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:

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

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. ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. _______________________________________________ lammps-users mailing list`

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

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.

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

Steve Plimpton wrote:

You can have overlaps at the periodic boundaries which are

hard to detect in VMD or any visualizer. The best thing

to do is start with a small system (few unit cells) and see if

you get exactly the number of atoms you expect, in the right

locations. With a rotated lattice, you may need to adjust

the box size slightly to avoid overlaps at the boundaries.

Steve