
"""
Write cdata in the Xcrysden format (XSF)
Args:
file:
file-like object.
structure:
Structure object.
cdata:
array-like object in C-order
add_replicas:
If True, cdata is padded with redundant data points.
in order to have a periodic 3D array of shape=(nx+1,ny+1,nz+1).
"""
# TODO
warnings.warn("This code should be checked.")
fwrite = file.write
# Check this one
if add_replicas:
cdata = add_periodic_replicas(cdata)
if cdata.dtype == complex:
raise NotImplementedError("Writing of complex arrays not coded yet.")
cdata = np.abs(cdata)
cshape = cdata.shape
ndim = cdata.ndim
if ndim == 3:
ngrids = 1
cdata = np.asarray([cdata])
elif ndim == 4:
ngrids = cshape[0]
else:
raise ValueError("ndim %d is not supported" % ndim)
# Xcrysden uses Fortran-order.
# Transpose (...,x,y,z) --> (...,z,y,x) to speed up the write below.
fdata = transpose_last3dims(cdata)
fgrid = fdata.shape[-3:]
cell = structure.lattice_vectors(space="r") #* Bohr_Ang
origin = np.zeros(3)
fwrite('BEGIN_BLOCK_DATAGRID_3D\n')
fwrite(' data\n')
for dg in range(ngrids):
fwrite(" BEGIN_DATAGRID_3Dgrid#" + str(dg+1) + "\n")
fwrite('%d %d %d\n' % cshape[-3:])
fwrite('%f %f %f\n' % tuple(origin))
for i in range(3):
fwrite('%f %f %f\n' % tuple(cell[i]))
for z in range(fgrid[0]):
for y in range(fgrid[1]):
slice_x = fdata[dg,z,y]
fwrite(' '.join(['%f' % d for d in slice_x]) )
#np.savetxt(file, slice_x)
fwrite('\n')
fwrite('\n')
fwrite(' END_DATAGRID_3D\n')
fwrite('END_BLOCK_DATAGRID_3D\n')