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 = 4.0500001 4.0500001 4.0500001
Created orthogonal box = (0.0000000 -43.242168 0.0000000) to (30.576830 43.242168 5.7275650)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 5.9007918 6.8277107 5.7275650
Created 456 atoms
using lattice units in orthogonal box = (0.0000000 -43.242168 0.0000000) to (30.576830 43.242168 5.7275650)
create_atoms CPU = 0.004 seconds
456 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 5.9007918 6.8277107 5.7275650
Created 458 atoms
using lattice units in orthogonal box = (0.0000000 -43.242168 0.0000000) to (30.576830 43.242168 5.7275650)
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 = 8.28721
ghost atom cutoff = 8.28721
binsize = 4.143605, bins = 8 21 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 8.28721
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_751354403791_005#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 = 8.28721
ghost atom cutoff = 8.28721
binsize = 4.143605, bins = 8 21 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.28721
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) = 4.980 | 4.980 | 4.980 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2996.8661 0 -2996.8661 3718.0028
95 0 -3040.8475 0 -3040.8475 1695.8952
Loop time of 2.46222 on 1 procs for 95 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 =
-2996.86614713512 -3040.84508137408 -3040.84745482604
Force two-norm initial, final = 36.666376 0.12442244
Force max component initial, final = 10.327766 0.030109149
Final line search alpha, max atom move = 1.0000000 0.030109149
Iterations, force evaluations = 95 169
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.3428 | 2.3428 | 2.3428 | 0.0 | 95.15
Neigh | 0.0741 | 0.0741 | 0.0741 | 0.0 | 3.01
Comm | 0.024202 | 0.024202 | 0.024202 | 0.0 | 0.98
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.02114 | | | 0.86
Nlocal: 908.000 ave 908 max 908 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5748.00 ave 5748 max 5748 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: 126324.0 ave 126324 max 126324 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 126324
Ave neighs/atom = 139.12335
Neighbor list builds = 4
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 = 8.28721
ghost atom cutoff = 8.28721
binsize = 4.143605, bins = 8 21 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.28721
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up cg style minimization ...
Unit style : metal
Current step : 95
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 4.980 | 4.980 | 4.980 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
95 0 -3040.8475 0 -3040.8475 1695.8952 15146.069
102 0 -3040.9994 0 -3040.9994 37.36298 15178.322
Loop time of 0.127807 on 1 procs for 7 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 =
-3040.84745482604 -3040.99913353817 -3040.99942679263
Force two-norm initial, final = 48.823310 0.66427416
Force max component initial, final = 48.814652 0.43230591
Final line search alpha, max atom move = 0.00075842860 0.00032787316
Iterations, force evaluations = 7 8
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12276 | 0.12276 | 0.12276 | 0.0 | 96.05
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0011053 | 0.0011053 | 0.0011053 | 0.0 | 0.86
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.003938 | | | 3.08
Nlocal: 908.000 ave 908 max 908 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5748.00 ave 5748 max 5748 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: 126280.0 ave 126280 max 126280 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 126280
Ave neighs/atom = 139.07489
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 = 8.28721
ghost atom cutoff = 8.28721
binsize = 4.143605, bins = 8 22 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.28721
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) = 5.118 | 5.118 | 5.118 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -3040.9994 0 -3040.9994 37.36298
Loop time of 6.515e-06 on 1 procs for 0 steps with 908 atoms
168.8% 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 | | 6.515e-06 | | |100.00
Nlocal: 908.000 ave 908 max 908 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5748.00 ave 5748 max 5748 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: 126244.0 ave 126244 max 126244 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 126244
Ave neighs/atom = 139.03524
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 = 8.28721
ghost atom cutoff = 8.28721
binsize = 4.143605, bins = 8 22 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.28721
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) = 5.118 | 5.118 | 5.118 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 -3040.9994 -3040.9994 30.510815 87.022775 5.7165899 37.36298 37.36298 28.132919 38.410596 45.545425 2.6561739 868.04402
Loop time of 6.415e-06 on 1 procs for 0 steps with 908 atoms
265.0% 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 | | 6.415e-06 | | |100.00
Nlocal: 908.000 ave 908 max 908 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5748.00 ave 5748 max 5748 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 63122.0 ave 63122 max 63122 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 126244.0 ave 126244 max 126244 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 126244
Ave neighs/atom = 139.03524
Neighbor list builds = 0
Dangerous builds = 0
908
-3040.99942675289 eV
2.65617392765616 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:03