# [lammps-users] Lammps input for a skewed cell

Hello,

I am a new lammps user having trouble lammps read my unit-cell! This is what it looks like :

a = {a, 0, 0}, b={a/2,a*sqrt(3)/2,0}, c={0,0,c}

I am not clear about the (xy,xz,yz) as defined in the manual i.e. is xy == yx? Given their definitions in terms of a,b,c and alpha,beta,gamma I entered this:

0 a xlo xhi
0 a*sqrt(3)/2 ylo yhi
0 c zlo zhi

a/2 0.0 0.0 xy xz yz

with the atom positions entered in cartesian coordinates. The resulting structure doesn't seem right (what is the best viewer? vmd crashes or shows a blank screen. ). I suspect lammps is looking for 'xy' while I want to enter my 'yx', but not sure. I am using the OCT-31/2010 release.

Is there a way to just enter {a,b,c,alpha,beta,gamma} directly or the full 3x3 rotation-matrix or read/convert from a .pdb or VASP-poscar file?

Thank you for any helpful response.

Sincerely,
Ganesh

ganesh,

Hello,

I am a new lammps user having trouble lammps read my unit-cell! This is what it looks like :

a = {a, 0, 0}, b={a/2,a*sqrt(3)/2,0}, c={0,0,c}

I am not clear about the (xy,xz,yz) as defined in the manual i.e. is xy == yx? Given their definitions in terms of a,b,c and alpha,beta,gamma I entered this:

0 a xlo xhi
0 a*sqrt(3)/2 ylo yhi
0 c zlo zhi

a/2 0.0 0.0 xy xz yz

with the atom positions entered in cartesian coordinates. The resulting structure doesn't seem right (what is the best viewer? vmd crashes or shows a blank screen. ). I suspect lammps is looking for 'xy' while I want to enter my 'yx', but not sure. I am using the OCT-31/2010 release.

what version of VMD are you using?
if there is a lammps data or trajectory file
that makes VMD crash, i'd like to have a
sample and sort it out.

Is there a way to just enter {a,b,c,alpha,beta,gamma} directly or the full 3x3 rotation-matrix or read/convert from a .pdb or VASP-poscar file?

the VMD poscar reader should be able to read coordinates as needed
and actually rotate them automatically as lammps needs it and then you
can use the writelammpsdata function of the topotools plugin to write out
a lammps compatible data file. you need the latest update for it from:

or use a recent VMD alpha or beta release:

http://www.ks.uiuc.edu/Research/vmd/alpha/

for that. the latter might also help with potential crashes.

cheers,
axel.

Section 4-12 of the manual explains how LAMMPS treats
triclinic boxes and a comparison to other conventions.

There is no yx in LAMMPS, just xy.

Steve