sisl.io.siesta.fdfSileSiesta¶
- class sisl.io.siesta.fdfSileSiesta(filename, mode='r', comment=None, *args, **kwargs)¶
Bases:
sisl.io.siesta.SileSiesta
FDF-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
Examples
>>> fdf = fdfSileSiesta('tmp/RUN.fdf') # reads output files in 'tmp/' folder >>> fdf = fdfSileSiesta('tmp/RUN.fdf', base='.') # reads output files in './' folder
Methods
dir_file
([filename, filename_base])File of the current Sile
exist
()Query whether the file exists
get
(label[, default, unit, with_unit])Retrieve fdf-keyword from the file
includes
()Return a list of all files that are included or otherwise necessary for reading the fdf file
print
(key, value)Return a string which is pretty-printing the key+value
read
(*args, **kwargs)Generic read method which should be overloaded in child-classes
read_basis
(*args, **kwargs)Read the atomic species and figure out the number of atomic orbitals in their basis
read_density_matrix
(*args, **kwargs)Try and read density matrix by reading the <>.nc, <>.TSDE files, <>.DM (in that order)
read_dynamical_matrix
(*args, **kwargs)Read dynamical matrix from output of the calculation
read_energy_density_matrix
(*args, **kwargs)Try and read energy density matrix by reading the <>.nc or <>.TSDE files (in that order)
read_fermi_level
(*args, **kwargs)Read fermi-level from output of the calculation
read_force
(*args, **kwargs)Read forces from the output of the calculation (forces are not defined in the input)
read_force_constant
(*args, **kwargs)Read force constant from the output of the calculation
read_geometry
([output])Returns Geometry object by reading fdf or Siesta output related files.
read_grid
(name, *args, **kwargs)Read grid related information from any of the output files
read_hamiltonian
(*args, **kwargs)Try and read the Hamiltonian by reading the <>.nc, <>.TSHS files, <>.HSX (in that order)
read_overlap
(*args, **kwargs)Try and read the overlap matrix by reading the <>.nc, <>.TSHS files, <>.HSX, <>.onlyS (in that order)
read_supercell
([output])Returns SuperCell object by reading fdf or Siesta output related files.
read_supercell_nsc
(*args, **kwargs)Read supercell size using any method available
set
(key, value[, keep])Add the key and value to the FDF file
type
(label)Return the type of the fdf-keyword
write
(*args, **kwargs)Generic write method which should be overloaded in child-classes
write_geometry
(geometry[, fmt])Writes the geometry to the contained file
write_supercell
(sc[, fmt])Writes the supercell to the contained file
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
- exist()¶
Query whether the file exists
- property file¶
File of the current Sile
- get(label, default=None, unit=None, with_unit=False)[source]¶
Retrieve fdf-keyword from the file
- Parameters
label (str) – the fdf-label to search for
default (optional) – if the label is not found, this will be the returned value (default to
None
)unit (str, optional) – unit of the physical quantity to return
with_unit (bool, optional) – whether the physical quantity gets returned with the found unit in the fdf file.
- Returns
value (the value of the fdf-label. If the label is a block, a list is returned, for) – a real value a float (or if the default is of float), for an integer, an int is returned.
unit (if with_unit is true this will contain the associated unit if it is specified)
Examples
>>> print(open(...).readlines()) LabeleV 1. eV LabelRy 1. Ry Label name FakeInt 1 %block Hello line 1 line2 %endblock >>> fdf.get('LabeleV') == 1. # default unit is eV >>> fdf.get('LabelRy') == unit.siesta.unit_convert('Ry', 'eV') >>> fdf.get('LabelRy', unit='Ry') == 1. >>> fdf.get('LabelRy', with_unit=True) == (1., 'Ry') >>> fdf.get('FakeInt', '0') == '1' >>> fdf.get('LabeleV', with_unit=True) == (1., 'eV') >>> fdf.get('Label', with_unit=True) == 'name' # no unit present on line >>> fdf.get('Hello') == ['line 1', 'line2']
- includes()[source]¶
Return a list of all files that are included or otherwise necessary for reading the fdf file
- 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)[source]¶
Read the atomic species and figure out the number of atomic orbitals in their basis
The order of the read is shown below.
One can limit the tried files to only one file by passing only a single file ending.
- Parameters
order (list of str, optional) – the order of which to try and read the basis information. By default this is
['nc', 'ion', 'ORB_INDX', 'fdf']
- read_density_matrix(*args, **kwargs)[source]¶
Try and read density matrix by reading the <>.nc, <>.TSDE files, <>.DM (in that order)
One can limit the tried files to only one file by passing only a single file ending.
- Parameters
order (list of str, optional) – the order of which to try and read the density matrix By default this is
['nc', 'TSDE', 'DM']
.
- read_dynamical_matrix(*args, **kwargs)[source]¶
Read dynamical matrix from output of the calculation
Generally the mass is stored in the basis information output, but for dynamical matrices it makes sense to let the user control this, e.g. through the fdf file. By default the mass will be read from the AtomicMass key in the fdf file and _not_ from the basis set information.
- Parameters
order (list of str, optional) – the order of which to try and read the dynamical matrix. By default this is
['nc', 'FC']
.cutoff_dist (float, optional) – cutoff value for the distance of the force-constants (everything farther than cutoff_dist will be set to 0 Ang). Default, no cutoff.
cutoff (float, optional) – absolute values below the cutoff are considered 0. Defaults to 0. eV/Ang**2.
trans_inv (bool, optional) – if true (default), the force-constant matrix will be fixed so that translational invariance will be enforced
sum0 (bool, optional) – if true (default), the sum of forces on atoms for each displacement will be forced to 0.
hermitian (bool, optional) – if true (default), the returned dynamical matrix will be hermitian
- Returns
dynamic_matrix – the dynamical matrix
- Return type
- read_energy_density_matrix(*args, **kwargs)[source]¶
Try and read energy density matrix by reading the <>.nc or <>.TSDE files (in that order)
One can limit the tried files to only one file by passing only a single file ending.
- Parameters
order (list of str, optional) – the order of which to try and read the density matrix By default this is
['nc', 'TSDE']
.
- read_fermi_level(*args, **kwargs)[source]¶
Read fermi-level from output of the calculation
- Parameters
order (list of str, optional) – the order of which to try and read the fermi-level. By default this is
['nc', 'TSDE', 'TSHS', 'EIG']
.- Returns
Ef – fermi-level
- Return type
- read_force(*args, **kwargs)[source]¶
Read forces from the output of the calculation (forces are not defined in the input)
- Parameters
order (list of str, optional) – the order of the forces we are trying to read, default to
['FA', 'nc']
- Returns
numpy.ndarray
- Return type
vector with forces for each of the atoms, along each Cartesian direction
- read_force_constant(*args, **kwargs)[source]¶
Read force constant from the output of the calculation
- Returns
force_constant – vector
[*, 3, 2, *, 3]
with force constant element for each of the atomic displacements- Return type
- read_geometry(output=False, *args, **kwargs)[source]¶
Returns Geometry object by reading fdf or Siesta output related files.
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 fdf file).
order (list of str, optional) – the order of which to try and read the geometry. By default this is
['XV', 'nc', 'fdf', 'TSHS']
if output is true If order is present output is disregarded.
Examples
>>> fdf = get_sile('RUN.fdf') >>> fdf.read_geometry() # read from fdf >>> fdf.read_geometry(True) # read from [XV, nc, fdf] >>> fdf.read_geometry(order=['nc']) # read from [nc] >>> fdf.read_geometry(True, order=['nc']) # read from [nc]
- read_grid(name, *args, **kwargs)[source]¶
Read grid related information from any of the output files
The order of the readed data is shown below.
One can limit the tried files to only one file by passing only a single file ending.
- Parameters
name (str) – name of data to read. The list of names correspond to the Siesta output manual (Rho, TotalPotential, etc.), the strings are case insensitive.
order (list of str, optional) – the order of which to try and read the geometry. By default this is
['nc', 'grid.nc', 'bin']
(bin refers to the binary files)
- read_hamiltonian(*args, **kwargs)[source]¶
Try and read the Hamiltonian by reading the <>.nc, <>.TSHS files, <>.HSX (in that order)
One can limit the tried files to only one file by passing only a single file ending.
- Parameters
order (list of str, optional) – the order of which to try and read the Hamiltonian. By default this is
['nc', 'TSHS', 'HSX']
.
- read_overlap(*args, **kwargs)[source]¶
Try and read the overlap matrix by reading the <>.nc, <>.TSHS files, <>.HSX, <>.onlyS (in that order)
One can limit the tried files to only one file by passing only a single file ending.
- Parameters
order (list of str, optional) – the order of which to try and read the overlap matrix By default this is
['nc', 'TSHS', 'HSX', 'onlyS']
.
- read_supercell(output=False, *args, **kwargs)[source]¶
Returns SuperCell object by reading fdf or Siesta output related files.
One can limit the tried files to only one file by passing only a single file ending.
- Parameters
output (bool, optional) – whether to read supercell from output files (default to read from the fdf file).
order (list of str, optional) – the order of which to try and read the supercell. By default this is
['XV', 'nc', 'fdf']
if output is true. If order is present output is disregarded.
Examples
>>> fdf = get_sile('RUN.fdf') >>> fdf.read_supercell() # read from fdf >>> fdf.read_supercell(True) # read from [XV, nc, fdf] >>> fdf.read_supercell(order=['nc']) # read from [nc] >>> fdf.read_supercell(True, order=['nc']) # read from [nc]
- read_supercell_nsc(*args, **kwargs)[source]¶
Read supercell size using any method available
- Raises
SislWarning if none of the files can be read –
- set(key, value, keep=True)[source]¶
Add the key and value to the FDF file
- Parameters
key (str) – the fdf-key value to be set in the fdf file
value (str or list of str) – the value of the string. If a str is passed a regular fdf-key is used, if a list it will be a %block.
keep (bool, optional) – whether old flags will be kept in the fdf file. In this case a time-stamp will be written to show when the key was overwritten.
- type(label)[source]¶
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.