Command line utilities

The available commands for sids are:

sgeom

Easy conversion tool for manipulation of geometries.

It reads various file formats which can be read and, some written again.

By default sgeom takes two arguments, the first is the geometry to be processed, the second is the output geometry.

sgeom can also be used via Unix pipes in which case the output has to be directly specified on the command-line. Hence

sgeom in.fdf out.fdf
sgeom in.fdf | sgeom -o out.fdf

are equivalent commands.

There are many possible ways to alter the geometries read by sgeom. To see all available modes, use this command

sgeom --help

Several common functionalities are existing in sgeom

1. Translate atoms to the origin (sgeom -O|--origin)

2. Translate to specific center (sgeom -co|--center-of opt)

   1. Unit cell center (opt=cell)
   2. Atomic mass center (opt=mass)
   3. Coordinate center (opt=position|xyz)

3. Translate coordinates into the unit cell (sgeom -uc|--unit-cell opt)

   1. Retain relative coordinates (opt=translate|tr|t)
   2. Only shift those coordinates outside the unit cell (opt=mod)

4. Rotate geometry (-R|--rotate angle dir)

   Where angle is an angle in degrees, suffixing with r for radians. dir is the direction of x, y or z direction.

5. Repeating the geometry in blocks (-t|--tile tile dir)

   Where tile is an integer larger than 0 and dir is either of the x, y or z direction.

6. Repeating the geometry in sequence, (-r|--repeat repeat dir) which roughly is the same as --tile, however, the sequence is first repeating the first atom, then the second, etc.

Accepted file formats

The currently accepted file formats are files with these endings:

1. xyz, standard coordinate format

   NOTE that sids uses the comment field in the xyz file to store the unit-cell. Hence, unit-cell sizes are preserved in *xyz files read/generated by sids.

2. gout, reads geometries from GULP output

   NOTE that sids currently does not implement writing GULP input files.

3. *nc, reads/writes NetCDF4 files created by SIESTA.

4. TBT.nc/PHT.nc, reads NetCDF4 files created by TBtrans/PHtrans.

5. tb, intrinsic file format for geometry/tight-binding models in pure ASCII format.

6. fdf, SIESTA native input file format.

7. XV, SIESTA native coordinate format for MD re-runs.

8. POSCAR/CONTCAR, VASP coordinate format.

   NOTE the current implementation does not contain atomic species, i.e. the returned geometry is made of Hydrogen atoms.