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 = 3.567323 3.567323 3.567323
Created orthogonal box = (0 -57.521355 0) to (28.760677 57.521355 3.567323)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 4.8671916 4.8671916 3.567323
Created 519 atoms
using lattice units in orthogonal box = (0 -57.521355 0) to (28.760677 57.521355 3.567323)
create_atoms CPU = 0.003 seconds
519 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 4.8671916 4.8671916 3.567323
Created 521 atoms
using lattice units in orthogonal box = (0 -57.521355 0) to (28.760677 57.521355 3.567323)
create_atoms CPU = 0.002 seconds
521 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 = 5.6
ghost atom cutoff = 5.6
binsize = 2.8, bins = 11 42 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 5.6
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Deleted 4 atoms, new total = 1036
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_058735400462_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 = 5.6
ghost atom cutoff = 5.6
binsize = 2.8, bins = 11 42 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 5.6
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) = 4.595 | 4.595 | 4.595 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -3992.1173 0 -3992.1173 54621.282
95 0 -4360.8945 0 -4360.8945 26615.222
Loop time of 12.2887 on 1 procs for 95 steps with 1036 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 =
-3992.11731781235 -4360.89096957734 -4360.89452405959
Force two-norm initial, final = 712.105 0.24142609
Force max component initial, final = 242.76104 0.047157322
Final line search alpha, max atom move = 1 0.047157322
Iterations, force evaluations = 95 170
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.233 | 12.233 | 12.233 | 0.0 | 99.55
Neigh | 0.010576 | 0.010576 | 0.010576 | 0.0 | 0.09
Comm | 0.021912 | 0.021912 | 0.021912 | 0.0 | 0.18
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.02287 | | | 0.19
Nlocal: 1036 ave 1036 max 1036 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5260 ave 5260 max 5260 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: 57868 ave 57868 max 57868 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 57868
Ave neighs/atom = 55.857143
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 = 5.6
ghost atom cutoff = 5.6
binsize = 2.8, bins = 11 42 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 5.6
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up cg style minimization ...
Unit style : metal
Current step : 95
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 4.595 | 4.595 | 4.595 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
95 0 -4360.8945 0 -4360.8945 26615.222 11803.224
135 0 -4365.5531 0 -4365.5531 640.04077 12240.015
Loop time of 2.68822 on 1 procs for 40 steps with 1036 atoms
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-4360.89452405959 -4365.55002111479 -4365.55305475187
Force two-norm initial, final = 386.59027 9.1449588
Force max component initial, final = 277.16623 5.4194277
Final line search alpha, max atom move = 0.00010092752 0.00054696937
Iterations, force evaluations = 40 41
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.6306 | 2.6306 | 2.6306 | 0.0 | 97.86
Neigh | 0.031346 | 0.031346 | 0.031346 | 0.0 | 1.17
Comm | 0.0056885 | 0.0056885 | 0.0056885 | 0.0 | 0.21
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.02058 | | | 0.77
Nlocal: 1036 ave 1036 max 1036 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5212 ave 5212 max 5212 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: 63956 ave 63956 max 63956 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 63956
Ave neighs/atom = 61.733591
Neighbor list builds = 3
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 = 5.6
ghost atom cutoff = 5.6
binsize = 2.8, bins = 11 43 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 5.6
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) = 4.804 | 4.804 | 4.804 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -4365.5531 0 -4365.5531 640.04077
Loop time of 6.535e-06 on 1 procs for 0 steps with 1036 atoms
214.2% 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 | | 6.535e-06 | | |100.00
Nlocal: 1036 ave 1036 max 1036 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5212 ave 5212 max 5212 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: 64146 ave 64146 max 64146 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 64146
Ave neighs/atom = 61.916988
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 = 5.6
ghost atom cutoff = 5.6
binsize = 2.8, bins = 11 43 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 5.6
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) = 4.804 | 4.804 | 4.804 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 -4365.5531 -4365.5531 29.578148 118.12528 3.5032258 640.04077 640.04077 586.27378 728.39267 605.45585 2.3114205 449.24076
Loop time of 6.876e-06 on 1 procs for 0 steps with 1036 atoms
320.0% 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 | | 6.876e-06 | | |100.00
Nlocal: 1036 ave 1036 max 1036 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5212 ave 5212 max 5212 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 32073 ave 32073 max 32073 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 64146 ave 64146 max 64146 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 64146
Ave neighs/atom = 61.916988
Neighbor list builds = 0
Dangerous builds = 0
1036
-4365.55305475186 eV
2.31142049403739 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:15