[lammps-users] simulation error for triclinic box

Dear all,

I am trying to simulate screw dislocation in BCC metals using a triclinic box. The system has 288,000 atoms and the boundary of the box is :

-99.298468 99.298468 xlo xhi
-59.456364 62.158925 ylo yhi
-70.214624 70.214624 zlo zhi
0.000 1.241231 0.000 xy xz yz

Units of all are in Angstrom.

According to the documents of LAMMPS, I set periodic boundary conditions along both X and Z directions, and fix outermost Y layers immobile. But after several simulating steps, there are only those immobile atoms staying in the box, all the others are lost.

The output file shows a very strange box shape, length along Y direction is so small:

-99.2985 100.54
-9.91777e-05 0.983433
-70.2146 70.2146

I cannot figure out what is wrong in my input script file. Would you please help me to solve this problem? Thank you very much.

Best Regards

Zhengzheng Chen
Department of Physics and Astronomy
California State University Northridge,
18111 Nordhoff St, Northridge, CA, 91330

PS: My input file

Molecular Dynamics with thermal equilibrium

units metal
boundary p s p

atom_style atomic
read_data Fe_work.atoms
lattice sc 1.0
pair_style eam/alloy
pair_coeff * * fe04_cu97_setfl Fe Cu

neighbor 0.2 bin
neigh_modify delay 10
region inner block INF INF -41.0 42.0 INF INF
region DisCore block INF INF -30.0 30.0 -40.0 30.0

group output region DisCore
group mobile region inner
group constrain subtract all mobile


velocity all create 5.0 74329830
velocity constrain set 0.0 0.0 0.0
compute OnlyMV mobile temp
fix 1 mobile nvt 5.0 5.0 0.45 drag 0.8
fix 2 constrain setforce 0.0 0.0 0.0
fix_modify 1 temp OnlyMV

thermo 500
thermo_style custom step temp c_OnlyMV pe ke etotal

log log.Fe_Cu10
dump backup all atom 15000 Fe_Cu10_result.*
dump_modify backup format ā€œ%10d %3d %12.6g %12.6g %12.6gā€ scale no
run 45000

Why don't you see if you can get one of the examples, like
examples/nemd/in.nemd to work with periodic xz and non-periodic y
with fixed walls and a deforming box (if that's what you want).

Once that works, you could then plug in your potential and atom lattice.