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 = 4.0446508 4.0446508 4.0446508
Created orthogonal box = (0 -43.562222 0) to (21.781111 43.562222 4.0446508)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 5.2575096 5.2575096 4.0446508
Created 231 atoms
using lattice units in orthogonal box = (0 -43.562222 0) to (21.781111 43.562222 4.0446508)
create_atoms CPU = 0.002 seconds
231 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 5.2575096 5.2575096 4.0446508
Created 233 atoms
using lattice units in orthogonal box = (0 -43.562222 0) to (21.781111 43.562222 4.0446508)
create_atoms CPU = 0.001 seconds
233 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 = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 7 26 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 6.8
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Deleted 0 atoms, new total = 464
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_618133763375_002#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 = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 7 26 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 6.8
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) = 4.455 | 4.455 | 4.455 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1363.9316 0 -1363.9316 50177.897
69 0 -1552.1089 0 -1552.1089 5722.1395
Loop time of 5.03925 on 1 procs for 69 steps with 464 atoms
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-1363.93163628368 -1552.10745664666 -1552.10886982242
Force two-norm initial, final = 299.26754 0.091622512
Force max component initial, final = 78.24407 0.016770188
Final line search alpha, max atom move = 1 0.016770188
Iterations, force evaluations = 69 112
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.0031 | 5.0031 | 5.0031 | 0.0 | 99.28
Neigh | 0.017105 | 0.017105 | 0.017105 | 0.0 | 0.34
Comm | 0.0095027 | 0.0095027 | 0.0095027 | 0.0 | 0.19
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.009502 | | | 0.19
Nlocal: 464 ave 464 max 464 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3020 ave 3020 max 3020 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: 35968 ave 35968 max 35968 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 35968
Ave neighs/atom = 77.517241
Neighbor list builds = 3
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 = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 7 26 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 6.8
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up cg style minimization ...
Unit style : metal
Current step : 69
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 4.455 | 4.455 | 4.455 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
69 0 -1552.1089 0 -1552.1089 5722.1395 7675.4011
82 0 -1552.4111 0 -1552.4111 2.8218015 7730.0664
Loop time of 0.668382 on 1 procs for 13 steps with 464 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 =
-1552.10886982242 -1552.41063747951 -1552.41110770075
Force two-norm initial, final = 58.301954 0.38427723
Force max component initial, final = 54.980189 0.079381958
Final line search alpha, max atom move = 0.00085751583 6.8071285e-05
Iterations, force evaluations = 13 14
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.65727 | 0.65727 | 0.65727 | 0.0 | 98.34
Neigh | 0.0055216 | 0.0055216 | 0.0055216 | 0.0 | 0.83
Comm | 0.0013025 | 0.0013025 | 0.0013025 | 0.0 | 0.19
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.004286 | | | 0.64
Nlocal: 464 ave 464 max 464 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3000 ave 3000 max 3000 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: 35928 ave 35928 max 35928 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 35928
Ave neighs/atom = 77.431034
Neighbor list builds = 1
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 = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 7 26 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 6.8
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) = 4.632 | 4.632 | 4.632 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1552.4111 0 -1552.4111 2.8218015
Loop time of 6.615e-06 on 1 procs for 0 steps with 464 atoms
211.6% 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 | | 6.615e-06 | | |100.00
Nlocal: 464 ave 464 max 464 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3000 ave 3000 max 3000 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: 35928 ave 35928 max 35928 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 35928
Ave neighs/atom = 77.431034
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 = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 7 26 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 6.8
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) = 4.632 | 4.632 | 4.632 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 -1552.4111 -1552.4111 21.743881 88.211961 4.0301266 2.8218015 2.8218015 16.108568 -14.562764 6.9196001 2.5560248 347.17436
Loop time of 6.505e-06 on 1 procs for 0 steps with 464 atoms
276.7% 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 | | 6.505e-06 | | |100.00
Nlocal: 464 ave 464 max 464 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3000 ave 3000 max 3000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 17964 ave 17964 max 17964 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 35928 ave 35928 max 35928 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 35928
Ave neighs/atom = 77.431034
Neighbor list builds = 0
Dangerous builds = 0
464
-1552.41110770075 eV
2.5560247589869 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:06