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 -76.314318 0) to (38.157159 76.314318 4.0446508)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 5.5735176 5.5735176 4.0446508
Created 712 atoms
using lattice units in orthogonal box = (0 -76.314318 0) to (38.157159 76.314318 4.0446508)
create_atoms CPU = 0.003 seconds
712 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 5.5735176 5.5735176 4.0446508
Created 714 atoms
using lattice units in orthogonal box = (0 -76.314318 0) to (38.157159 76.314318 4.0446508)
create_atoms CPU = 0.003 seconds
714 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 = 12 45 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 = 1426
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 = 12 45 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) = 5.083 | 5.083 | 5.083 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -4634.9801 0 -4634.9801 18429.684
86 0 -4780.8463 0 -4780.8463 3828.9098
Loop time of 19.1478 on 1 procs for 86 steps with 1426 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 =
-4634.98006488203 -4780.84186577958 -4780.84631210485
Force two-norm initial, final = 202.41582 0.17089419
Force max component initial, final = 64.159898 0.031602187
Final line search alpha, max atom move = 1 0.031602187
Iterations, force evaluations = 86 158
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 19.055 | 19.055 | 19.055 | 0.0 | 99.51
Neigh | 0.034764 | 0.034764 | 0.034764 | 0.0 | 0.18
Comm | 0.030289 | 0.030289 | 0.030289 | 0.0 | 0.16
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.02789 | | | 0.15
Nlocal: 1426 ave 1426 max 1426 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7824 ave 7824 max 7824 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: 110808 ave 110808 max 110808 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 110808
Ave neighs/atom = 77.70547
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 = 12 45 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 : 86
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 5.075 | 5.075 | 5.075 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
86 0 -4780.8463 0 -4780.8463 3828.9098 23555.541
94 0 -4781.1721 0 -4781.1721 11.296283 23667.826
Loop time of 1.17776 on 1 procs for 8 steps with 1426 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 =
-4780.84631210485 -4781.17201492581 -4781.17210512109
Force two-norm initial, final = 113.83583 0.71518701
Force max component initial, final = 104.24255 0.49340273
Final line search alpha, max atom move = 0.00049269016 0.00024309467
Iterations, force evaluations = 8 9
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.1534 | 1.1534 | 1.1534 | 0.0 | 97.93
Neigh | 0.016342 | 0.016342 | 0.016342 | 0.0 | 1.39
Comm | 0.001947 | 0.001947 | 0.001947 | 0.0 | 0.17
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.006106 | | | 0.52
Nlocal: 1426 ave 1426 max 1426 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6974 ave 6974 max 6974 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: 110744 ave 110744 max 110744 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 110744
Ave neighs/atom = 77.660589
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 = 12 46 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) = 5.303 | 5.303 | 5.303 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -4781.1721 0 -4781.1721 11.296283
Loop time of 6.115e-06 on 1 procs for 0 steps with 1426 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 | | 6.115e-06 | | |100.00
Nlocal: 1426 ave 1426 max 1426 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6974 ave 6974 max 6974 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: 110744 ave 110744 max 110744 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 110744
Ave neighs/atom = 77.660589
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 = 12 46 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) = 5.303 | 5.303 | 5.303 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 -4781.1721 -4781.1721 38.13126 153.69307 4.0385264 11.296283 11.296283 33.377872 21.834512 -21.323536 2.5312115 544.44354
Loop time of 7.327e-06 on 1 procs for 0 steps with 1426 atoms
327.6% 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 | | 7.327e-06 | | |100.00
Nlocal: 1426 ave 1426 max 1426 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6974 ave 6974 max 6974 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 55372 ave 55372 max 55372 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 110744 ave 110744 max 110744 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 110744
Ave neighs/atom = 77.660589
Neighbor list builds = 0
Dangerous builds = 0
1426
-4781.17210512109 eV
2.53121146250942 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:21