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 = 4.049999 4.049999 4.049999
Created orthogonal box = (0 -76.415228 0) to (38.207614 76.415228 4.049999)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 5.5808875 5.5808875 4.049999
Created 712 atoms
using lattice units in orthogonal box = (0 -76.415228 0) to (38.207614 76.415228 4.049999)
create_atoms CPU = 0.003 seconds
712 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 5.5808875 5.5808875 4.049999
Created 714 atoms
using lattice units in orthogonal box = (0 -76.415228 0) to (38.207614 76.415228 4.049999)
create_atoms CPU = 0.002 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 = 8
ghost atom cutoff = 8
binsize = 4, bins = 10 39 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
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_093637366498_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 = 8
ghost atom cutoff = 8
binsize = 4, bins = 10 39 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 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) = 5.11 | 5.11 | 5.11 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -4615.6513 0 -4615.6513 26023.34
74 0 -4780.1903 0 -4780.1903 3877.837
Loop time of 35.98 on 1 procs for 74 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 =
-4615.65128929718 -4780.18723365939 -4780.19032784857
Force two-norm initial, final = 201.91114 0.16346789
Force max component initial, final = 42.698878 0.030740791
Final line search alpha, max atom move = 1 0.030740791
Iterations, force evaluations = 74 136
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 35.925 | 35.925 | 35.925 | 0.0 | 99.85
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.030726 | 0.030726 | 0.030726 | 0.0 | 0.09
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.02436 | | | 0.07
Nlocal: 1426 ave 1426 max 1426 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9774 ave 9774 max 9774 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: 190928 ave 190928 max 190928 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 190928
Ave neighs/atom = 133.8906
Neighbor list builds = 0
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 = 8
ghost atom cutoff = 8
binsize = 4, bins = 10 39 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up cg style minimization ...
Unit style : metal
Current step : 74
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 5.11 | 5.11 | 5.11 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
74 0 -4780.1903 0 -4780.1903 3877.837 23649.107
82 0 -4780.5412 0 -4780.5412 69.503206 23760.423
Loop time of 2.62376 on 1 procs for 8 steps with 1426 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 =
-4780.19032784857 -4780.54095541259 -4780.54119885736
Force two-norm initial, final = 117.813 1.9982276
Force max component initial, final = 109.16226 1.6641459
Final line search alpha, max atom move = 0.00047494954 0.00079038534
Iterations, force evaluations = 8 9
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.589 | 2.589 | 2.589 | 0.0 | 98.68
Neigh | 0.024296 | 0.024296 | 0.024296 | 0.0 | 0.93
Comm | 0.0026968 | 0.0026968 | 0.0026968 | 0.0 | 0.10
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.007743 | | | 0.30
Nlocal: 1426 ave 1426 max 1426 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9729 ave 9729 max 9729 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: 190328 ave 190328 max 190328 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 190328
Ave neighs/atom = 133.46985
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 = 8
ghost atom cutoff = 8
binsize = 4, bins = 10 39 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 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) = 5.353 | 5.353 | 5.353 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -4780.5412 0 -4780.5412 69.503206
Loop time of 6.335e-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 | | 6.335e-06 | | |100.00
Nlocal: 1426 ave 1426 max 1426 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9729 ave 9729 max 9729 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: 190328 ave 190328 max 190328 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 190328
Ave neighs/atom = 133.46985
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 = 8
ghost atom cutoff = 8
binsize = 4, bins = 10 39 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 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) = 5.353 | 5.353 | 5.353 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 -4780.5412 -4780.5412 38.177874 153.91247 4.0436039 69.503206 69.503206 64.856461 113.0086 30.644554 2.5438551 559.17053
Loop time of 6.786e-06 on 1 procs for 0 steps with 1426 atoms
294.7% 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: 1426 ave 1426 max 1426 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9729 ave 9729 max 9729 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 95164 ave 95164 max 95164 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 190328 ave 190328 max 190328 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 190328
Ave neighs/atom = 133.46985
Neighbor list builds = 0
Dangerous builds = 0
1426
-4780.54119885736 eV
2.54385508678326 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:40