LAMMPS (30 Jul 2021)
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 = 3.5240105 3.5240105 3.5240105
Created orthogonal box = (0.0000000 -37.626136 0.0000000) to (26.605696 37.626136 4.9837035)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 5.1344325 5.9409688 4.9837035
Created 456 atoms
using lattice units in orthogonal box = (0.0000000 -37.626136 0.0000000) to (26.605696 37.626136 4.9837035)
create_atoms CPU = 0.003 seconds
456 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 5.1344325 5.9409688 4.9837035
Created 458 atoms
using lattice units in orthogonal box = (0.0000000 -37.626136 0.0000000) to (26.605696 37.626136 4.9837035)
create_atoms CPU = 0.003 seconds
458 atoms in group lower
Displacing atoms ...
System init for delete_atoms ...
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.65
ghost atom cutoff = 7.65
binsize = 3.825, bins = 7 20 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 7.65
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Deleted 6 atoms, new total = 908
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_535504325462_003#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:189)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.65
ghost atom cutoff = 7.65
binsize = 3.825, bins = 7 20 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 7.65
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) = 4.994 | 4.994 | 4.994 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -4022.5522 0 -4022.5522 11529.808
100 0 -4092.0101 0 -4092.0101 7154.9428
Loop time of 3.54743 on 1 procs for 100 steps with 908 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 =
-4022.55220269691 -4092.00624684301 -4092.01014734892
Force two-norm initial, final = 47.672026 0.22679611
Force max component initial, final = 11.544830 0.052967913
Final line search alpha, max atom move = 1.0000000 0.052967913
Iterations, force evaluations = 100 186
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.4227 | 3.4227 | 3.4227 | 0.0 | 96.48
Neigh | 0.070754 | 0.070754 | 0.070754 | 0.0 | 1.99
Comm | 0.029866 | 0.029866 | 0.029866 | 0.0 | 0.84
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.02414 | | | 0.68
Nlocal: 908.000 ave 908 max 908 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6402.00 ave 6402 max 6402 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 157780.0 ave 157780 max 157780 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 157780
Ave neighs/atom = 173.76652
Neighbor list builds = 3
Dangerous builds = 0
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.65
ghost atom cutoff = 7.65
binsize = 3.825, bins = 7 20 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 7.65
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up cg style minimization ...
Unit style : metal
Current step : 100
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 4.994 | 4.994 | 4.994 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
100 0 -4092.0101 0 -4092.0101 7154.9428 9978.0674
105 0 -4092.1861 0 -4092.1861 226.6431 10016.745
Loop time of 0.1264 on 1 procs for 5 steps with 908 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 =
-4092.01014734892 -4092.18536692193 -4092.18611299319
Force two-norm initial, final = 92.370641 2.7955274
Force max component initial, final = 85.814817 2.1157079
Final line search alpha, max atom move = 0.00022844181 0.00048331613
Iterations, force evaluations = 5 6
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12233 | 0.12233 | 0.12233 | 0.0 | 96.78
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00095169 | 0.00095169 | 0.00095169 | 0.0 | 0.75
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.003118 | | | 2.47
Nlocal: 908.000 ave 908 max 908 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6404.00 ave 6404 max 6404 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 157844.0 ave 157844 max 157844 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 157844
Ave neighs/atom = 173.83700
Neighbor list builds = 0
Dangerous builds = 0
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.65
ghost atom cutoff = 7.65
binsize = 3.825, bins = 7 20 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 7.65
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) = 5.132 | 5.132 | 5.132 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -4092.1861 0 -4092.1861 226.6431
Loop time of 6.285e-06 on 1 procs for 0 steps with 908 atoms
190.9% 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 | | 6.285e-06 | | |100.00
Nlocal: 908.000 ave 908 max 908 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6396.00 ave 6396 max 6396 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 157684.0 ave 157684 max 157684 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 157684
Ave neighs/atom = 173.66079
Neighbor list builds = 0
Dangerous builds = 0
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.65
ghost atom cutoff = 7.65
binsize = 3.825, bins = 7 20 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 7.65
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) = 5.132 | 5.132 | 5.132 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 -4092.1861 -4092.1861 26.600922 75.561713 4.9834273 226.6431 226.6431 59.296101 282.24486 338.38834 2.2856492 631.53558
Loop time of 6.956e-06 on 1 procs for 0 steps with 908 atoms
258.8% 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 | | 6.956e-06 | | |100.00
Nlocal: 908.000 ave 908 max 908 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6396.00 ave 6396 max 6396 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 78842.0 ave 78842 max 78842 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 157684.0 ave 157684 max 157684 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 157684
Ave neighs/atom = 173.66079
Neighbor list builds = 0
Dangerous builds = 0
908
-4092.18611299319 eV
2.28564923357877 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:04