sisl.io.siesta.outSileSiesta
- class sisl.io.siesta.outSileSiesta(filename, mode='r', comment=None, *args, **kwargs)
Bases:
sisl.io.siesta.SileSiesta
Output file from Siesta
This enables reading the output quantities from the Siesta output.
Methods
True if the full file has been read and "Job completed" was found.
dir_file
([filename, filename_base])File of the current Sile
read
(*args, **kwargs)Generic read method which should be overloaded in child-classes
Reads the basis as found in the output file
read_charge
(name[, iscf, imd, key_scf, ...])Read charges calculated in SCF loop or MD loop (or both)
read_data
(*args, **kwargs)Read specific content in the Siesta out file
Reads the final energy distribution
read_force
([last, all, total, max])Reads the forces from the Siesta output file
read_geometry
([last, all])Reads the geometry from the Siesta output file
read_moment
([orbitals, quantity, last, all])Reads the moments from the Siesta output file
read_scf
([key, iscf, imd, as_dataframe])Parse SCF information and return a table of SCF information depending on what is requested
read_stress
([key, last, all])Reads the stresses from the Siesta output file
write
(*args, **kwargs)Generic write method which should be overloaded in child-classes
File of the current Sile
File of the current Sile
- __init__(filename, mode='r', comment=None, *args, **kwargs)
- property base_file
File of the current Sile
- dir_file(filename=None, filename_base='')
File of the current Sile
- property file
File of the current Sile
- 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()[source]
Reads the basis as found in the output file
This parses 3 things:
At the start of the file there are some initatom output specifying which species in the calculation.
Reading the <basis_specs> entries for the masses
Reading the PAO.Basis block output for orbital information
- read_charge(name, iscf=Opt.ANY, imd=Opt.ANY, key_scf='scf', as_dataframe=False)[source]
Read charges calculated in SCF loop or MD loop (or both)
Siesta enables many different modes of writing out charges.
NOTE: currently Mulliken charges are not implemented.
The below table shows a list of different cases that may be encountered, the letters are referred to in the return section to indicate what is returned.
Case
A
B
C
D
E
Charge
MD
SCF
MD+SCF
Final
Orbital resolved
Voronoi
Hirshfeld
Mulliken
Notes
Errors will be raised if one requests information not present. I.e. passing an integer or Opt.ALL for iscf will raise an error if the SCF charges are not present. For Opt.ANY it will return the most information, effectively SCF will be returned if present.
Currently Mulliken is not implemented, any help in reading this would be very welcome.
- Parameters
name ({"voronoi", "hirshfeld"}) – the name of the charges that you want to read
iscf (int or Opt, optional) – index (0-based) of the scf iteration you want the charges for. If the enum specifier Opt.ANY or Opt.ALL are used, then the returned quantities depend on what is present. If
None/Opt.NONE
it will not return any SCF charges. If both imd and iscf areNone
then only the final charges will be returned.imd (int or Opt, optional) – index (0-based) of the md step you want the charges for. If the enum specifier Opt.ANY or Opt.ALL are used, then the returned quantities depend on what is present. If
None/Opt.NONE
it will not return any MD charges. If both imd and iscf areNone
then only the final charges will be returned.key_scf (str, optional) – the key lookup for the scf iterations (a “:” will automatically be appended)
as_dataframe (boolean, optional) – whether charges should be returned as a pandas dataframe.
- Returns
numpy.ndarray – if a specific MD+SCF index is requested (or special cases where output is not complete)
list of numpy.ndarray – if one both iscf or imd is different from
None/Opt.NONE
.pandas.DataFrame – if as_dataframe is requested. The dataframe will have multi-indices if multiple SCF or MD steps are requested.
- read_data(*args, **kwargs)[source]
Read specific content in the Siesta out file
The currently implemented things are denoted in the parameters list. Note that the returned quantities are in the order of keywords, so:
>>> read_data(geometry=True, force=True) <geometry>, <force> >>> read_data(force=True, geometry=True) <force>, <geometry>
- Parameters
geometry (bool, optional) – read geometry, args are passed to
read_geometry
force (bool, optional) – read force, args are passed to
read_force
stress (bool, optional) – read stress, args are passed to
read_stress
moment (bool, optional) – read moment, args are passed to
read_moment
(only for spin-orbit calculations)energy (bool, optional) – read final energies, args are passed to
read_energy
- read_energy()[source]
Reads the final energy distribution
Currently the energies translated are:
band
band structure energy
kinetic
electronic kinetic energy
hartree
electronic electrostatic Hartree energy
dftu
DFT+U energy
spin_orbit
spin-orbit energy
extE
external field energy
xc
exchange-correlation energy
exchange
exchange energy
correlation
correlation energy
bulkV
bulk-bias correction energy
total
total energy
negf
NEGF energy
fermi
Fermi energy
ion.electron
ion-electron interaction energy
ion.ion
ion-ion interaction energy
ion.kinetic
kinetic ion energy
Any unrecognized key gets added as is.
Examples
>>> energies = sisl.get_sile("RUN.out").read_energy() >>> ion_energies = energies.ion >>> ion_energies.ion # ion-ion interaction energy >>> ion_energies.kinetic # ion kinetic energy >>> energies.fermi # fermi energy
- Returns
PropertyDict
- Return type
dictionary like lookup table ionic energies are stored in a nested PropertyDict at the key
ion
(all energies in eV)
- read_force(last=True, all=False, total=False, max=False)[source]
Reads the forces from the Siesta output file
- Parameters
last (bool, optional) – only read the last force
all (bool, optional) – return a list of all forces (like an MD) If True last is ignored
total (bool, optional) – return the total forces instead of the atomic forces.
max (bool, optional) –
whether only the maximum atomic force should be returned for each step.
Setting it to True is equivalent to max(outSile.read_force()) in case atomic forces are written in the output file (WriteForces .true. in the fdf file)
Note that this is not the same as doing max(outSile.read_force(total=True)) since the forces returned in that case are averages on each axis.
- Returns
returns
None
if the forces are not found in the output, otherwise forces will be returned- The shape of the array will be different depending on the type of forces requested:
atomic (default): (nMDsteps, nAtoms, 3)
total: (nMDsteps, 3)
max: (nMDsteps, )
If all is False, the first dimension does not exist. In the case of max, the returned value will therefore be just a float, not an array.
If total and max are both True, they are returned separately as a tuple:
(total, max)
- Return type
numpy.ndarray or None
- read_geometry(last=True, all=False)[source]
Reads the geometry from the Siesta output file
- Parameters
- Returns
geometries – if all is False only one geometry will be returned (or None). Otherwise a list of geometries corresponding to the MD-runs.
- Return type
- read_moment(orbitals=False, quantity='S', last=True, all=False)[source]
Reads the moments from the Siesta output file
These will only be present in case of spin-orbit coupling.
- read_scf(key='scf', iscf=- 1, imd=None, as_dataframe=False)[source]
Parse SCF information and return a table of SCF information depending on what is requested
- Parameters
key ({'scf', 'ts-scf'}) – parse SCF information from Siesta SCF or TranSiesta SCF
iscf (int, optional) – which SCF cycle should be stored. If
-1
only the final SCF step is stored, for None all SCF cycles are returned. When iscf values queried are not found they will be truncated to the nearest SCF step.imd (int or None, optional) – whether only a particular MD step is queried, if None, all MD steps are parsed and returned. A negative number wraps for the last MD steps.
as_dataframe (boolean, optional) – whether the information should be returned as a
pandas.DataFrame
. The advantage of this format is that everything is indexed and therefore you know what each value means.You can also perform operations very easily on a dataframe.
- read_stress(key='static', last=True, all=False)[source]
Reads the stresses from the Siesta output file
- Parameters
- Returns
returns
None
if the stresses are not found in the output, otherwise stresses will be returned- Return type
numpy.ndarray or None
- 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.