omxSileOpenMX

class sisl.io.openmx.omxSileOpenMX(filename, mode='r', comment=None, *args, **kwargs)

Bases: sisl.io.openmx.sile.SileOpenMX

OpenMX-input file

By supplying base you can reference files in other directories. By default the base is the directory given in the file name.

Parameters

• filename (str) – input file

• mode (str, optional) – opening mode, default to read-only

• base (str, optional) – base-directory to read output files from.

Examples

>>> omx = omxSileOpenMX("tmp/input.dat") # reads output files in 'tmp/' folder
>>> omx = omxSileOpenMX("tmp/input.dat", base=".") # reads output files in './' folder

When using this file in conjunction with the sgeom script while your input data-files are named input.dat, please do this:

sgeom input.dat{omx} output.xyz

which forces the use of the omx file.

Attributes

__dict__
__doc__
__module__
__weakref__	list of weak references to the object (if defined)
_write_default
_write_default_only
base_file	File of the current Sile
file	Return the current file name (without the directory prefix)

Methods

_ArgumentParser_args_single()	Default arguments for the Sile
__delattr__	Implement delattr(self, name).
__dir__	Default dir() implementation.
__enter__()	Opens the output file and returns it self
__eq__	Return self==value.
__exit__(type, value, traceback)
__format__	Default object formatter.
__ge__	Return self>=value.
__getattr__(name)	Override to check the handle
__getattribute__	Return getattr(self, name).
__gt__	Return self>value.
__hash__	Return hash(self).
__init__(filename[, mode, comment])	Initialize self.
__init_subclass__	This method is called when a class is subclassed.
__iter__()	Iterator for file
__le__	Return self<=value.
__lt__	Return self<value.
__ne__	Return self!=value.
__new__	Create and return a new object.
__reduce__	Helper for pickle.
__reduce_ex__	Helper for pickle.
__repr__	Return repr(self).
__setattr__	Implement setattr(self, name, value).
__sizeof__	Size of object in memory, in bytes.
__str__()	Return a representation of the Sile
__subclasshook__	Abstract classes can override this to customize issubclass().
_base_file(f)	Make f refer to the file with the appropriate base directory
_base_setup(*args, **kwargs)	Setup the Sile after initialization
_open()
_popfile()
_pushfile(f)
_r_basis_omx()
_r_geometry_dat(*args, **kwargs)	Returns Geometry
_r_geometry_omx(*args, **kwargs)	Returns Geometry
_r_supercell_dat(*args, **kwargs)	Returns SuperCell object from the omx file
_r_supercell_omx(*args, **kwargs)	Returns SuperCell object from the omx file
_read_key(key)	Try and read the first occurence of a key
_seek()	Closes all files, and starts over from beginning
_setup(*args, **kwargs)	Setup the omxSileOpenMX after initialization
_type(value)	Determine the type by the value
_write(*args, **kwargs)	Wrapper to default the write statements
dir_file([filename])	File of the current Sile
exist()	Query whether the file exists
get(key[, default])	Retrieve keyword from the file
read(*args, **kwargs)	Generic read method which should be overloaded in child-classes
read_basis(*args, **kwargs)	Reads basis
read_geometry([output])	Returns Geometry object
read_supercell([output])	Reads supercell
type(label)	Return the type of the fdf-keyword
write(*args, **kwargs)	Generic write method which should be overloaded in child-classes

property base_file

File of the current Sile

dir_file(filename=None)

File of the current Sile

exist()

Query whether the file exists

property file

Return the current file name (without the directory prefix)

get(key, default=None)

Retrieve keyword from the file

Parameters

• key (str) – the key to search for

• default (optional) – if the key is not found, this will be the returned value (default to None)

Returns

value – a real value a float (or if the default is of float), for an integer, an int is returned.

Return type

the value of the key. If the key is a block, a list is returned, for

read(*args, **kwargs)

Generic read method which should be overloaded in child-classes

Parameters

kwargs – keyword arguments will try and search for the attribute read_<> and call it with the remaining **kwargs as arguments.

read_basis(*args, **kwargs)

Reads basis

Parameters

• output (bool, optional) – whether to read supercell from output files (default to read from the input file).

• order ({'dat', 'omx'}) – the order of which to try and read the supercell. If order is present output is disregarded.

read_geometry(output=False, *args, **kwargs)

Returns Geometry object

One can limit the tried files to only one file by passing only a single file ending.

Parameters

• output (bool, optional) – whether to read geometry from output files (default to read from the input file).

• order ({'dat', 'omx'}) – the order of which to try and read the geometry. If order is present output is disregarded.

read_supercell(output=False, *args, **kwargs)

Reads supercell

One can limit the tried files to only one file by passing only a single file ending.

Parameters

• output (bool, optional) – whether to read supercell from output files (default to read from the input file).

• order ({'dat', 'omx'}) – the order of which to try and read the supercell. If order is present output is disregarded.

type(label)

Return the type of the fdf-keyword

Parameters

label (str) – the label to look-up

write(*args, **kwargs)

Generic write method which should be overloaded in child-classes

Parameters

**kwargs – keyword arguments will try and search for the attribute write_ and call it with the remaining **kwargs as arguments.