sisl.io.openmx.omxSileOpenMX

class sisl.io.openmx.omxSileOpenMX(filename, *args, **kwargs)

Bases: 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.

Methods

close()
dir_file([filename, filename_base])	File of the current Sile
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_lattice([output])	Reads lattice
type(label)	Return the type of the fdf-keyword
write(*args, **kwargs)	Generic write method which should be overloaded in child-classes
base_file	File of the current Sile
file	Return the current file name (without the directory prefix)

class InfoAttr(attr, regex, parser, doc='', updatable=False, default=None, found=False)

Bases: object

Holder for parsing lines and extracting information from text files

This consists of:

attr:

the name of the attribute This will be the sile.info. access point.

regex:

the regular expression used to match a line. If a str, it will be compiled as is to a regex pattern. regex.match(line) will be used to check if the value should be updated.

parser:

if regex.match(line) returns a match that is true, then this parser will be executed. The parser must be a function accepting two arguments:

def parser(attr, match)

where attr is this object, and match is the match done on the line. (Note that match.string will return the full line used to match against).

updatable:

control whether a new match on the line will update using parser. If false, only the first match will update the value

default:

the default value of the attribute

found:

whether the value has been found in the file.

__init__(attr, regex, parser, doc='', updatable=False, default=None, found=False)

attr

copy()

doc

documentation()

Returns a documentation string for this object

found

parser

process(line)

regex

updatable

value

__init__(filename, mode='r', *args, **kwargs)

Just to pass away the args and kwargs

property base_file

File of the current Sile

close()

dir_file(filename=None, filename_base='')

File of the current Sile

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

plot

Handles all plotting possibilities for a class

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 lattice from output files (default to read from the input file).

• order ({'dat', 'omx'}) – the order of which to try and read the lattice 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_lattice(output=False, *args, **kwargs)

Reads lattice

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

Parameters

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

• order ({'dat', 'omx'}) – the order of which to try and read the lattice. 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.