Ubuntu Manpage: c2x - converts various crystal formats including density grid data

NAME

       c2x - converts various crystal formats including density grid data

SYNOPSIS

       c2x [-OPTIONS] [--FORMAT] [--OPERATION] infile [outfile]

DESCRIPTION

       c2x  converts  primarily  a  CASTEP  .check  file  to various output formats, additionally
       extracting densities (charge, spin, band or psi) and forces. It can also read CASTEP .cell
       files  and  PDB  files, Onetep .dat files, and several input and output files from Abinit,
       Quantum Espresso and VASP, with some support for Siesta too. It is a sort  of  Babel  with
       support  for gridded data and .check files, and the ability to transform cells and perform
       simple analysis  (integration,  interpolation,  dipole  moment  calculation,  band  parity
       identification).

       It may have been compiled to give access to symmetry functions from spglib too.

       An  input  file whose name ends '.pdb' is assumed to be in pdb format, ending in '.cif' is
       assumed to be in cif format, ending in '.res' is assumed to be in shelx97,  ending  '.cub'
       or  '.cube'  is  assumed  to be in cube format, ending '.in' is assumed to be an Abinit or
       Quantum Espresso input file, ending '.xml' is assumed to  be  a  Quantum  Espresso  output
       file,  ending  in  '.xsf'  is  assumed to be in xsf format, and ending in '.xv' or 'XV' is
       assumed to be in Siesta's XV format.  Input files ending  CHG,  CHGCAR,  POSCAR,  CONTCAR,
       LOCPOT  or WAVECAR are assumed to be in VASP 5.x format. Input files ending in DEN, POT or
       WFK are assumed to be in Abinit format. Otherwise, if the first byte is either zero, 10 or
       30  it  is assumed to be a .check file, else it is assumed to be a .cell file. It can also
       read .orbitals files (which are identical to .check  files  in  format),  and  .castep_bin
       files  (which  lack  wavefunctions).  Furthermore,  it can read .chdiff files and .cst_esp
       files. In these cases it needs a .cell or a .check file as well in order  to  obtain  unit
       cell information.

OPTIONS

-a rotate as though outputing in abc format, i.e. place a along x axis, b in xy plane,
and abc form a right hand set. Useful if one wants a dx file consistent with a pdb
file. See also -3.

-A accumulate (sum) bands requested by -b= or -B=.

-b[=range]
include specified bands as psi (real).

-B[=range]
include specified bands as densities (psi*conjg(psi)).

-c include charge density (units electrons per cubic Angstrom).

--calc evaluate next arg with arithmetic parser and exit.

--constants
report internal conversion constants and exit.

-C find "compact" (near-cubic) set of cell vectors.

-d read also a corresponding .chdiff file, and output its contents. The filename given
must still be that of a .cell or .check file, as a .chdiff file contains no axes.

-D=[x,y,z]
if charge density read (-c), calculate dipole moment about fractional co-ordinates
x,y,z, or 0.5,0.5,0.5 if co-ordinates not given. Assumes density has been read as
eA^-3.

-Da=[x,y,z]
as above, but also report post-hoc energy correction for slab geometry for the a
axis being the non-periodic axis. Valid values of a: a, b and c.

-Dm=[x,y,z]
as above, but also report post-hoc energy correction for a molecule in a cubic box,
or for a molecule in a tetragonal box if dipole moment is parallel to c.

-e read also a corresponding .cst_esp file, and output its contents. The filename
given must still be that of a .cell or .check file, as a .cst_esp file contains no
axes.

-e=tol set symmetry tolerance to given number of Angstroms.

-E[=[-][mu]]
calculate electrostatic potential, assuming that an electron density has been read
(implies -c). Ions are treated as Gaussian blobs of charge of extent exp(-mu^2r^2).
If the ionic charge differs from the atomic number, a further localised smoothing
of the atomic potential occurs, unless the first character after the = is -. With
-E=0, a bare Coulomb potential is used.

-f calculate first failure start of k-point set.

--formats
list supported formats.

--frame=N
extract single frame from series of time steps. Frames are numbered from zero, and
negative numbers represent offsets from the end of the sequence, so --frame=-1 will
extract the final frame. --gap print band gap in eV. -H shift atoms by half a
grid cell. For use with xplor data format, see below.

-i=nx,ny,nz
Fourier interpolate onto specified grid size. New grid may be coarser or finer than
original. Any dimension given as zero is replaced by old grid size. If reading
wavefunction, any grid truncation is done after transforming back to real space and
converting to density etc.

-I[=range]
report whether bands have inversion, and parity under inversion. If combined with
-b or -B, the last range given is used.

-k[=range]
include given kpoints for bands (default range is 1).

-l if k-points are to be included in a .cell file, explicitly list them rather than
using the MP generation parameters.

-L output in abc format assuming that abc describes a left-handed set of axes. Do not
use this unless you understand why you should not!

-m[=a,b,c]
assume input is molecule, not crystal. Try to avoid outputing a cell, shift if some
co-ordinates are negative, or if a,b,c given shift by those numbers of FFT grid
cells.

-m=(a,b,c)
assume input is molecule, not crystal. Try to avoid outputing a cell, shift atoms
by fractional co-ordinates given.

-n discard symmetry information, and, if output is XSF, discard forces. Give twice to
discard k-points too.

-N normalise by reducing fractional coords to 0<=x<1. In conjunction with -m, do
output a cell.

-O print band occupancies and evalues to stderr.

-P find primitive cell with own internal algorithm, not spglib.

-P=p1:p2:nn
output data as line of nn points from p1 to p2. Express p's as either fractional
co-ordinates in the form (x,y,z), or an atom position as, e.g., Si3 for silicon
atom number 3, or simply Si for the first Si atom. Using a 0 (zero) for a p is
equivalent to (0,0,0), and the three cell axes "(0,0,0):(1,0,0):ngx+1" (etc.) can
be specified as a, b and c. Each co-ordinate is passed to the arithmetic parser, so
1/3 is acceptable for a third, etc.

-P=p1:rl:nn
output data with cylindrical averaging. p1 is the centre of the cylinder, rl
(literal "r", followed by a length, suffixed by "B" if Bohr) is the radius, and nn
the number of points. The axis of the cylinder must be the c axis, and alpha and
beta must be 90 degrees. Data are averaged over c and theta. Append "w" to number
of points to weight samples by two pi times radius, or "a" to weight and
accumulate.

-P=p1:Rl:nn
output data with spherical averaging. p1 is the centre of the sphere, Rl (literal
"R", followed by a length, suffixed by "B" if Bohr) is the radius, and nn the
number of points output. The number of points for sampling around the spherical
surface is chosen to give a similar point separation to that along the line. A
length of zero will set the length to the maximum possible given the periodicity.
Data are averaged over theta and phi. Append "w" to number of points to weight
samples by four pi times radius squared, or "a" to weight and accumulate.

-q calculate post hoc energy correction for charged isolated system. Implies -c.

-q[abc]
calculate post hoc energy correction for charged 2D system. The axis given (a, b or
c) is the aperiodic one. Implies -c.

-Q sort the atoms on output in descending atomic order

-Q2 sort the atoms on output in ascending atomic order

-R don't attempt to rescale densities, but output them raw. Charge density becomes
electrons per unit cell if reading from Castep, for instance. Also do not attempt
to adjust radius to maintain bond length on nanotube creation.

-R=x rescale grid data by factor x, not whatever factor (if any) would normally be used.
If the factor is suffixed by an "x", do include c2x's usual conversion factor too.

-s include spin density.

--sym_list
list symmetry elements found in input, without calling SPGlib.

-S[=range]
include specified spins or spinors for bands (default range is -, and the spins are
numbered 0 and 1).

-t=(x1,y1,z1)(x2,y2,z2)[(x3,y3,z3)]
rotate co-ordinate system so that the first vector becomes the second. First vector
given in relative co-ordinates. If third axis given, it is used as the rotation
axis. Else the rotation axis will be perpendicular to the two axes given.

--tricubic
when interpolating, using tricubic (spline) interpolation in place of trilinear
interpolation. Slower, might not preserve monotonicity, but does keep first
derivative continuous.

-T=(x1,y1,z1)(x2,y2,z2)[(x3,y3,z3)]
rotate co-ordinate system so that the first vector becomes the second. All vectors
given in absolute co-ordinates. If third axis given, it is used as the rotation
axis. Else the rotation axis will be perpendicular to the two axes given.

-u use atomic units (Bohrs) when writing .cell files and 1D data. Scale densities from
A^-3 to Bohr^-3 when writing .cube files.

-U scale densities from Bohr^-3 to A^-3 when reading .cube files.

-v be verbose. Far too much output can be generated if specified more than twice.

--version
print version information. If preceeded by -v, also print internal conversion
factors.

-w weight bands by occupancies, or sqrt(occ) if not calculating density.

-w=k weight bands by k-point weight, but not occupancy.

-W weight bands by occupancies and k-point weight, or sqrt thereof if not calculating
density.

-x=(x1,x2,x3)(y1,y2,y3)(z1,z2,z3)
expand unit cell to new cell specified in terms of the old cell axes. Each co-
ordinate is passed to the arithmetic parser, so 'sqrt(3)/2' etc is acceptable.

-x=ixjxk
expand cell with a trivial tiling.

-X=(x1,x2,x3)(y1,y2,y3)(z1,z2,z3)
expand unit cell to new cell specified in absolute co-ordinates.

-X[abc]=x
change given axis/axes to new length by inserting / removing vacuum around the
origin. Removing non-existent vacuum will produce nonsense. Length may be suffixed
with B (for Bohr) or nm.

-y=i,j[:x]
make nanotube. The input cell must have c perpendicular to the ab plane, and c as
the nonperiodic direction of the sheet to be rolled. The circumference is then
defined by the vector i*a+j*b. The vector along the tube's length found
automatically, and the size of the cell perpendicular to the tube's length is given
by the optional parameter x, which may be suffixed with B (for Bohr) or nm.

-z=p1 print to stdout data at given point, and set output type to null. For specification
of p1, see -P= option.

-Z=p1 ditto, but assume that data represents an electron density in A^-3, and also output
Perdew Zunger 81 XC energy.

-3 when moving from a left hand set of axes to a right hand set, rather than
exchanging the 2nd and 3rd axes, preserve the 3rd and exchange the 1st and 2nd.
This transformation is required if the input is cartesian and left handed, and an
abc output is requested. Specifying this flag twice will cause the 1st and 3rd axes
to be exchanged.

COMBINING OPERATIONS

       The  following  options expect multiple input files to be given, and perform the specified
       operation.

       --add  Add datasets element-wise.

       --diff Subtract datasets element-wise.

       --mask Multiply datasets element-wise. Although it is assumed that one dataset will  be  a
              mask of ones and zeros, it need not be so.

       --merge
              Merge  datasets.  The  expected use is merging an atoms-only format with a density-
              only format to create an output containing both atoms and density.

       --mult Alternative for --mask.

       --sub  Alternative for --diff.

       --sum  Alternative for --add.

       When merging, if files contain  conflicting  data,  the  one  on  the  right  usually  has
       precidence.

       When  performing  operations on grids, the grids must be the same size.  The use of -i may
       assist. In all cases, the cells must be the same.

FORMATS

The following output formats are recognised. (See the output of the --formats option for
the complete list. Most are also recognised for input provided that their filenames have
the expected suffix.)

--abinit
Abinit .abi file (for Abinit version 9 and beyond).

--abinit8
Abinit .in file. The output is insufficient to be a valid input file to Abinit, but
can easily be made so.

--bands
CASTEP .bands file, no sorting of bands.

--bxsf XCrysDen / FermiSurfer file for plotting Fermi surfaces. A symmetry-reduced kpoint
set will be expanded. (Not accepted as input.)

--ccp4 CCP4 density map format. Note no atomic positions can be recorded in this format,
and c2x will always produce a right-hand set of axes unless the input is a lhs and
the option -L is given.

--cell CASTEP .cell, cartesian cell, fractional co-ordinates.

--cell_abc
CASTEP .cell, abc cell, fractional co-ordinates.

--cell_abs
CASTEP .cell, cartesian cell, absolute co-ordinates.

--cell_abc_abs
CASTEP .cell, abc cell, absolute co-ordinates.

--chgcar
VASP 5.x chgcar output.

--cif a very basic and rigid format which may be compatible with some CIF-reading
software.

--cml Chemical Markup Language.

--cube Gaussian cube. Atoms and at most one data set.

--dx Data Explorer. Data set only.

--denfmt
CASTEP formatted density

--elk Elk elk.in format.

--fdf Siesta. If a density has been read, a corresponding .RHO file will be written.

--gcoeff
An ASCII wavefunction coefficient representation

--gcoeff_sorted
The same, sorted by |g|

--gnu Gnuplot command file for 1D data.

--npy Numpy array, single dataset, as doubles with -15, else single precision.

--null Null output. Throw away all output, but still write some useful information the
input to stderr.

--one Onetep .dat, very similar to .cell. Also one_abc, one_abs, and one_abc_abs.

--pdb PDB

--pdbn PDB, but label the atoms with element symbol and number within that species, e.g.
C8, H24, Ca2, rather than just with element symbol. The whole string can contain no
more than four characters, so * is used for the numeric part if it would not
otherwise fit.

--py a python dictionary, compatible with the Atoms data structure from ASE.

--pya a python ASE Atoms data structure.

--qe Quantum Espresso. Non colinear spins not supported.

--qef Ditto, atoms in fractional co-ordinates.

--shelx
a subset of the SHELX97 format.

--vasp VASP 5.x output (poscar or chg).

--xplor
Xplor format. Data set only. The grid used in this format is offset by half a grid
cell compared to Castep, and as interpolating is inexact, this program does not in
this case. Also the grid axes are described in terms of a, b, c, alpha, beta,
gamma, so information about orientation in space is lost. To produce a compatible
pdb file of atomic co-ordinates, specify -Hc when creating the pdb file.

--xsf XCrysDen format. Default. The only format in which multiple data sets are
supported.

--xv Siesta's .XV format (positions only, velocities written as zero). Will also write a
.RHO file if grid data have been read.

--xyz XYZ format. Atoms only, no unit cell.

Where a range is required, it can be specified as a single integer, two integers separated
by a hyphen (all integers in the given range), or a comma-separated list of any of these
elements. Only for the xsf output format is a range including more than a single integer
meaningful.

OPERATION

       If c2x has been compiled with spglib, the following spglib operations are available.

       --int  call spg_get_dataset() and report international symbol

       --list call spg_get_dataset() and list symmetry ops

       --point
              call spg_get_dataset() followed by spg_get_pointgroup()

       --primitive
              call  spg_find_primitive(),  equivalent   to   spg_standardize_cell(to_primitive=1,
              no_idealize=0). This may rotate the cell to a standardised orientation.

       --primitive_nr
              call spg_standardize_cell(to_primitive=1, no_idealize=1), so primitive no rotation

       --refine
              call spg_refine_cell()

       --schoen
              call spg_get_schoenflies()

       --snap call  spg_standardize_cell()  then expand back to a snapped version of the original
              cell

       --snap_tr
              ditto, but include any translation introduced by spglib

       --standardise
              call spg_standardize_cell(no_idealize=1)

       --std_ideal
              call spg_standardize_cell(no_idealize=0)

       --symmetry or --symm
              call spg_get_dataset() and keep symmetry ops

NOTES

For the pdb formats, just the unit cell and atomic positions are read or written. For the
dx and xplor formats, just a single data set is written. For the Gaussian cube format
atomic positions and at most one data set are recorded, and for the XCrysDen format the
unit cell, atomic positions, forces, and any number of data sets are recorded.

When reading a .geom file and writing a format containing a single frame, the last frame
is written, unless the --frame option is given.

When reporting symmetry operations, all co-ordinates are fractional.

Note that the pdb format offers a very low precision for storing co-ordinates, and,
because it stores the unit cell in abc format, and the atoms in absolute coordinates, a
rotation is likely to be required to place a on the cartesian x axis, etc. If so, it will
be done automatically. The same is true for the abc varients of the cell format and for
the Xplor and cif file formats. This rotation can be specified explicitly for other
formats. Additionally the axes must form a right-handed set. If this is not the case, two
axes will be interchanged. By default, b and c are exchanged, but the flag -3 will cause
a and b to be exchanged instead.

The cif reader reads little more than c2x's cif output. It is very basic, and will fail to
read correctly a large number of valid cif files. There is currently no intention to
produce a proper cif reader.

When outputting psi it is assumed that it is possible to make psi real by unwinding any
phase produced by the k-point, and then multiplying all points by the same arbitrary
complex constant. If this is not so, the band was probably nonsense anyway. The final
choice of a factor of -1 is arbitrary. This scheme produces nonsense if one attempts to
plot a degenerate band.

When doing the conversions resulting from -x, a new grid will be chosen of similar density
to the old, and the data interpolated onto the new using trilinear interpolation.
Extrapolating psis (rather than densities) is meaningless except at gamma, for the phase
due to the k point is not considered.

Densities by default are in Angstroms**-3, and psis in Angstroms**-1.5, save that .RHO
files are written in Bohr**-3 as expected.

EXAMPLES

       To extract the charge density in xsf format

              c2x -c input.check output.xsf

       To extract the first four bands as psi at the second k-point in xsf format

              c2x -b=1-4 -k=2 input.check output.xsf

       To convert a check file to a pdb file

              c2x --pdb input.check output.pdb

       To  convert a cell to something containing two repeat units in the a and b directions, and
       one in the c direction

              c2x --cell -x='(2,0,0)(0,2,0)(0,0,1)' in.cell out.cell

              or, from c2x version 2.30,

              c2x --cell -x=2x2x1 in.cell out.cell

       Assuming the above cell was a 3.5A cube, the same in absolute co-ordinates

              c2x --cell -X='(7,0,0)(0,7,0)(0,0,3.5)' in.cell out.cell

       To change a cell containing one layer of bulk in the c direction to  one  containing  four
       layers, and sufficient vacuum to make a total length of 30A

              c2x --cell -x=1x1x4 -Xc=30 in.cell out.cell

VIEWERS

       The following viewers have been used during the development of c2x: Avogadro, FermiSurfer,
       gabedit, Jmol, pymol, VESTA, VMD and XCrysDen.

BUGS

       None known.

       Please report others to MJR.

ACKNOWLEGEMENTS

       If you wish to cite, please do so as "C2x: a tool for visualisation and input  preparation
       for   Castep   and   other  electronic  structure  codes",  MJ  Rutter,  Computer  Physics
       Communications, vol 225 pages 174-179 (2018). http://dx.doi.org/10.1016/j.cpc.2017.12.008

       Details of spglib can be found at https://atztogo.github.io/spglib/