Provided by: python3-cif2cell_2.1.0+dfsg-1_all bug

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,
              crymol,  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.