iotools Package

iotools Package

class abipy.iotools.ETSF_Reader(path)

Bases: EtsfReader

Provides high-level API to read data from netcdf files written following the ETSF-IO specifications described in [Caliste2008]

read_structure()

Overrides the read_structure method so that we always return an instance of AbiPy abipy.core.structure.Structure object

typeidx_from_symbol(symbol: str) → int

Returns the type index from the chemical symbol. Note python convention.

chemical_symbols()

Chemical symbols char [number of atom species][symbol length].

read_string(varname: str)

Parameters:

varname – Name of the variable

none_if_masked_array(arr)

Return None if arr is a MaskedArray else None.

read_amu_symbol() → dict

Read atomic masses and return dictionary element_symbol –> amu.

Note

Only netcdf files with phonon-related quantities contain this variable.

read_ngfft3() → array

Return the number of FFT divisions.

visualizer Module

Classes used to execute a visualizer within the Python interpreter.

class abipy.iotools.visualizer.Visualizer(filepath: str)

Bases: object

Handle the visualization of data.

is_macosx_app = False

Error

alias of VisualizerError

property cmdarg

Arguments that must be used to visualize the file.

binpath()

Absolute path of the binary. None if app is not found

property is_available: bool

True is the visualizer is available on the local machine.

classmethod get_available(ext=None) → list

List of visualizers available on the local host. If ext is not None, only the visualizers supporting this extension are returned.

classmethod support_ext(ext) → bool

True if visualizer supports the extension ext.

classmethod from_file(filepath: str)

Initialize a subclass of Visualizer from filepath, the application is chosen automatically depending on the file extension.

Raises:

VisualizerError –

classmethod supported_extensions() → list

List of file extensions supported by the visualizer.

classmethod from_name(appname)

Return the visualizer class from the name of the application.

classmethod all_visunames()

List with the names of the visualizers supported.

xsf Module

Tools for writing Xcrysden files.

abipy.iotools.xsf.xsf_write_structure_and_data_to_path(filepath, structure, datar, **kwargs) → None

Simplified interface to write structure and data to filepath in XSF format.

abipy.iotools.xsf.xsf_write_structure(file, structures: list) → None

Write the crystalline structure in the Xcrysden format (XSF)

Parameters:

• file – file-like object.

• structures – Structure or list of Structure objects.

abipy.iotools.xsf.xsf_write_data(file, structure, data, add_replicas=True, cplx_mode=None, idname='data', tag='_UNKNOWN') → None

Write data in the Xcrysden format (XSF)

Parameters:

• file – file-like object.

• structure – Structure object.

• data – array-like object in C-order, i.e data[nx, ny, nz] or data[ngrids, 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

abipy.iotools.xsf.bxsf_write(file, structure, nsppol, nband, ngkpt, ucdata_sbk, fermie, unit='eV') → None

Write band structure data in the Xcrysden format (XSF)

Parameters:

• file – file-like object.

• structure – Structure object.

• nsppol – Number of spins.

• nband – Number of bands.

• ngkpt – Number of divisions of the full k-mesh.

• ucdata_sbk – Array [nsppol, nband, ngkpt[0], ngkpt[1], ngkpt[2]] with energies in the unit cell mesh in unit unit.

• fermie – Fermi energy.

• writing. (unit=Unit of input ucdata_sbk and fermie. Energies will be converted to Hartree before)

Note

1. The k-points must span the reciprocal unit cell, not the Brillouin zone.

2. The mesh must be closed and centered on Gamma.

3. Energies are written in row-major (i.e. C) order.

# Energies are in Hartree.

See also http://www.xcrysden.org/doc/XSF.html