sisl.io.fhiaims.inSileFHIaims
- class sisl.io.fhiaims.inSileFHIaims(filename, *args, **kwargs)
Bases:
SileFHIaims
FHI-aims
geometry.in
file objectMethods
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
Reads supercell object from the file
Reads initial moment in the file
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
File of the current Sile
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:
- 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
- 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