sisl.io.fhiaims.inSileFHIaims

class sisl.io.fhiaims.inSileFHIaims(filename, *args, **kwargs)

Bases: SileFHIaims

FHI-aims geometry.in file object

Methods

base_directory([relative_to])

Retrieve the base directory of the file, relative to the path relative_to

close()

dir_file([filename, filename_base])

File of the current Sile

read(*args, **kwargs)

Generic read method which should be overloaded in child-classes

read_geometry([velocity, moment])

Reads Geometry object from the file

read_lattice()

Reads supercell object from the file

read_moment()

Reads initial moment in the file

read_velocity()

Reads velocity in the file

write(*args, **kwargs)

Generic write method which should be overloaded in child-classes

write_geometry(geometry[, fmt, as_frac, ...])

Writes the geometry to the contained file

write_lattice(lattice[, fmt])

Writes the supercell to the contained file

base_file

File of the current Sile

file

File of the current Sile

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

base_directory(relative_to='.')

Retrieve the base directory of the file, relative to the path relative_to

property base_file

File of the current Sile

close()
dir_file(filename=None, filename_base='')

File of the current Sile

property file

File of the current Sile

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_geometry(velocity=False, moment=False)[source]

Reads Geometry object from the file

Parameters:
  • velocity (bool, optional) – also return the velocities in the file, if not present, it will return a 0 array

  • moment (bool, optional) – also return the moments specified in the file, if not present, it will return a 0 array

Returns:

  • Geometry – geometry found in file

  • velocity (array_like) – array of velocities in Ang/ps for each atom, will only be returned if velocity is true

  • moment (array_like) – array of initial moments of each atom, will only be returned if moment is true

read_lattice()[source]

Reads supercell object from the file

read_moment()[source]

Reads initial moment in the file

read_velocity()[source]

Reads velocity in the file

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.

write_geometry(geometry, fmt='.8f', as_frac=False, velocity=None, moment=None)[source]

Writes the geometry to the contained file

Parameters:
  • geometry (Geometry) – the geometry to be written

  • fmt (str, optional) – used format for the precision of the data

  • as_frac (bool, optional) – whether coordinates are written as fractional coordinates

  • velocity (array_like, optional) – also write the velocity fields in [Ang/ps]

  • moment (array_like, optional) – also write an initial moment for each atom

write_lattice(lattice, fmt='.8f')[source]

Writes the supercell to the contained file

Parameters:
  • lattice (Lattice) – the supercell to be written

  • fmt (str, optional) – used format for the precision of the data