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 -58.891004 0) to (29.445502 58.891004 4.0446508)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 5.0001796 5.0001796 4.0446508
Created 424 atoms
using lattice units in orthogonal box = (0 -58.891004 0) to (29.445502 58.891004 4.0446508)
create_atoms CPU = 0.002 seconds
424 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 5.0001796 5.0001796 4.0446508
Created 426 atoms
using lattice units in orthogonal box = (0 -58.891004 0) to (29.445502 58.891004 4.0446508)
create_atoms CPU = 0.001 seconds
426 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 = 9 35 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 = 848
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 = 9 35 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) = 4.55 | 4.55 | 4.55 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2771.3257 0 -2771.3257 15576.066
79 0 -2840.3177 0 -2840.3177 3959.3713
Loop time of 10.6294 on 1 procs for 79 steps with 848 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2771.32573385551 -2840.31529199265 -2840.31768679987
Force two-norm initial, final = 132.93002 0.10455652
Force max component initial, final = 44.430635 0.009826372
Final line search alpha, max atom move = 1 0.009826372
Iterations, force evaluations = 79 148
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 10.586 | 10.586 | 10.586 | 0.0 | 99.59
Neigh | 0.01006 | 0.01006 | 0.01006 | 0.0 | 0.09
Comm | 0.017158 | 0.017158 | 0.017158 | 0.0 | 0.16
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01666 | | | 0.16
Nlocal: 848 ave 848 max 848 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4672 ave 4672 max 4672 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: 65776 ave 65776 max 65776 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 65776
Ave neighs/atom = 77.566038
Neighbor list builds = 1
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 = 9 35 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 : 79
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 4.55 | 4.55 | 4.55 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
79 0 -2840.3177 0 -2840.3177 3959.3713 14027.457
89 0 -2840.5972 0 -2840.5972 -29.064908 14097.237
Loop time of 0.902382 on 1 procs for 10 steps with 848 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 =
-2840.31768679987 -2840.5972028947 -2840.59721309215
Force two-norm initial, final = 74.008257 0.52067529
Force max component initial, final = 69.771214 0.27820359
Final line search alpha, max atom move = 0.0059937311 0.0016674775
Iterations, force evaluations = 10 11
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.88562 | 0.88562 | 0.88562 | 0.0 | 98.14
Neigh | 0.010097 | 0.010097 | 0.010097 | 0.0 | 1.12
Comm | 0.0015304 | 0.0015304 | 0.0015304 | 0.0 | 0.17
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.005132 | | | 0.57
Nlocal: 848 ave 848 max 848 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4652 ave 4652 max 4652 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: 65824 ave 65824 max 65824 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 65824
Ave neighs/atom = 77.622642
Neighbor list builds = 1
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 = 9 35 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) = 4.747 | 4.747 | 4.747 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2840.5972 0 -2840.5972 -29.064908
Loop time of 6.615e-06 on 1 procs for 0 steps with 848 atoms
0.0% 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 | | 6.615e-06 | | |100.00
Nlocal: 848 ave 848 max 848 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4652 ave 4652 max 4652 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: 65824 ave 65824 max 65824 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 65824
Ave neighs/atom = 77.622642
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 = 9 35 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) = 4.747 | 4.747 | 4.747 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 -2840.5972 -2840.5972 29.411879 118.84475 4.0330279 -29.064908 -29.064908 -27.835879 -27.831364 -31.527481 2.5998282 451.29836
Loop time of 7.136e-06 on 1 procs for 0 steps with 848 atoms
224.2% 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 | | 7.136e-06 | | |100.00
Nlocal: 848 ave 848 max 848 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4652 ave 4652 max 4652 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 32912 ave 32912 max 32912 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 65824 ave 65824 max 65824 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 65824
Ave neighs/atom = 77.622642
Neighbor list builds = 0
Dangerous builds = 0
848
-2840.59721309215 eV
2.59982822687154 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:12