wojdyr / gosam

generator of simple atomistic models

gosam is a bunch of Python scripts:

• bicryst.py -- to generate atomistic model of grain boundary (bicrystal) with a coincidence site lattice (CSL) boundary in the PBC box,
• monocryst.py -- to generate monocrystal in PBC box (atomistic model),
• graingen.py -- create crystalline grains of given shape, with vacancies, thermal vibrations, etc.
• mdfile.py -- convert between several file formats (AtomEye cfg, VASP POSCAR, LAMMPS, DL_POLY, XMOL XYZ).
• csl.py -- to list coincident site lattice (CSL) grain boundaries in cubic crystals

Prerequisites: Python 2 and numpy. graingen.py additionally requires the qhull program.

Installation: download, unpack if you've downloaded zip file, and use from command line.

Usage: See documentation in the wiki and feel free to e-mail me with questions. Or open Github issue. Also, most of the programs print basic usage instructions when invoked without parameters.

License: GPLv2+ (I'll consider changing it to a more liberal license if there is a good reason)

Citing: you may cite Marcin Wojdyr et al 2010 Modelling Simul. Mater. Sci. Eng. 18 075009 (preprint), especially if you use bicryst.py.

See also: debyer - a bunch of tools coded in C and C++

contact: [email protected]

gosam's Issues

Grain boundary of Graphene

Dear gosam developer,

I would like to generate grain boundary of graphene? Would you please guide me 
how to make from a xyz file containing coordinates of graphene.

Many thanks and looking forward to your attention.

Regards,

Rajib 

Original issue reported on code.google.com by [email protected] on 7 Jun 2012 at 7:52

A bug in "find_orthorhombic_pbc(M)"

Problems happened when I tried this command:

./bicrystal.py 100 m001 3,8 3 12 24 remove:2.3 lattice:cu a.cfg

The following code needs to be modified a little bit (line 6):

1 # optionally swap x2 with y2
2    id = identity(3)
3    if (pbc[1] == id[0]).all() or (pbc[0] == -id[1]).all():
4        pbc[0], pbc[1] = pbc[1], -pbc[0]
5    elif (pbc[1] == -id[0]).all() or (pbc[0] == id[1]).all():
6        pbc[0], pbc[1] = -pbc[1], pbc[0]
7    return pbc

Correct way:

1 # optionally swap x2 with y2
2    id = identity(3)
3    if (pbc[1] == id[0]).all() or (pbc[0] == -id[1]).all():
4        pbc[0], pbc[1] = pbc[1], -pbc[0]
5    elif (pbc[1] == -id[0]).all() or (pbc[0] == id[1]).all():
6        pbc[1], pbc[0] = pbc[0], -pbc[1]
7    return pbc

Original issue reported on code.google.com by [email protected] on 5 Jun 2012 at 6:01