Ubuntu Manpage: cif2cell - prepare CIF files for electronic structure calculations

Provided by: python3-cif2cell_2.0.0a3+dfsg-1_all

NAME

       cif2cell - prepare CIF files for electronic structure calculations

SYNOPSIS

       cif2cell FILE [-p PROGRAM] [other options]

DESCRIPTION

       A  program  for  generating  input lattice structures to various electronic structure programs from a CIF
       (Crystallographic Information Framework) file.  This code was published in  Comput.  Phys.  Commun.  182,
       1183 (2011). Please cite generously.

OPTIONS

-h, --help
show this help message and exit

--version
Print version number.

-v, --verbose
Be as verbose as possible.

-q, --quiet
Suppress all but explicitly requested screen output. Overrides --verbose flag.

General options:

-f FILE, --file=FILE
Input CIF file, unless given as first argument to the program.

-p PROGRAM, --program=PROGRAM
The electronic structure code you want to create input file(s) for. Currently supports: abinit,
ase, atat, bmdl, castep, cellgen, cfg, cif, coo, cp2k, cpmd, crystal09, elk, emto, exciting,
fhi-aims, fleur, hutsepot, kfcd, kgrn, kstr, lammps, mopac, ncol, pwscf, quantum-espresso, rspt,
shape, siesta, spacegroup, spc, sprkkr, vasp, xband, xyz. This keyword is case insensitive.

-o FILE, --outputfile=FILE
Name of output file (if other than default for you electronic structure code).

-a, --append
Append the output to given output file rather than overwriting.

--grammar=GRAMMAR
Set the CIF grammar to be used when parsing the input file (default is 1.1).

--which-filename
If given together with the --program option, the name of the output file will be printed to
screen.

-b BLOCK, --block=BLOCK
Block of data in input file (if there are more than one block in the CIF file).

Cell generation options:

--no-reduce
Do not reduce to the primitive cell.

--force
Attempt to force generation of output file despite problems and/or ambiguities in the input file.
There are no guarantees that what you get makes sense, but the program makes an honest attempt.
Implies --forcealloy.

--force-alloy
Force generation of output file for an alloy compound for an electronic structure code that does
not implement any alloy theory (such as CPA).

--vca Set up an alloy using the virtual crystal approximation (VCA). Currently only supported by the
CASTEP interface.

--cartesian
Make the program generate any output in cartesian coordinates.

--coordinate-tolerance=COORDTOL
Parameter for determining when two coordinates are the same (default=0.0002).

--setup-all
Make a more complete setup, not just the geometrical part. This is currently only available for
mopac, pwscf, quantum-espresso, rspt, vasp.

--k-resolution=KRESOLUTION
The desired resolution in k-space (default=0.2). Used for generating k-space grid options if
--setup-all is specified.

--transform-cell=[[],[],[]]
Transformation matrix applied to the lattice vectors and the symmetry operations if you, for
example, want to realign the cell.

--body-centred-setting=0,1
If set to 1, use the more symmetrical set of primitive translation vectors used for the bcc
structure also for other body-centred crystals.

--cubic-diagonal-z
Set up cubic cell with [111] direction along the z-axis.

--rhombohedral-diagonal
Set up rhombohedral cell with threefold axis along pseudocubic [111] direction.

--random-displacements=displacementsize
Randomly displace all atoms. Depending on the distribution, the displacement size is either the
maximal displacement (for uniform distribution) or the standard deviation (for gaussian
distribution) in Angstrom.

--random-displacements-distribution=uniform/gaussian
The distribution used for displacing the atoms.

--export-cif-labels
Export atom labels from the CIF file (currently only supported for castep and RSPt).

Supercell generation options:

--supercell=[k,l,m]/[[],[],[]]
Three integers separated with commas and enclosed in square brackets that specify the dimensions
of a supercell OR three vectors of integers that gives the map to the supercell to be constructed
from the primitive cell. If combined with the --no-reduce option the supercell will instead be
generated based on the conventional cell.

--supercell-dimensions=[x,y,z]/[[],[],[]]
Three numbers separated with commas and enclosed in square brackets that specify the desired
ABSOLUTE dimensions of a supercell (in angstrom) OR three vectors of numbers that gives the
desired lattice vectors. The program will automatically generate a supercell, attempting to get as
close as possible to the desired dimensions.

--supercell-vacuum=[k,l,m]
Three numbers >=0 separated with commas and enclosed in square brackets that specify a number of
unit cell units of vacuum to be added along the first, second or third of the generated lattice
vectors.

--supercell-translation-vector=[k,l,m], --supercell-prevacuum-translation=[k,l,m]
Three numbers separated with commas and enclosed in square brackets that specify a shift of all
atomic positions in the cell prior to vacuum generation (in units of the lattice vectors of the
supercell).

--supercell-postvacuum-translation=[k,l,m]
Three numbers separated with commas and enclosed in square brackets that specify a final shift of
all atomic positions in the final cell (in units of the lattice vectors of the new cell).

--supercell-realign=0,1
Realign the supercell lattice vectors with respect to the cartesian reference frame. For
orthorhombic cells, it puts the first, second and third lattice vectors along x, y and z,
respectively.

--supercell-sort=SUPERCELLSORT
Sort the atom positions by some scheme. Currently available are: 1) By cartesian coordinate -
example: xzy will sort first on x then on z then on y. 2) by lattice vector - example: 132 will
sort first by lattice vector 1 then by lattice vector 3 and last by lattice vector 2.

Surface generation options:

--surface-wizard=[h,k,l]
Three integers separated with commas and enclosed in square brackets that specify a (hkl) plane.
The wizard will suggest a supercell map that gives the first two lattice vectors in the (hkl)
plane. The third lattice vector is selected as the [hkl] direction, or reasonably orthogonal to
the (hkl) plane (if the [hkl] direction is far from orthogonal to this plane).

Printing options:

--print-digits=PRINTDIGITS
Number of digits used when printing coordinates etc. to screen (default=8). Useful if you need to
tweak the screen output for cutting and pasting into some unsupported program. There is no point
in going over 16 because of the floating point accuracy.

--print-atomic-units
Output lattice parameters in bohrradii rather than angstrom.

--print-cartesian
Atomic sites printed to screen in cartesian rather than lattice coordinates.

--print-symmetry-operations
Print symmetry operations of the generated cell.

--print-seitz-matrices
Print symmetry operations of the generated cell in Seitz matrix form.

--print-charge-state, --print-oxidation-numbers
Print information about the oxidation state from the CIF file.

--print-reference-bibtex
Print citation in BibTeX format and exit.

Program specific options:

--abinit-braces
Put curly braces around input values for ABINIT.

--cellgen-map=[[k,l,m],[n,o,p],[q,r,s]]
Nine integers separated with commas and enclosed three and three in square brackets (this is a
matrix in Python) that specify the map to a supercell to be output for the RSPt supercell
generator 'cellgen'. Overrides --cellgen-supercell-dims.

--cellgen-supercell-dimensions=[k,l,m]
Three integers separated with commas and enclosed in square brackets that specify the dimensions
of a supercell to be output to the RSPt supercell generator 'cellgen' (the diagonal elements of
the 'map').

--cellgen-reference-vector=[x,y,z]
Three reals separated with commas and enclosed in square brackets that specify an optional shift
of the origin used by the RSPt supercell generator 'cellgen'.

--castep-cartesian
Output atom positions in cartesian rather than lattice coordinates.

--castep-atomic-units
Output to CASTEP in atomic units (bohr radii) rather than angstrom.

--cpmd-cutoff=CPMDCUTOFF
Set the cutoff written to the &SYSTEM block (default=100.0 Ry).

--crystal09-rhombohedral-setting
For trigonal spacegroups where this is possible, specify the rhombohedral cell in the Crystal09
input.

--emto-hard-sphere-radii=HARDSPHERERADII
Set hard spheres in KSTR to something other than the default (=0.67).

--fhi-aims-cartesian
Store the coordinates for FHI-AIMS in cartesian format.

--mopac-first-line="string"
String to be used for the first line (the run commands) of the MOPAC input.

--mopac-second-line="string"
String to be used for the second line (documentation) of the MOPAC input.

--mopac-third-line="string"
String to be used for the third line (documentation) of the MOPAC input.

--mopac-freeze-structure=T/F
If set to 'T' then add a 0 after each coordinate (freezing the structure), if set to 'F' then add
a 1 (allowing everything to relax).

--pwscf-pseudostring=_PSEUDO
String to attach to the element name to identify the pseudopotential file (e.g. something like
"_HSCV_PBE-1.0.UPF").

--pwscf-atomic-units
Write PWSCF .in file in atomic units (bohr) rather than angstrom.

--pwscf-alat-units
Use 'alat' units for the positions in the PWSCF .in file.

--pwscf-cartesian
Write lattice vectors and positions to PWSCF .in file in cartesian coordinates and set the lengths
scale to 1.

--pwscf-cartesian-latticevectors
Write lattice vectors to PWSCF .in file in cartesian coordinates and set the lengths scale to 1.

--pwscf-cartesian-positions
Write lattice positions to PWSCF .in file in cartesian coordinates.

--rspt-new
Generate a symt.inp file in the new format.

--rspt-spinpol
Generate new format symt.inp file with spin polarization.

--rspt-relativistic
Generate new format symt.inp file with relativistic effects.

--rspt-spinaxis=[x,y,z]
Spin axis for symt.inp (default is [0.0,0.0,0.0].

--rspt-no-spin
Force a nonmagnetic setup in conjunction with --setupall.

--rspt-mtradii=N
Integer that gives the method for setting muffin tin radii.

--rspt-cartesian-latticevectors
Put lattice vectors in atomic units and the lenght scale parameter to 1.

--rspt-pass-wyckoff
Pass wyckoff labels from CIF file to the symt/rspt.inp file.

--sprkkr-minangmom=SPRKKRMINANGMOM
Enforce minimum onsite angular momentum (=l+1, so that 3 will be d-states).

--spacegroup-supercell=[k,l,m]
Three integers separated with commas and enclosed in square brackets that specify the dimensions
of a supercell to be output to the elk input generator 'spacegroup'.

--vasp-format=VASPFORMAT
Format of the generated POSCAR file, either 4 or 5. Default is 4.

--vasp-print-species
Print the atomic species to screen in the order they are put in the POSCAR file (useful for
scripting).

--vasp-cartesian
Write lattice vectors and positions to POSCAR file in cartesian coordinates and set length to 1.

--vasp-cartesian-lattice-vectors
Write lattice vectors to POSCAR file in cartesian coordinates and set the length scale to 1.

--vasp-cartesian-positions
Write atomic positions to POSCAR file in Cartesian rather than Direct coordinates.

--vasp-selective-dynamics
Output POSCAR in selective dynamics format (without any constrained atoms).

--vasp-pseudo-libdr=VASPPSEUDOLIB
Path to the VASP pseudopotential library. Also settable by the VASP_PAWLIB environment variable.

--vasp-pseudo-priority="_d,_pv,_sv,_h,_s"
Set the priority of different pseudopotentials by a list of suffixes. Also available via the
VASP_PP_PRIORITY environment variable.

--vasp-encutfac=1.5
Factor that multiplies the maximal ENCUT found in the POTCAR file.

--xyz-atomic-units
Output xyz file in atomic units (bohr radii) rather than angstrom.

cif2cell 2.0.0a3+dfsg May 2021 CIF2CELL(1)