sisl.io.vasp.stdoutSileVASP

class sisl.io.vasp.stdoutSileVASP(filename, *args, **kwargs)

Bases: SileVASP

Output file from VASP

Methods

accuracy_reached()	True if the line "reached required accuracy" was found.
close()
completed()	True if the line "General timing and accounting" was found.
cpu_time([flag])	Returns the consumed cpu time (in seconds) from a given section
dir_file([filename, filename_base])	File of the current Sile
geometry_group(geometry[, ret_index])	Order atoms in geometry according to species such that all of one specie is consecutive
read(*args, **kwargs)	Generic read method which should be overloaded in child-classes
write(*args, **kwargs)	Generic write method which should be overloaded in child-classes
base_file	File of the current Sile
file	File of the current Sile
read_energy
read_trajectory

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

accuracy_reached()

True if the line “reached required accuracy” was found.

property base_file

File of the current Sile

close()

completed()

True if the line “General timing and accounting” was found.

cpu_time(flag='General timing and accounting')

Returns the consumed cpu time (in seconds) from a given section

dir_file(filename=None, filename_base='')

File of the current Sile

property file

File of the current Sile

static geometry_group(geometry, ret_index=False)

Order atoms in geometry according to species such that all of one specie is consecutive

When creating VASP input files (poscarSileVASP for instance) the equivalent POTCAR file needs to contain the pseudos for each specie as they are provided in blocks.

I.e. for a geometry like this: .. code:

[Atom(6), Atom(4), Atom(6)]

the resulting POTCAR needs to contain the pseudo for Carbon twice.

This method will re-order atoms according to the species”

Parameters

• geometry (Geometry) – geometry to be re-ordered

• ret_index (bool, optional) – return sorted indices

Returns

geometry

Return type

reordered geometry

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_energy = <sisl.io._multiple.SileBound object>

read_trajectory = <sisl.io._multiple.SileBound object>

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.