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 -69.586803 0) to (34.793402 69.586803 4.0446508)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 5.6421732 5.6421732 4.0446508
Created 592 atoms
using lattice units in orthogonal box = (0 -69.586803 0) to (34.793402 69.586803 4.0446508)
create_atoms CPU = 0.003 seconds
592 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 5.6421732 5.6421732 4.0446508
Created 594 atoms
using lattice units in orthogonal box = (0 -69.586803 0) to (34.793402 69.586803 4.0446508)
create_atoms CPU = 0.002 seconds
594 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 = 11 41 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 = 1186
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 = 11 41 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) = 4.642 | 4.642 | 4.642 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -3872.4214 0 -3872.4214 17747.776
78 0 -3976.5031 0 -3976.5031 3825.4625
Loop time of 14.5709 on 1 procs for 78 steps with 1186 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 =
-3872.42138367903 -3976.49977776229 -3976.5031006167
Force two-norm initial, final = 132.71501 0.15280333
Force max component initial, final = 39.360119 0.026685184
Final line search alpha, max atom move = 1 0.026685184
Iterations, force evaluations = 78 144
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 14.495 | 14.495 | 14.495 | 0.0 | 99.48
Neigh | 0.029986 | 0.029986 | 0.029986 | 0.0 | 0.21
Comm | 0.024223 | 0.024223 | 0.024223 | 0.0 | 0.17
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.02151 | | | 0.15
Nlocal: 1186 ave 1186 max 1186 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6959 ave 6959 max 6959 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: 92200 ave 92200 max 92200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 92200
Ave neighs/atom = 77.740304
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 = 11 41 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 : 78
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 4.642 | 4.642 | 4.642 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
78 0 -3976.5031 0 -3976.5031 3825.4625 19585.506
85 0 -3976.7532 0 -3976.7532 -67.025066 19680.742
Loop time of 0.884918 on 1 procs for 7 steps with 1186 atoms
100.1% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-3976.50310061669 -3976.75121247373 -3976.75321971048
Force two-norm initial, final = 92.994834 1.5019651
Force max component initial, final = 83.962967 1.1140737
Final line search alpha, max atom move = 0.00022720148 0.0002531192
Iterations, force evaluations = 7 8
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.87889 | 0.87889 | 0.87889 | 0.0 | 99.32
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0013082 | 0.0013082 | 0.0013082 | 0.0 | 0.15
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.004721 | | | 0.53
Nlocal: 1186 ave 1186 max 1186 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6955 ave 6955 max 6955 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: 92208 ave 92208 max 92208 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 92208
Ave neighs/atom = 77.747049
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 = 11 42 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) = 4.866 | 4.866 | 4.866 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -3976.7532 0 -3976.7532 -67.025066
Loop time of 6.284e-06 on 1 procs for 0 steps with 1186 atoms
222.8% 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 | | 6.284e-06 | | |100.00
Nlocal: 1186 ave 1186 max 1186 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6955 ave 6955 max 6955 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: 92128 ave 92128 max 92128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 92128
Ave neighs/atom = 77.679595
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 = 11 42 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) = 4.866 | 4.866 | 4.866 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 -3976.7532 -3976.7532 34.78523 140.0953 4.0385274 -67.025066 -67.025066 -41.808985 -68.708631 -90.557582 2.536511 375.2365
Loop time of 6.696e-06 on 1 procs for 0 steps with 1186 atoms
298.7% 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 | | 6.696e-06 | | |100.00
Nlocal: 1186 ave 1186 max 1186 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6955 ave 6955 max 6955 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 46064 ave 46064 max 46064 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 92128 ave 92128 max 92128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 92128
Ave neighs/atom = 77.679595
Neighbor list builds = 0
Dangerous builds = 0
1186
-3976.75321971048 eV
2.53651098843538 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:16