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 -43.749587 0) to (14.583196 43.749587 4.0446508)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 5.6089215 5.6089215 4.0446508
Created 156 atoms
using lattice units in orthogonal box = (0 -43.749587 0) to (14.583196 43.749587 4.0446508)
create_atoms CPU = 0.002 seconds
156 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 5.6089215 5.6089215 4.0446508
Created 158 atoms
using lattice units in orthogonal box = (0 -43.749587 0) to (14.583196 43.749587 4.0446508)
create_atoms CPU = 0.001 seconds
158 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 = 5 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 2 atoms, new total = 312
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 = 5 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) = 4.427 | 4.427 | 4.427 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1025.944 0 -1025.944 15573.722
45 0 -1044.6797 0 -1044.6797 4274.0518
Loop time of 2.35577 on 1 procs for 45 steps with 312 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 =
-1025.94401017168 -1044.67894747678 -1044.67966459921
Force two-norm initial, final = 36.828789 0.064361389
Force max component initial, final = 11.498897 0.013417077
Final line search alpha, max atom move = 1 0.013417077
Iterations, force evaluations = 45 84
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.3451 | 2.3451 | 2.3451 | 0.0 | 99.55
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0056501 | 0.0056501 | 0.0056501 | 0.0 | 0.24
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.005047 | | | 0.21
Nlocal: 312 ave 312 max 312 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2820 ave 2820 max 2820 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: 24352 ave 24352 max 24352 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 24352
Ave neighs/atom = 78.051282
Neighbor list builds = 0
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 = 5 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 : 45
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 4.426 | 4.426 | 4.426 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
45 0 -1044.6797 0 -1044.6797 4274.0518 5161.0456
54 0 -1044.7865 0 -1044.7865 10.76389 5188.5145
Loop time of 0.31474 on 1 procs for 9 steps with 312 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 =
-1044.67966459921 -1044.78572602757 -1044.78653073036
Force two-norm initial, final = 29.104378 0.21929407
Force max component initial, final = 27.329178 0.13806589
Final line search alpha, max atom move = 0.00076511707 0.00010563657
Iterations, force evaluations = 9 10
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.31165 | 0.31165 | 0.31165 | 0.0 | 99.02
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00069683 | 0.00069683 | 0.00069683 | 0.0 | 0.22
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.002393 | | | 0.76
Nlocal: 312 ave 312 max 312 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2784 ave 2784 max 2784 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: 24208 ave 24208 max 24208 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 24208
Ave neighs/atom = 77.589744
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 = 5 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) = 4.599 | 4.599 | 4.599 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1044.7865 0 -1044.7865 10.76389
Loop time of 6.405e-06 on 1 procs for 0 steps with 312 atoms
203.0% 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 | | 6.405e-06 | | |100.00
Nlocal: 312 ave 312 max 312 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2784 ave 2784 max 2784 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: 24160 ave 24160 max 24160 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 24160
Ave neighs/atom = 77.435897
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 = 5 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) = 4.599 | 4.599 | 4.599 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 -1044.7865 -1044.7865 14.573369 88.262919 4.033711 10.76389 10.76389 42.605041 -3.3967057 -6.9166657 2.5494949 196.26082
Loop time of 6.515e-06 on 1 procs for 0 steps with 312 atoms
230.2% 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 | | 6.515e-06 | | |100.00
Nlocal: 312 ave 312 max 312 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2784 ave 2784 max 2784 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 12080 ave 12080 max 12080 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 24160 ave 24160 max 24160 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 24160
Ave neighs/atom = 77.435897
Neighbor list builds = 0
Dangerous builds = 0
312
-1044.78653073036 eV
2.54949492462016 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:03