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 = 3.5242205 3.5242205 3.5242205
Created orthogonal box = (0.0000000 -37.628378 0.0000000) to (26.607281 37.628378 4.9840004)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 5.1347384 5.9413228 4.9840004
Created 456 atoms
using lattice units in orthogonal box = (0.0000000 -37.628378 0.0000000) to (26.607281 37.628378 4.9840004)
create_atoms CPU = 0.004 seconds
456 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 5.1347384 5.9413228 4.9840004
Created 458 atoms
using lattice units in orthogonal box = (0.0000000 -37.628378 0.0000000) to (26.607281 37.628378 4.9840004)
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 = 6.3171695
ghost atom cutoff = 6.3171695
binsize = 3.1585848, bins = 9 24 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 6.3171695
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Deleted 0 atoms, new total = 914
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_769632475533_000#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 = 6.3171695
ghost atom cutoff = 6.3171695
binsize = 3.1585848, bins = 9 24 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 6.3171695
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) = 4.577 | 4.577 | 4.577 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -3436.7048 0 -3436.7048 208606.99
69 0 -4054.3848 0 -4054.3848 30230.661
Loop time of 1.12738 on 1 procs for 69 steps with 914 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-3436.70477952193 -4054.38130909328 -4054.38476544914
Force two-norm initial, final = 1034.2334 0.25003886
Force max component initial, final = 234.14672 0.061531744
Final line search alpha, max atom move = 1.0000000 0.061531744
Iterations, force evaluations = 69 120
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.085 | 1.085 | 1.085 | 0.0 | 96.24
Neigh | 0.013813 | 0.013813 | 0.013813 | 0.0 | 1.23
Comm | 0.013913 | 0.013913 | 0.013913 | 0.0 | 1.23
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01462 | | | 1.30
Nlocal: 914.000 ave 914 max 914 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4588.00 ave 4588 max 4588 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: 79260.0 ave 79260 max 79260 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 79260
Ave neighs/atom = 86.717724
Neighbor list builds = 1
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 = 6.3171695
ghost atom cutoff = 6.3171695
binsize = 3.1585848, bins = 9 24 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 6.3171695
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) = 4.577 | 4.577 | 4.577 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
69 0 -4054.3848 0 -4054.3848 30230.661 9979.8508
84 0 -4056.7749 0 -4056.7749 -166.80062 10112.124
Loop time of 0.170806 on 1 procs for 15 steps with 914 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 =
-4054.38476544914 -4056.77448593564 -4056.77489945812
Force two-norm initial, final = 396.05993 2.1211712
Force max component initial, final = 371.10392 1.2834971
Final line search alpha, max atom move = 0.00031901183 0.00040945076
Iterations, force evaluations = 15 17
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.14786 | 0.14786 | 0.14786 | 0.0 | 86.57
Neigh | 0.013522 | 0.013522 | 0.013522 | 0.0 | 7.92
Comm | 0.0021166 | 0.0021166 | 0.0021166 | 0.0 | 1.24
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.007309 | | | 4.28
Nlocal: 914.000 ave 914 max 914 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4560.00 ave 4560 max 4560 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: 78516.0 ave 78516 max 78516 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 78516
Ave neighs/atom = 85.903720
Neighbor list builds = 1
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 = 6.3171695
ghost atom cutoff = 6.3171695
binsize = 3.1585848, bins = 9 25 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 6.3171695
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) = 4.715 | 4.715 | 4.715 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -4056.7749 0 -4056.7749 -166.80062
Loop time of 6.114e-06 on 1 procs for 0 steps with 914 atoms
196.3% 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 | | 6.114e-06 | | |100.00
Nlocal: 914.000 ave 914 max 914 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4560.00 ave 4560 max 4560 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: 78512.0 ave 78512 max 78512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 78512
Ave neighs/atom = 85.899344
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 = 6.3171695
ghost atom cutoff = 6.3171695
binsize = 3.1585848, bins = 9 25 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 6.3171695
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) = 4.715 | 4.715 | 4.715 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 -4056.7749 -4056.7749 26.588754 76.297608 4.9846362 -166.80062 -166.80062 -186.72697 -206.17135 -107.50353 2.2811978 670.89152
Loop time of 6.987e-06 on 1 procs for 0 steps with 914 atoms
200.4% 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 | | 6.987e-06 | | |100.00
Nlocal: 914.000 ave 914 max 914 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4560.00 ave 4560 max 4560 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 39256.0 ave 39256 max 39256 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 78512.0 ave 78512 max 78512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 78512
Ave neighs/atom = 85.899344
Neighbor list builds = 0
Dangerous builds = 0
914
-4056.77489945812 eV
2.28119782969476 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:01