sisl.io.vasp.carSileVASP
- class sisl.io.vasp.carSileVASP(filename, *args, **kwargs)
Bases:
SileVASP
CAR VASP files for defining geometries
This file-object handles both POSCAR and CONTCAR files
Plotting
Plotting functions for the
carSileVASP
class.plot.geometry
([ret_dynamic, ...])Calls
read_geometry
and creates aGeometryPlot
from its output.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
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
read_geometry
([ret_dynamic])Returns Geometry object from this Sile
Returns Lattice object from this Sile
write
(*args, **kwargs)Generic write method which should be overloaded in child-classes
write_geometry
(geometry[, dynamic, ...])Writes the geometry to the contained file
Attributes
File of the current Sile
File of the current Sile
- base_directory(relative_to='.')
Retrieve the base directory of the file, relative to the path relative_to
- close()
- dir_file(filename=None, filename_base='')
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:
[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-orderedret_index (
bool
, optional) – return sorted indices
- Returns:
geometry (
Geometry
) – reordered geometry
- plot.geometry(ret_dynamic: bool = False, *, axes: Axes = ['x', 'y', 'z'], atoms: AtomsIndex = None, atoms_style: Sequence[AtomsStyleSpec] = [], atoms_scale: float = 1.0, atoms_colorscale: Colorscale | None = None, drawing_mode: Literal['scatter', 'balls', None] = None, bind_bonds_to_ats: bool = True, points_per_bond: int = 20, bonds_style: StyleSpec = {}, bonds_scale: float = 1.0, bonds_colorscale: Colorscale | None = None, show_atoms: bool = True, show_bonds: bool = True, show_cell: Literal['box', 'axes', False] = 'box', cell_style: StyleSpec = {}, nsc: tuple[int, int, int] = (1, 1, 1), atoms_ndim_scale: tuple[float, float, float] = (16, 16, 1), bonds_ndim_scale: tuple[float, float, float] = (1, 1, 10), dataaxis_1d: np.ndarray | Callable | None = None, arrows: Sequence[AtomArrowSpec] = (), backend='plotly') GeometryPlot
Calls
read_geometry
and creates aGeometryPlot
from its output.- Parameters:
ret_dynamic (
bool
, optional) – also return selective dynamics (if present), if not, None will be returned.axes – The axes to project the geometry to.
atoms – The atoms to plot. If None, all atoms are plotted.
atoms_style – List of style specifications for the atoms. See the showcase notebooks for examples.
atoms_scale – Scaling factor for the size of all atoms.
atoms_colorscale – Colorscale to use for the atoms in case the color attribute is an array of values. If None, the default colorscale is used for each backend.
drawing_mode – The method used to draw the atoms.
bind_bonds_to_ats – Whether to display only bonds between atoms that are being displayed.
points_per_bond – When the points are drawn using points instead of lines (e.g. in some frameworks to draw multicolor bonds), the number of points used per bond.
bonds_style – Style specification for the bonds. See the showcase notebooks for examples.
bonds_scale – Scaling factor for the width of all bonds.
bonds_colorscale – Colorscale to use for the bonds in case the color attribute is an array of values. If None, the default colorscale is used for each backend.
show_atoms – Whether to display the atoms.
show_bonds – Whether to display the bonds.
show_cell – Mode to display the cell. If False, the cell is not displayed.
cell_style – Style specification for the cell. See the showcase notebooks for examples.
nsc – Number of unit cells to display in each direction.
atoms_ndim_scale – Scaling factor for the size of the atoms for different dimensionalities (1D, 2D, 3D).
bonds_ndim_scale – Scaling factor for the width of the bonds for different dimensionalities (1D, 2D, 3D).
dataaxis_1d – Only meaningful for 1D plots. The data to plot on the Y axis.
arrows – List of arrow specifications to display. See the showcase notebooks for examples.
backend – The backend to use to generate the figure.
See also
GeometryPlot
The plot class used to generate the plot.
read_geometry
The method called to get the data.
- 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(ret_dynamic: bool = False) Geometry [source]
Returns Geometry object from this Sile
Possibly also return the dynamics (if present).
- Parameters:
ret_dynamic (
bool
, optional) – also return selective dynamics (if present), if not, None will be returned.- Returns:
Geometry
– the contained geometrynumpy.ndarray
– which Cartesian directions are allowed to move (only if ret_dynamic)
- 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: Geometry, dynamic=True, group_species: bool = False)[source]
Writes the geometry to the contained file
- Parameters:
geometry – geometry to be written to the file
dynamic (
None
,bool
orlist
, optional) – define which atoms are dynamic in the VASP run (default is True, which means all atoms are dynamic). If None, the resulting file will not contain any dynamic flagsgroup_species – before writing geometry first re-order species to have species in consecutive blocks (see
geometry_group
)
Examples
>>> car = carSileVASP('POSCAR', 'w') >>> geom = geom.graphene() >>> geom.write(car) # regular car without Selective Dynamics >>> geom.write(car, dynamic=False) # fix all atoms >>> geom.write(car, dynamic=[False, (True, False, True)]) # fix 1st and y coordinate of 2nd
See also
geometry_group
method used to group atoms together according to their species
- property base_file
File of the current Sile
- property file
File of the current Sile
- plot
Plotting functions for the
carSileVASP
class.