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 -50.029567 0) to (23.584164 50.029567 5.72)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 6.9365189 6.8668033 5.72
Created 408 atoms
using lattice units in orthogonal box = (0 -50.029567 0) to (23.584164 50.029567 5.72)
create_atoms CPU = 0.004 seconds
408 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 6.9365189 6.8668033 5.72
Created 412 atoms
using lattice units in orthogonal box = (0 -50.029567 0) to (23.584164 50.029567 5.72)
create_atoms CPU = 0.003 seconds
412 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 30 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 4 atoms, new total = 816
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 30 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) = 4.55 | 4.55 | 4.55 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2678.6503 0 -2678.6503 14932.187
77 0 -2734.2547 0 -2734.2547 3476.5379
Loop time of 10.0281 on 1 procs for 77 steps with 816 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 =
-2678.65026525161 -2734.2520345813 -2734.25470986654
Force two-norm initial, final = 82.066277 0.12020746
Force max component initial, final = 17.498034 0.010775945
Final line search alpha, max atom move = 1 0.010775945
Iterations, force evaluations = 77 147
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.9756 | 9.9756 | 9.9756 | 0.0 | 99.48
Neigh | 0.021437 | 0.021437 | 0.021437 | 0.0 | 0.21
Comm | 0.015454 | 0.015454 | 0.015454 | 0.0 | 0.15
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01563 | | | 0.16
Nlocal: 816 ave 816 max 816 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3934 ave 3934 max 3934 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: 63352 ave 63352 max 63352 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 63352
Ave neighs/atom = 77.637255
Neighbor list builds = 2
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 30 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 : 77
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 4.55 | 4.55 | 4.55 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
77 0 -2734.2547 0 -2734.2547 3476.5379 13498.119
83 0 -2734.3932 0 -2734.3932 -169.16549 13560.127
Loop time of 0.537038 on 1 procs for 6 steps with 816 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 =
-2734.25470986654 -2734.39089639001 -2734.39323309924
Force two-norm initial, final = 57.994134 2.5349121
Force max component initial, final = 52.175521 1.7368267
Final line search alpha, max atom move = 0.00021239901 0.00036890028
Iterations, force evaluations = 6 7
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.5336 | 0.5336 | 0.5336 | 0.0 | 99.36
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00068433 | 0.00068433 | 0.00068433 | 0.0 | 0.13
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.00275 | | | 0.51
Nlocal: 816 ave 816 max 816 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3905 ave 3905 max 3905 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: 63296 ave 63296 max 63296 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 63296
Ave neighs/atom = 77.568627
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 30 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) = 4.738 | 4.738 | 4.738 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2734.3932 0 -2734.3932 -169.16549
Loop time of 6.255e-06 on 1 procs for 0 steps with 816 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 | | 6.255e-06 | | |100.00
Nlocal: 816 ave 816 max 816 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3905 ave 3905 max 3905 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: 63288 ave 63288 max 63288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 63288
Ave neighs/atom = 77.558824
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 30 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) = 4.738 | 4.738 | 4.738 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 -2734.3932 -2734.3932 23.578058 100.6416 5.7144994 -169.16549 -169.16549 -179.87523 -122.60642 -205.01482 2.699917 567.61298
Loop time of 7.688e-06 on 1 procs for 0 steps with 816 atoms
247.1% 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 | | 7.688e-06 | | |100.00
Nlocal: 816 ave 816 max 816 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3905 ave 3905 max 3905 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 31644 ave 31644 max 31644 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 63288 ave 63288 max 63288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 63288
Ave neighs/atom = 77.558824
Neighbor list builds = 0
Dangerous builds = 0
816
-2734.39323309924 eV
2.69991704377537 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:11