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 = 4.0500001 4.0500001 4.0500001
Created orthogonal box = (0.0000000 -46.530958 0.0000000) to (32.902356 46.530958 5.7275650)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 6.9792877 6.3451307 5.7275650
Created 528 atoms
using lattice units in orthogonal box = (0.0000000 -46.530958 0.0000000) to (32.902356 46.530958 5.7275650)
create_atoms CPU = 0.004 seconds
528 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 6.9792877 6.3451307 5.7275650
Created 532 atoms
using lattice units in orthogonal box = (0.0000000 -46.530958 0.0000000) to (32.902356 46.530958 5.7275650)
create_atoms CPU = 0.003 seconds
532 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 = 8.28721
ghost atom cutoff = 8.28721
binsize = 4.143605, bins = 8 23 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 8.28721
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Deleted 12 atoms, new total = 1048
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_751354403791_005#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 = 8.28721
ghost atom cutoff = 8.28721
binsize = 4.143605, bins = 8 23 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.28721
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) = 5.009 | 5.009 | 5.009 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -3480.8246 0 -3480.8246 -555.55618
78 0 -3513.6627 0 -3513.6627 -2944.0834
Loop time of 2.25267 on 1 procs for 78 steps with 1048 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 =
-3480.82461085016 -3513.65952530581 -3513.66273722601
Force two-norm initial, final = 18.200299 0.13617759
Force max component initial, final = 3.5978682 0.023110620
Final line search alpha, max atom move = 1.0000000 0.023110620
Iterations, force evaluations = 78 134
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.1696 | 2.1696 | 2.1696 | 0.0 | 96.31
Neigh | 0.044251 | 0.044251 | 0.044251 | 0.0 | 1.96
Comm | 0.020169 | 0.020169 | 0.020169 | 0.0 | 0.90
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01863 | | | 0.83
Nlocal: 1048.00 ave 1048 max 1048 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5924.00 ave 5924 max 5924 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: 146160.0 ave 146160 max 146160 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 146160
Ave neighs/atom = 139.46565
Neighbor list builds = 2
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 = 8.28721
ghost atom cutoff = 8.28721
binsize = 4.143605, bins = 8 23 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.28721
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up cg style minimization ...
Unit style : metal
Current step : 78
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 5.009 | 5.009 | 5.009 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
78 0 -3513.6627 0 -3513.6627 -2944.0834 17537.554
82 0 -3513.7341 0 -3513.7341 -14.250885 17472.302
Loop time of 0.128926 on 1 procs for 4 steps with 1048 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 =
-3513.66273722599 -3513.73411367174 -3513.73411894881
Force two-norm initial, final = 57.088103 0.33170843
Force max component initial, final = 41.689235 0.22131280
Final line search alpha, max atom move = 0.014065611 0.0031128999
Iterations, force evaluations = 4 7
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.12444 | 0.12444 | 0.12444 | 0.0 | 96.52
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00098575 | 0.00098575 | 0.00098575 | 0.0 | 0.76
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.003503 | | | 2.72
Nlocal: 1048.00 ave 1048 max 1048 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5892.00 ave 5892 max 5892 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: 146080.0 ave 146080 max 146080 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 146080
Ave neighs/atom = 139.38931
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 = 8.28721
ghost atom cutoff = 8.28721
binsize = 4.143605, bins = 8 23 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.28721
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) = 5.147 | 5.147 | 5.147 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -3513.7341 0 -3513.7341 -14.250885
Loop time of 6.315e-06 on 1 procs for 0 steps with 1048 atoms
190.0% 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 | | 6.315e-06 | | |100.00
Nlocal: 1048.00 ave 1048 max 1048 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5892.00 ave 5892 max 5892 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: 146168.0 ave 146168 max 146168 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 146168
Ave neighs/atom = 139.47328
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 = 8.28721
ghost atom cutoff = 8.28721
binsize = 4.143605, bins = 8 23 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.28721
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) = 5.147 | 5.147 | 5.147 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 -3513.7341 -3513.7341 32.873252 92.812819 5.7266347 -14.250885 -14.250885 -4.9309071 -17.531085 -20.290663 2.6581083 598.61344
Loop time of 6.966e-06 on 1 procs for 0 steps with 1048 atoms
258.4% 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 | | 6.966e-06 | | |100.00
Nlocal: 1048.00 ave 1048 max 1048 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5892.00 ave 5892 max 5892 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 73084.0 ave 73084 max 73084 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 146168.0 ave 146168 max 146168 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 146168
Ave neighs/atom = 139.47328
Neighbor list builds = 0
Dangerous builds = 0
1048
-3513.73411890294 eV
2.6581082604409 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:03