Dear Lammps users/developers,
I am trying to run a simulation having a layer of uranium metal and a layer of supercritical co2 (sco2). To do so I have used the pair_style hybrid. I have used lj/cut/coul/cut for co2 and COMB potential for U-metal. Here is my input file and I have attached my data file as well.
units metal
atom_style full
dimension 3
boundary p p p
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
kspace_style ewald 0.000001
read_data u-pure-co2.data
pair_style hybrid lj/cut/coul/cut 10.0 comb
pair_coeff * * comb ffield.comb U NULL NULL
pair_coeff 2 2 lj/cut/coul/long 0.056 2.757
pair_coef 2 3 lj/cut/coul/long 0.066 2.895
pair_coeff 3 3 lj/cut/coul/long 0.16 3.033
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
timestep 0.00020
min_style cg
minimize 1.0e-4 1.0e-4 100 1000
fix 3 all nve
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly
lz xz
thermo_modify norm yes
thermo 1
dump coords1 all custom 10 u-pure-co2.lammpstrj id x y z
dump_modify coords1 sort id
restart 100 u+pure-co2.rst1 u-pure-co2.rst2
run 1000
When I ran this I encounter the following message, which I am not sure what is the source of error. I would appreciate any help and suggestion.
LAMMPS (6 Mar 2015)
Reading data file …
orthogonal box = (0 0 0) to (50 40 61)
4 by 2 by 4 MPI processor grid
reading atoms …
6904 atoms
scanning bonds …
2 = max bonds/atom
scanning angles …
1 = max angles/atom
reading bonds …
2064 bonds
reading angles …
1032 angles
Finding 1-2 1-3 1-4 neighbors …
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
Reading potential file ffield.comb with DATE: 2011-02-22
Pair COMB:
generating Coulomb integral lookup table …
Application 8642754 exit codes: 139
Application 8642754 resources: utime ~2s, stime ~8s, Rss ~12996,
inblocks ~15246, outblocks ~47926
pmiu_daemon(SIGCHLD): [NID 02088] [c4-5c1s4n2] [Thu Jun 4 19:21:28
2015] PE RANK 11 exit signal Segmentation fault
_pmiu_daemon(SIGCHLD): [NID 02089] [c4-5c1s4n3] [Thu Jun 4 19:21:28
2015] PE RANK 27 exit signal Segmentation fault
[NID 02088] 2015-06-04 19:21:28 Apid 8642754: initiated application
termination
Thanks,
Yasaman
u-pure-co2.data (588 KB)
Dear Lammps users/developers,
I am trying to run a simulation having a layer of uranium metal and a layer
of supercritical co2 (sco2). To do so I have used the pair_style hybrid. I
have used lj/cut/coul/cut for co2 and COMB potential for U-metal. Here is my
input file and I have attached my data file as well.
units metal
atom_style full
dimension 3
boundary p p p
bond_style harmonic
angle_style harmonic
dihedral_style none
improper_style none
kspace_style ewald 0.000001
read_data u-pure-co2.data
pair_style hybrid lj/cut/coul/cut 10.0 comb
pair_coeff * * comb ffield.comb U NULL NULL
pair_coeff 2 2 lj/cut/coul/long 0.056 2.757
pair_coef 2 3 lj/cut/coul/long 0.066 2.895
pair_coeff 3 3 lj/cut/coul/long 0.16 3.033
neighbor 0.5 bin
neigh_modify every 1 delay 1 check yes
timestep 0.00020
min_style cg
minimize 1.0e-4 1.0e-4 100 1000
fix 3 all nve
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly
lz xz
thermo_modify norm yes
thermo 1
dump coords1 all custom 10 u-pure-co2.lammpstrj id x y z
dump_modify coords1 sort id
restart 100 u+pure-co2.rst1 u-pure-co2.rst2
run 1000
When I ran this I encounter the following message, which I am not sure what
is the source of error. I would appreciate any help and suggestion.
LAMMPS (6 Mar 2015)
Reading data file ...
orthogonal box = (0 0 0) to (50 40 61)
4 by 2 by 4 MPI processor grid
reading atoms ...
6904 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
2064 bonds
reading angles ...
1032 angles
Finding 1-2 1-3 1-4 neighbors ...
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
Reading potential file ffield.comb with DATE: 2011-02-22
Pair COMB:
generating Coulomb integral lookup table ...
Application 8642754 exit codes: 139
Application 8642754 resources: utime ~2s, stime ~8s, Rss ~12996,
inblocks ~15246, outblocks ~47926
pmiu_daemon(SIGCHLD): [NID 02088] [c4-5c1s4n2] [Thu Jun 4 19:21:28
2015] PE RANK 11 exit signal Segmentation fault
_pmiu_daemon(SIGCHLD): [NID 02089] [c4-5c1s4n3] [Thu Jun 4 19:21:28
2015] PE RANK 27 exit signal Segmentation fault
[NID 02088] 2015-06-04 19:21:28 Apid 8642754: initiated application
termination
most of the error output is from your batch system. however, the
"Segmentation fault" line indicates that there is something that is
crashing the application at that point.
upon closer inspections it turns out that, both, COMB and COMB3 pair
styles are not fully compatible with using them as a hybrid pair
style.
the attached patch lifts this restriction, as far as i could test.
since your input has many, many other (obvious) errors, i could not
test whether this is sufficient for your case. the patch is relative
to the latest version of LAMMPS (15 May 2015).
axel.
lammps-comb-hybrid.diff.gz (795 Bytes)