lattice_command

LAMMPS LAMMPS Mailing List Mirror
1

Dear LAMMPSER,

I am trying to make a rutile lattice by lattice command as below.
unfortunately, as you know LAMMPS does not understand symmetry groups and
So I applied 4 Wyckoff positions for O and 2 Wyckoff positions for Ti in
basises as below. I extracted the wyckoff positions from existing texts.

but actually one of these wyckoff positions,i.e. red lines, is negative
which is not acceptable with lammps for fractional coordinates and so I
face with an Error. how can I substitute this basis (wyckoff position) with
a positive basis to pass this error?!

So, any constructive comments is highly appreciated.

*dimension 3*
*units metal*
*boundary s s s*
*atom_style atomic*

*region box block 0 4.59373 0 4.59373 0 2.95812 units box*
*create_box 2 box #2 is number of atoms*

*lattice custom 1 a1 4.59373 0.00000 0.00000 a2 0.0000 4.59373
0.00000 a3 0.00000 0.00000 2.95812 &*
*basis 0 0 0 &*
*basis 0.5 0.5 0.5 &*
*basis 0.3053 0.3053 0 &*
*basis -0.3053 -0.3053 0 &*
*basis 0.8053 0.1947 0.5 &*
*basis 0.1947 0.8053 0.5 &*
*mass 1 47.86*
*mass 2 16.00*

*create_atoms 2 region box &*
*basis 1 1 &*
*basis 2 1 &*
*basis 3 2 &*
*basis 4 2 &*
*basis 5 2 &*
*basis 6 2 &*

*write_dump all image snap*.png type type adiam 0.5 shiny 0.5 zoom 1.0
view 80 -30 axes yes 0.1 0.01 modify backcolor white*

With the best regards,
Bahman Daneshian

2

Dear LAMMPSER,

I am trying to make a rutile lattice by lattice command as below.
unfortunately, as you know LAMMPS does not understand symmetry groups and So
I applied 4 Wyckoff positions for O and 2 Wyckoff positions for Ti in
basises as below. I extracted the wyckoff positions from existing texts.

but actually one of these wyckoff positions,i.e. red lines, is negative
which is not acceptable with lammps for fractional coordinates and so I face
with an Error. how can I substitute this basis (wyckoff position) with a
positive basis to pass this error?!

you get an error, because the atom is outside the principal cell,
which is required. thus you can simply use the position of the same
atom wrapped back into the principal cell, i.e. with one lattice unit
added in x and y.

So, any constructive comments is highly appreciated.

if you'd read up a little bit on crystallography, you wouldn't need to
ask such (essentially trivial) questions.

axel.

3

Create the atoms on positive basis and displace it to negative side.

4

Create the atoms on positive basis and displace it to negative side.

that is bad advice; complicated, unneeded, and error prone.

it also neglects the basic property of lattice positions, that
locations differing by one lattice unit in any direction refer to the
same position.
specifying space group positions outside the principal unit cell can
be convenient to expose symmetries, but since LAMMPS doesn't make any
use of them, there is no benefit, and using the equivalent in-cell
position(s) the best and safest way to move forward.

axel.