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 -51.796803 0) to (25.898401 51.796803 4.0446508)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 5.6850149 5.6850149 4.0446508
Created 328 atoms
using lattice units in orthogonal box = (0 -51.796803 0) to (25.898401 51.796803 4.0446508)
create_atoms CPU = 0.002 seconds
328 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 5.6850149 5.6850149 4.0446508
Created 330 atoms
using lattice units in orthogonal box = (0 -51.796803 0) to (25.898401 51.796803 4.0446508)
create_atoms CPU = 0.001 seconds
330 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 = 8 31 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 = 658
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 = 8 31 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) = 4.509 | 4.509 | 4.509 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2111.6684 0 -2111.6684 26945.153
71 0 -2205.6167 0 -2205.6167 5012.531
Loop time of 7.67034 on 1 procs for 71 steps with 658 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 =
-2111.66835178874 -2205.61503390412 -2205.61669476489
Force two-norm initial, final = 143.03744 0.10908035
Force max component initial, final = 38.135506 0.027295399
Final line search alpha, max atom move = 1 0.027295399
Iterations, force evaluations = 71 129
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 7.6238 | 7.6238 | 7.6238 | 0.0 | 99.39
Neigh | 0.019197 | 0.019197 | 0.019197 | 0.0 | 0.25
Comm | 0.014307 | 0.014307 | 0.014307 | 0.0 | 0.19
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01303 | | | 0.17
Nlocal: 658 ave 658 max 658 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4220 ave 4220 max 4220 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: 51212 ave 51212 max 51212 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 51212
Ave neighs/atom = 77.829787
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 = 8 31 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 : 71
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 4.505 | 4.505 | 4.505 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
71 0 -2205.6167 0 -2205.6167 5012.531 10851.429
80 0 -2205.8286 0 -2205.8286 12.503666 10918.986
Loop time of 0.669881 on 1 procs for 9 steps with 658 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 =
-2205.61669476489 -2205.82859424798 -2205.82863098166
Force two-norm initial, final = 66.045851 0.36416362
Force max component initial, final = 58.427174 0.30731589
Final line search alpha, max atom move = 0.0011301316 0.00034730739
Iterations, force evaluations = 9 11
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.66509 | 0.66509 | 0.66509 | 0.0 | 99.28
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0009792 | 0.0009792 | 0.0009792 | 0.0 | 0.15
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.003814 | | | 0.57
Nlocal: 658 ave 658 max 658 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3882 ave 3882 max 3882 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: 51200 ave 51200 max 51200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 51200
Ave neighs/atom = 77.81155
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 = 8 31 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) = 4.693 | 4.693 | 4.693 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2205.8286 0 -2205.8286 12.503666
Loop time of 6.516e-06 on 1 procs for 0 steps with 658 atoms
245.5% 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 | | 6.516e-06 | | |100.00
Nlocal: 658 ave 658 max 658 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3882 ave 3882 max 3882 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: 51164 ave 51164 max 51164 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 51164
Ave neighs/atom = 77.756839
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 = 8 31 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) = 4.693 | 4.693 | 4.693 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 -2205.8286 -2205.8286 25.897069 104.41602 4.0379841 12.503666 12.503666 45.091085 1.2950112 -8.8750985 2.5599771 180.99983
Loop time of 6.786e-06 on 1 procs for 0 steps with 658 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: 658 ave 658 max 658 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3882 ave 3882 max 3882 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 25582 ave 25582 max 25582 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 51164 ave 51164 max 51164 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 51164
Ave neighs/atom = 77.756839
Neighbor list builds = 0
Dangerous builds = 0
658
-2205.82863098166 eV
2.55997712648802 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:08