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 -42.995228 0) to (42.995228 42.995228 4.0446508)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 5.7073311 5.7073311 4.0446508
Created 452 atoms
using lattice units in orthogonal box = (0 -42.995228 0) to (42.995228 42.995228 4.0446508)
create_atoms CPU = 0.003 seconds
452 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 5.7073311 5.7073311 4.0446508
Created 454 atoms
using lattice units in orthogonal box = (0 -42.995228 0) to (42.995228 42.995228 4.0446508)
create_atoms CPU = 0.002 seconds
454 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 = 13 26 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 0 atoms, new total = 906
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 = 13 26 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) = 4.556 | 4.556 | 4.556 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2979.496 0 -2979.496 17384.159
69 0 -3037.5846 0 -3037.5846 3992.4594
Loop time of 9.09133 on 1 procs for 69 steps with 906 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 =
-2979.49604173576 -3037.58213975861 -3037.58460999271
Force two-norm initial, final = 48.084733 0.1222513
Force max component initial, final = 12.161758 0.020103964
Final line search alpha, max atom move = 1 0.020103964
Iterations, force evaluations = 69 110
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.0385 | 9.0385 | 9.0385 | 0.0 | 99.42
Neigh | 0.023633 | 0.023633 | 0.023633 | 0.0 | 0.26
Comm | 0.0145 | 0.0145 | 0.0145 | 0.0 | 0.16
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01469 | | | 0.16
Nlocal: 906 ave 906 max 906 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5321 ave 5321 max 5321 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: 70524 ave 70524 max 70524 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 70524
Ave neighs/atom = 77.84106
Neighbor list builds = 2
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 = 13 26 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 : 69
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 4.556 | 4.556 | 4.556 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
69 0 -3037.5846 0 -3037.5846 3992.4594 14953.799
76 0 -3037.7731 0 -3037.7731 -0.37223829 15028.367
Loop time of 0.701013 on 1 procs for 7 steps with 906 atoms
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-3037.58460999271 -3037.77237710314 -3037.77308702643
Force two-norm initial, final = 72.579826 0.26915986
Force max component initial, final = 64.153423 0.17257379
Final line search alpha, max atom move = 0.00050761041 8.7600252e-05
Iterations, force evaluations = 7 8
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.69613 | 0.69613 | 0.69613 | 0.0 | 99.30
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0011437 | 0.0011437 | 0.0011437 | 0.0 | 0.16
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.003742 | | | 0.53
Nlocal: 906 ave 906 max 906 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5333 ave 5333 max 5333 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: 70572 ave 70572 max 70572 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 70572
Ave neighs/atom = 77.89404
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 = 13 26 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) = 4.759 | 4.759 | 4.759 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -3037.7731 0 -3037.7731 -0.37223829
Loop time of 6.415e-06 on 1 procs for 0 steps with 906 atoms
218.2% 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 | | 6.415e-06 | | |100.00
Nlocal: 906 ave 906 max 906 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5320 ave 5320 max 5320 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: 70492 ave 70492 max 70492 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 70492
Ave neighs/atom = 77.80574
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 = 13 26 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) = 4.759 | 4.759 | 4.759 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 -3037.7731 -3037.7731 43.003118 86.539223 4.0383026 -0.37223829 -0.37223829 18.401494 -10.118703 -9.3995064 2.5639412 173.63089
Loop time of 6.735e-06 on 1 procs for 0 steps with 906 atoms
282.1% 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 | | 6.735e-06 | | |100.00
Nlocal: 906 ave 906 max 906 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5320 ave 5320 max 5320 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 35246 ave 35246 max 35246 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 70492 ave 70492 max 70492 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 70492
Ave neighs/atom = 77.80574
Neighbor list builds = 0
Dangerous builds = 0
906
-3037.77308702643 eV
2.56394118606115 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:10