LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.05 4.05 4.05
Created orthogonal box = (0 -74.67831 0) to (37.339155 74.67831 4.05)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 5.7106943 5.7106943 4.05
Created 680 atoms
using lattice units in orthogonal box = (0 -74.67831 0) to (37.339155 74.67831 4.05)
create_atoms CPU = 0.003 seconds
680 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 5.7106943 5.7106943 4.05
Created 682 atoms
using lattice units in orthogonal box = (0 -74.67831 0) to (37.339155 74.67831 4.05)
create_atoms CPU = 0.002 seconds
682 atoms in group lower
Displacing atoms ...
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7
ghost atom cutoff = 7
binsize = 3.5, bins = 11 43 2
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) command delete_atoms, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) pair kim, perpetual
attributes: full, newton off, cut 7
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Deleted 0 atoms, new total = 1362
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- OpenKIM: https://doi.org/10.1007/s11837-011-0102-6
- OpenKIM potential: https://openkim.org/cite/MO_971738391444_001#item-citation
The log file lists these citations in BibTeX format.
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7
ghost atom cutoff = 7
binsize = 3.5, bins = 11 43 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 7
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up cg style minimization ...
Unit style : metal
Current step : 0
Per MPI rank memory allocation (min/avg/max) = 5.052 | 5.052 | 5.052 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -4497.7359 0 -4497.7359 6297.2479
40 0 -4559.0197 0 -4559.0197 1559.0543
Loop time of 11.6393 on 1 procs for 40 steps with 1362 atoms
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-4497.73585176631 -4559.01822688288 -4559.01974975909
Force two-norm initial, final = 70.006457 0.25371526
Force max component initial, final = 25.284438 0.042174131
Final line search alpha, max atom move = 0.25 0.010543533
Iterations, force evaluations = 40 72
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.597 | 11.597 | 11.597 | 0.0 | 99.63
Neigh | 0.017435 | 0.017435 | 0.017435 | 0.0 | 0.15
Comm | 0.012494 | 0.012494 | 0.012494 | 0.0 | 0.11
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01257 | | | 0.11
Nlocal: 1362 ave 1362 max 1362 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6830 ave 6830 max 6830 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 108172 ave 108172 max 108172 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 108172
Ave neighs/atom = 79.421439
Neighbor list builds = 1
Dangerous builds = 0
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7
ghost atom cutoff = 7
binsize = 3.5, bins = 11 43 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 7
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up cg style minimization ...
Unit style : metal
Current step : 40
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 5.055 | 5.055 | 5.055 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
40 0 -4559.0197 0 -4559.0197 1559.0543 22586.242
42 0 -4559.0428 0 -4559.0428 -1.5805028 22631.888
Loop time of 0.860725 on 1 procs for 2 steps with 1362 atoms
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-4559.01974975909 -4559.04236331578 -4559.04279733185
Force two-norm initial, final = 38.309084 0.30521246
Force max component initial, final = 24.297236 0.15668501
Final line search alpha, max atom move = 0.00040656989 6.3703406e-05
Iterations, force evaluations = 2 4
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.85597 | 0.85597 | 0.85597 | 0.0 | 99.45
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00093562 | 0.00093562 | 0.00093562 | 0.0 | 0.11
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.003816 | | | 0.44
Nlocal: 1362 ave 1362 max 1362 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6830 ave 6830 max 6830 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 108260 ave 108260 max 108260 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 108260
Ave neighs/atom = 79.48605
Neighbor list builds = 0
Dangerous builds = 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7
ghost atom cutoff = 7
binsize = 3.5, bins = 11 43 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 7
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) compute centro/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(3) compute pair/local, occasional
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 5.278 | 5.278 | 5.278 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -4559.0428 0 -4559.0428 -1.5805028
Loop time of 6.155e-06 on 1 procs for 0 steps with 1362 atoms
0.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 6.155e-06 | | |100.00
Nlocal: 1362 ave 1362 max 1362 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6830 ave 6830 max 6830 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 107996 ave 107996 max 107996 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 107996
Ave neighs/atom = 79.292217
Neighbor list builds = 0
Dangerous builds = 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7
ghost atom cutoff = 7
binsize = 3.5, bins = 11 43 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 7
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(2) compute centro/atom, occasional
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
(3) compute pair/local, occasional
attributes: half, newton on
pair build: half/bin/atomonly/newton
stencil: half/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 5.278 | 5.278 | 5.278 Mbytes
Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal
0 -4559.0428 -4559.0428 37.368019 149.49198 4.0513784 -1.5805028 -1.5805028 -11.100757 4.5522113 1.8070377 1.8909015 141.37938
Loop time of 6.906e-06 on 1 procs for 0 steps with 1362 atoms
289.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 6.906e-06 | | |100.00
Nlocal: 1362 ave 1362 max 1362 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6830 ave 6830 max 6830 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 53998 ave 53998 max 53998 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 107996 ave 107996 max 107996 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 107996
Ave neighs/atom = 79.292217
Neighbor list builds = 0
Dangerous builds = 0
1362
-4559.04279733185 eV
1.89090153387431 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:13