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 -45.123463 0) to (11.280866 45.123463 3.567323)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 4.5123463 4.5123463 3.567323
Created 160 atoms
using lattice units in orthogonal box = (0 -45.123463 0) to (11.280866 45.123463 3.567323)
create_atoms CPU = 0.002 seconds
160 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 4.5123463 4.5123463 3.567323
Created 162 atoms
using lattice units in orthogonal box = (0 -45.123463 0) to (11.280866 45.123463 3.567323)
create_atoms CPU = 0.001 seconds
162 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 = 5 33 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 0 atoms, new total = 322
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 = 5 33 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) = 4.426 | 4.426 | 4.426 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1256.9477 0 -1256.9477 85071.395
43 0 -1353.3534 0 -1353.3534 51012.092
Loop time of 1.96974 on 1 procs for 43 steps with 322 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 =
-1256.94769650663 -1353.35223761109 -1353.35339009412
Force two-norm initial, final = 187.16889 0.30117543
Force max component initial, final = 73.004481 0.049258414
Final line search alpha, max atom move = 1 0.049258414
Iterations, force evaluations = 43 77
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9562 | 1.9562 | 1.9562 | 0.0 | 99.31
Neigh | 0.0033993 | 0.0033993 | 0.0033993 | 0.0 | 0.17
Comm | 0.0051798 | 0.0051798 | 0.0051798 | 0.0 | 0.26
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.00495 | | | 0.25
Nlocal: 322 ave 322 max 322 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2502 ave 2502 max 2502 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: 19056 ave 19056 max 19056 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19056
Ave neighs/atom = 59.180124
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 = 5 33 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 : 43
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 4.427 | 4.427 | 4.427 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
43 0 -1353.3534 0 -1353.3534 51012.092 3631.7612
97 0 -1356.5963 0 -1356.5963 -117.87512 3761.6822
Loop time of 1.32255 on 1 procs for 54 steps with 322 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 =
-1353.35339009412 -1356.59599309867 -1356.59630885062
Force two-norm initial, final = 217.15606 1.682711
Force max component initial, final = 181.99587 1.2363997
Final line search alpha, max atom move = 0.00028149688 0.00034804265
Iterations, force evaluations = 54 57
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.2917 | 1.2917 | 1.2917 | 0.0 | 97.67
Neigh | 0.013388 | 0.013388 | 0.013388 | 0.0 | 1.01
Comm | 0.0040229 | 0.0040229 | 0.0040229 | 0.0 | 0.30
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01342 | | | 1.01
Nlocal: 322 ave 322 max 322 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2646 ave 2646 max 2646 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: 18760 ave 18760 max 18760 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18760
Ave neighs/atom = 58.26087
Neighbor list builds = 4
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 = 4 34 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) = 4.6 | 4.6 | 4.6 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1356.5963 0 -1356.5963 -117.87512
Loop time of 5.904e-06 on 1 procs for 0 steps with 322 atoms
203.3% 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 | | 5.904e-06 | | |100.00
Nlocal: 322 ave 322 max 322 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2654 ave 2654 max 2654 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: 19460 ave 19460 max 19460 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19460
Ave neighs/atom = 60.434783
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 = 4 34 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) = 4.6 | 4.6 | 4.6 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 -1356.5963 -1356.5963 11.191041 94.946972 3.5402219 -117.87512 -117.87512 110.32862 58.652968 -522.60695 2.2995445 154.6746
Loop time of 7.086e-06 on 1 procs for 0 steps with 322 atoms
239.9% 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 | | 7.086e-06 | | |100.00
Nlocal: 322 ave 322 max 322 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2654 ave 2654 max 2654 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9730 ave 9730 max 9730 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 19460 ave 19460 max 19460 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 19460
Ave neighs/atom = 60.434783
Neighbor list builds = 0
Dangerous builds = 0
322
-1356.59630885062 eV
2.29954448831171 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:03