LAMMPS (23 Jun 2022)
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 = 4.0446508 4.0446508 4.0446508
Created orthogonal box = (0 -42.033244 0) to (9.9073306 42.033244 5.72)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 6.6048871 7.0055406 5.72
Created 144 atoms
using lattice units in orthogonal box = (0 -42.033244 0) to (9.9073306 42.033244 5.72)
create_atoms CPU = 0.002 seconds
144 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 6.6048871 7.0055406 5.72
Created 152 atoms
using lattice units in orthogonal box = (0 -42.033244 0) to (9.9073306 42.033244 5.72)
create_atoms CPU = 0.002 seconds
152 atoms in group lower
Displacing atoms ...
System init for delete_atoms ...
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 3 25 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 6.8
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Deleted 8 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_618133763375_002#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:187)
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 3 25 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 6.8
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) = 4.436 | 4.436 | 4.436 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -967.14882 0 -967.14882 305.32806
4 0 -967.16361 0 -967.16361 308.71512
Loop time of 0.216005 on 1 procs for 4 steps with 288 atoms
100.1% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-967.148821483419 -967.162642108025 -967.16360676425
Force two-norm initial, final = 0.30398531 0.062059501
Force max component initial, final = 0.053737524 0.010880397
Final line search alpha, max atom move = 1 0.010880397
Iterations, force evaluations = 4 8
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.21497 | 0.21497 | 0.21497 | 0.0 | 99.52
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00049736 | 0.00049736 | 0.00049736 | 0.0 | 0.23
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0005369 | | | 0.25
Nlocal: 288 ave 288 max 288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2299 ave 2299 max 2299 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 22304 ave 22304 max 22304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 22304
Ave neighs/atom = 77.444444
Neighbor list builds = 0
Dangerous builds = 0
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:187)
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 3 25 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 6.8
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up cg style minimization ...
Unit style : metal
Current step : 4
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 4.436 | 4.436 | 4.436 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
4 0 -967.16361 0 -967.16361 308.71512 4764.042
6 0 -967.16703 0 -967.16703 242.80122 4764.4351
Loop time of 0.097664 on 1 procs for 2 steps with 288 atoms
100.2% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-967.163606764249 -967.166262012328 -967.167026000525
Force two-norm initial, final = 3.9917115 1.4886133
Force max component initial, final = 3.907046 1.3799104
Final line search alpha, max atom move = 0.00065469645 0.00090342247
Iterations, force evaluations = 2 3
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.096749 | 0.096749 | 0.096749 | 0.0 | 99.06
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00022825 | 0.00022825 | 0.00022825 | 0.0 | 0.23
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0006872 | | | 0.70
Nlocal: 288 ave 288 max 288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2299 ave 2299 max 2299 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 22304 ave 22304 max 22304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 22304
Ave neighs/atom = 77.444444
Neighbor list builds = 0
Dangerous builds = 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 3 25 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 6.8
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) = 4.603 | 4.603 | 4.603 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -967.16703 0 -967.16703 242.80122
Loop time of 6.364e-06 on 1 procs for 0 steps with 288 atoms
282.8% 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 | | 6.364e-06 | | |100.00
Nlocal: 288 ave 288 max 288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2299 ave 2299 max 2299 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 22304 ave 22304 max 22304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 22304
Ave neighs/atom = 77.444444
Neighbor list builds = 0
Dangerous builds = 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 6.8
ghost atom cutoff = 6.8
binsize = 3.4, bins = 3 25 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 6.8
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) = 4.603 | 4.603 | 4.603 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 -967.16703 -967.16703 9.9015445 84.171712 5.7166594 242.80122 242.80122 131.89439 464.61486 131.89439 2.8579662 130.76651
Loop time of 6.135e-06 on 1 procs for 0 steps with 288 atoms
244.5% 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 | | 6.135e-06 | | |100.00
Nlocal: 288 ave 288 max 288 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2299 ave 2299 max 2299 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 11152 ave 11152 max 11152 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 22304 ave 22304 max 22304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 22304
Ave neighs/atom = 77.444444
Neighbor list builds = 0
Dangerous builds = 0
288
-967.167026000525 eV
2.85796619804591 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:00