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 = 3.6043435 3.6043435 3.6043435
Created orthogonal box = (0.0000000 -43.255726 0.0000000) to (15.291934 43.255726 5.0973115)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 5.0973115 6.0072392 5.0973115
Created 292 atoms
using lattice units in orthogonal box = (0.0000000 -43.255726 0.0000000) to (15.291934 43.255726 5.0973115)
create_atoms CPU = 0.002 seconds
292 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 5.0973115 6.0072392 5.0973115
Created 292 atoms
using lattice units in orthogonal box = (0.0000000 -43.255726 0.0000000) to (15.291934 43.255726 5.0973115)
create_atoms CPU = 0.002 seconds
292 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
ghost atom cutoff = 6
binsize = 3, bins = 6 29 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
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Deleted 16 atoms, new total = 568
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_492310898779_001#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
ghost atom cutoff = 6
binsize = 3, bins = 6 29 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 6
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) = 4.503 | 4.503 | 4.503 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2391.1596 0 -2391.1596 -4263.8365
23 0 -2401.8135 0 -2401.8135 -17276.571
Loop time of 1.55071 on 1 procs for 23 steps with 568 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 =
-2391.15964410114 -2401.81136312675 -2401.81345661778
Force two-norm initial, final = 10.254722 0.13458841
Force max component initial, final = 2.5819049 0.015119303
Final line search alpha, max atom move = 1.0000000 0.015119303
Iterations, force evaluations = 23 39
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.546 | 1.546 | 1.546 | 0.0 | 99.69
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0023006 | 0.0023006 | 0.0023006 | 0.0 | 0.15
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.00243 | | | 0.16
Nlocal: 568.000 ave 568 max 568 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3138.00 ave 3138 max 3138 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: 43664.0 ave 43664 max 43664 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 43664
Ave neighs/atom = 76.873239
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 = 6
ghost atom cutoff = 6
binsize = 3, bins = 6 29 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 6
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up cg style minimization ...
Unit style : metal
Current step : 23
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 4.504 | 4.504 | 4.504 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
23 0 -2401.8135 0 -2401.8135 -17276.571 6743.3733
39 0 -2402.4929 0 -2402.4929 -1065.1624 6673.4434
Loop time of 0.712896 on 1 procs for 16 steps with 568 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 =
-2401.81345661778 -2402.49213215897 -2402.49287452295
Force two-norm initial, final = 108.21613 0.43978730
Force max component initial, final = 100.64145 0.085393971
Final line search alpha, max atom move = 0.00064079987 5.4720445e-05
Iterations, force evaluations = 16 17
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.70756 | 0.70756 | 0.70756 | 0.0 | 99.25
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00090961 | 0.00090961 | 0.00090961 | 0.0 | 0.13
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.004426 | | | 0.62
Nlocal: 568.000 ave 568 max 568 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3192.00 ave 3192 max 3192 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: 43888.0 ave 43888 max 43888 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 43888
Ave neighs/atom = 77.267606
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
ghost atom cutoff = 6
binsize = 3, bins = 6 29 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 6
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) = 4.642 | 4.642 | 4.642 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2402.4929 0 -2402.4929 -1065.1624
Loop time of 2.947e-06 on 1 procs for 0 steps with 568 atoms
169.7% 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 | | 2.947e-06 | | |100.00
Nlocal: 568.000 ave 568 max 568 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3192.00 ave 3192 max 3192 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: 43952.0 ave 43952 max 43952 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 43952
Ave neighs/atom = 77.380282
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
ghost atom cutoff = 6
binsize = 3, bins = 6 29 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 6
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) = 4.642 | 4.642 | 4.642 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 -2402.4929 -2402.4929 15.054723 86.511453 5.1239349 -1065.1624 -1065.1624 20.183567 -3205.4729 -10.197871 2.3427682 364.74689
Loop time of 3.121e-06 on 1 procs for 0 steps with 568 atoms
160.2% 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 | | 3.121e-06 | | |100.00
Nlocal: 568.000 ave 568 max 568 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3192.00 ave 3192 max 3192 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 21976.0 ave 21976 max 21976 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 43952.0 ave 43952 max 43952 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 43952
Ave neighs/atom = 77.380282
Neighbor list builds = 0
Dangerous builds = 0
568
-2402.49287452295 eV
2.34276820950817 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:02