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 -36.622591 0.0000000) to (8.6320276 36.622591 4.9837035)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 5.7546851 6.1037652 4.9837035
Created 143 atoms
using lattice units in orthogonal box = (0.0000000 -36.622591 0.0000000) to (8.6320276 36.622591 4.9837035)
create_atoms CPU = 0.003 seconds
143 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 5.7546851 6.1037652 4.9837035
Created 151 atoms
using lattice units in orthogonal box = (0.0000000 -36.622591 0.0000000) to (8.6320276 36.622591 4.9837035)
create_atoms CPU = 0.002 seconds
151 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 = 3 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 = 288
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 = 3 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) = 4.471 | 4.471 | 4.471 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1298.1339 0 -1298.1339 7221.7142
60 0 -1303.6169 0 -1303.6169 2099.8638
Loop time of 0.708755 on 1 procs for 60 steps with 288 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 =
-1298.13389147509 -1303.61563290321 -1303.61687777179
Force two-norm initial, final = 12.734911 0.10900419
Force max component initial, final = 7.9517531 0.013457812
Final line search alpha, max atom move = 1.0000000 0.013457812
Iterations, force evaluations = 60 114
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.69337 | 0.69337 | 0.69337 | 0.0 | 97.83
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0090526 | 0.0090526 | 0.0090526 | 0.0 | 1.28
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.006334 | | | 0.89
Nlocal: 288.000 ave 288 max 288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3852.00 ave 3852 max 3852 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: 50592.0 ave 50592 max 50592 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 50592
Ave neighs/atom = 175.66667
Neighbor list builds = 0
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 = 3 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 : 60
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 4.470 | 4.470 | 4.470 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
60 0 -1303.6169 0 -1303.6169 2099.8638 3150.9686
63 0 -1303.6248 0 -1303.6248 -8.1452835 3154.5867
Loop time of 0.0383787 on 1 procs for 3 steps with 288 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 =
-1303.61687777178 -1303.62479059423 -1303.6248016499
Force two-norm initial, final = 10.404497 0.11215152
Force max component initial, final = 10.296870 0.022681969
Final line search alpha, max atom move = 0.0029012550 6.5806175e-05
Iterations, force evaluations = 3 5
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.036569 | 0.036569 | 0.036569 | 0.0 | 95.29
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00046458 | 0.00046458 | 0.00046458 | 0.0 | 1.21
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.001345 | | | 3.50
Nlocal: 288.000 ave 288 max 288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3726.00 ave 3726 max 3726 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: 50368.0 ave 50368 max 50368 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 50368
Ave neighs/atom = 174.88889
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 = 3 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) = 4.608 | 4.608 | 4.608 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1303.6248 0 -1303.6248 -8.1452835
Loop time of 5.944e-06 on 1 procs for 0 steps with 288 atoms
151.4% 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 | | 5.944e-06 | | |100.00
Nlocal: 288.000 ave 288 max 288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3726.00 ave 3726 max 3726 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: 50368.0 ave 50368 max 50368 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 50368
Ave neighs/atom = 174.88889
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 = 3 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) = 4.608 | 4.608 | 4.608 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 -1303.6248 -1303.6248 8.6299134 73.361404 4.982742 -8.1452835 -8.1452835 -11.517076 -9.1842304 -3.7345436 2.4885386 99.217997
Loop time of 6.465e-06 on 1 procs for 0 steps with 288 atoms
232.0% 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 | | 6.465e-06 | | |100.00
Nlocal: 288.000 ave 288 max 288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3726.00 ave 3726 max 3726 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 25184.0 ave 25184 max 25184 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 50368.0 ave 50368 max 50368 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 50368
Ave neighs/atom = 174.88889
Neighbor list builds = 0
Dangerous builds = 0
288
-1303.6248016499 eV
2.48853863449799 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:01