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 -40.446508 0) to (20.223254 40.446508 4.0446508)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 5.6625111 5.6625111 4.0446508
Created 200 atoms
using lattice units in orthogonal box = (0 -40.446508 0) to (20.223254 40.446508 4.0446508)
create_atoms CPU = 0.002 seconds
200 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 5.6625111 5.6625111 4.0446508
Created 202 atoms
using lattice units in orthogonal box = (0 -40.446508 0) to (20.223254 40.446508 4.0446508)
create_atoms CPU = 0.001 seconds
202 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 = 6 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 6.8
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Deleted 2 atoms, new total = 400
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 = 6 24 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) = 4.442 | 4.442 | 4.442 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1306.1877 0 -1306.1877 18218.139
41 0 -1339.5019 0 -1339.5019 3813.7913
Loop time of 2.71147 on 1 procs for 41 steps with 400 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 =
-1306.1877304982 -1339.50110013757 -1339.50193594357
Force two-norm initial, final = 66.860309 0.064305496
Force max component initial, final = 22.600735 0.013733931
Final line search alpha, max atom move = 1 0.013733931
Iterations, force evaluations = 41 76
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.7002 | 2.7002 | 2.7002 | 0.0 | 99.59
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0057771 | 0.0057771 | 0.0057771 | 0.0 | 0.21
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.005456 | | | 0.20
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3122 ave 3122 max 3122 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: 31192 ave 31192 max 31192 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 31192
Ave neighs/atom = 77.98
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 = 6 24 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 : 41
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 4.441 | 4.441 | 4.441 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
41 0 -1339.5019 0 -1339.5019 3813.7913 6616.7251
49 0 -1339.6065 0 -1339.6065 35.87684 6647.9838
Loop time of 0.357984 on 1 procs for 8 steps with 400 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 =
-1339.50193594357 -1339.60590152652 -1339.60652073525
Force two-norm initial, final = 32.935889 0.32503689
Force max component initial, final = 30.703683 0.25597631
Final line search alpha, max atom move = 0.0008154485 0.0002087355
Iterations, force evaluations = 8 9
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.35467 | 0.35467 | 0.35467 | 0.0 | 99.07
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00068559 | 0.00068559 | 0.00068559 | 0.0 | 0.19
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.002627 | | | 0.73
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3081 ave 3081 max 3081 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: 31072 ave 31072 max 31072 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 31072
Ave neighs/atom = 77.68
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 = 6 24 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) = 4.617 | 4.617 | 4.617 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1339.6065 0 -1339.6065 35.87684
Loop time of 6.334e-06 on 1 procs for 0 steps with 400 atoms
205.2% 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 | | 6.334e-06 | | |100.00
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3081 ave 3081 max 3081 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: 30992 ave 30992 max 30992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 30992
Ave neighs/atom = 77.48
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 = 6 24 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) = 4.617 | 4.617 | 4.617 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 -1339.6065 -1339.6065 20.216409 81.50224 4.0347478 35.87684 35.87684 61.669887 25.165568 20.795064 2.5537549 189.77569
Loop time of 6.786e-06 on 1 procs for 0 steps with 400 atoms
265.3% 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 | | 6.786e-06 | | |100.00
Nlocal: 400 ave 400 max 400 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3081 ave 3081 max 3081 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 15496 ave 15496 max 15496 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 30992 ave 30992 max 30992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 30992
Ave neighs/atom = 77.48
Neighbor list builds = 0
Dangerous builds = 0
400
-1339.60652073525 eV
2.55375489134499 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:03