[lammps-users] setting input commands for grain boundary simulation

Prithwish · July 29, 2009, 11:38am

Hi,
I was trying to make a configuration file using lattice command with different orientation, as suggested in LAMMPS users' forum. My input file is as follows:

sjplimp · July 29, 2009, 2:39pm

The hi initial energy means there are overlaps, probably at the
boundaries. Have you visualized your system to make sure
you are getting no extra atoms? Are you sure the box size is
periodic for the orientation you've chosen?

Steve

Prithwish · July 30, 2009, 6:17am

Steve Plimpton wrote:

The hi initial energy means there are overlaps, probably at the
boundaries.  Have you visualized your system to make sure
you are getting no extra atoms?  Are you sure the box size is
periodic for the orientation you've chosen?

Steve

Hi,
I was trying to make a configuration file using lattice command with
different orientation, as suggested in LAMMPS users' forum. My input
file is as follows:

****************************************************
units           metal
dimension       3
atom_style      atomic

lattice         bcc 2.86
region          box block 0 10 0 10 0 10
create_box      1 box
region          rGB block INF INF INF INF INF INF
region          rGB1 block 0 4.999 0 INF 0 INF
region          rGB2 block 0 4.999 0 INF 0 INF side out
create_atoms    1 region rGB1 basis 1 1 basis 2 1
lattice         bcc 2.86 origin 0.0 0.0 0.0 orient x  1  1  0  orient y
-1  1  0
create_atoms    1 region rGB2 basis 1 1 basis 2 1
mass            1 55.845

pair_style      eam/fs
pair_coeff      * * Fe_mm.eam.fs  Fe

neighbor        0.5 bin
neigh_modify    delay 0 every 1 check yes

dump    startdump all atom 2 start.dump
run 5
undump startdump
****************************************************************
Screen Output is as follows :
*****************************************************************
LAMMPS (22 Jun 2007)
Lattice spacing in x,y,z = 2.86 2.86 2.86
Created orthogonal box = (0 0 0) to (28.6 28.6 28.6)
 1 by 1 by 1 processor grid
Created 1000 atoms
Lattice spacing in x,y,z = 4.04465 4.04465 2.86
Created 1050 atoms
WARNING: No fixes defined, atoms won't move
Setting up run ...
Memory usage per processor = 2.12106 Mbytes
Step Temp E_pair E_mol TotEng Press
      0            0 3.3131975e+14            0 3.3131975e+14 7.5637702e+15
      5            0 3.3131975e+14            0 3.3131975e+14 7.5637702e+15
Loop time of 0.154984 on 1 procs for 5 steps with 2050 atoms

Pair  time (%) = 0.113832 (73.4476)
Neigh time (%) = 0 (0)
Comm  time (%) = 0.00133258 (0.85982)
Outpt time (%) = 0.0385349 (24.8638)
Other time (%) = 0.00128453 (0.828814)

Nlocal:    2050 ave 2050 max 2050 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:    4170 ave 4170 max 4170 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    70600 ave 70600 max 70600 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 70600
Ave neighs/atom = 34.439
Neighbor list builds = 0
Dangerous builds = 0
************************************************************************

First, for bcc Fe, we must expect 2000 atoms for a 10*10*10 supercell.
We are getting (1000 + 1050) = 2050 atoms.
Secondly, in region rGB1, lattice spacings are 2.86 2.86 2.86 (which is
cubic), but in region rGB2, lattice spacings are
4.04465 4.04465 2.86, i.e. in region rGB2, its no longer a bcc lattice,
rather we are getting a tetragonal network.
Can anybody please tell where am I making the mistake ?

Best regards.
Prithwish.

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Hi Steve,
As I mentioned in my previous mail, I am getting 50 extra atoms. Apparently this means that overlaps are there. But, I have visualized the dump file with VMD. It seems that there is no overlap at the boundary of two grains, rather the space between two boundaries are somewhat large. You also suggested to check whether the box size is periodic for the orientation I have chosen. I have redone the calculation by setting “boundary p p p”; anyway its giving the same result. But the above command will make the boundary periodic along x, y and z directions; but for the second grain obtained by rotating the lattice around z direction, I am not sure how to make the box size periodic along this particular orientation. Again, in this run also for the second grain I am getting a tetragonal lattice though I have asked to create a bcc lattice. I am little bit confused.

Again, as suggested by Dr. Evans, I have run the calculation by seeting a fix nve, it results in an error. Anyway, I am again giving the fresh input as well as the output attached with this mail.
Any suggestion is highly welcome.
Regards.
Prithwish

My INPUT:

units metal
dimension 3
atom_style atomic
boundary p p p

lattice bcc 2.86
region box block 0 10 0 10 0 10
create_box 1 box
region rGB block INF INF INF INF INF INF
region rGB1 block 0 4.999 0 INF 0 INF
region rGB2 block 0 4.999 0 INF 0 INF side out
create_atoms 1 region rGB1 basis 1 1 basis 2 1
lattice bcc 2.86 origin 0.0 0.0 0.0 orient x 1 1 0 orient y -1 1 0
create_atoms 1 region rGB2 basis 1 1 basis 2 1
mass 1 55.845
fix 1 all nve

pair_style eam/fs
pair_coeff * * Fe_mm.eam.fs Fe

neighbor 0.5 bin
neigh_modify delay 0 every 1 check yes

dump startdump all atom 2 start.dump
run 5
undump startdump

OUTPUT :
LAMMPS (22 Jun 2007)
Lattice spacing in x,y,z = 2.86 2.86 2.86
Created orthogonal box = (0 0 0) to (28.6 28.6 28.6)
1 by 1 by 1 processor grid
Created 1000 atoms
Lattice spacing in x,y,z = 4.04465 4.04465 2.86
Created 1050 atoms
Setting up run …
Memory usage per processor = 2.12106 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 3.3131975e+14 0 3.3131975e+14 7.5637702e+15
ERROR: Lost atoms: original 2050 current 1880

Prithwish · July 30, 2009, 6:20am

Hi ,
As I mentioned in my previous mail, I am getting 50 extra atoms. Apparently this means that overlaps are there. But, I have visualized the dump file with VMD. It seems that there is no overlap at the boundary of two grains, rather the space between two boundaries are somewhat large. You also suggested to check whether the box size is periodic for the orientation I have chosen. I have redone the calculation by setting “boundary p p p”; anyway its giving the same result. But the above command will make the boundary periodic along x, y and z directions; but for the second grain obtained by rotating the lattice around z direction, I am not sure how to make the box size periodic along this particular orientation. Again, in this run also for the second grain I am getting a tetragonal lattice though I have asked to create a bcc lattice. I am little bit confused.