Command line utilities

The available commands for sisl 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.

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

See external accepted file formats for a list of recognised file formats.