LAMMPS (30 Jul 2021)
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 = 4.0500001 4.0500001 4.0500001
Created orthogonal box = (0.0000000 -49.931754 0.0000000) to (17.653541 49.931754 5.7275650)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 6.5039362 5.2559741 5.7275650
Created 304 atoms
using lattice units in orthogonal box = (0.0000000 -49.931754 0.0000000) to (17.653541 49.931754 5.7275650)
create_atoms CPU = 0.002 seconds
304 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 6.5039362 5.2559741 5.7275650
Created 306 atoms
using lattice units in orthogonal box = (0.0000000 -49.931754 0.0000000) to (17.653541 49.931754 5.7275650)
create_atoms CPU = 0.002 seconds
306 atoms in group lower
Displacing atoms ...
System init for delete_atoms ...
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.28721
ghost atom cutoff = 8.28721
binsize = 4.143605, bins = 5 25 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 8.28721
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Deleted 6 atoms, new total = 604
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_751354403791_005#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:189)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.28721
ghost atom cutoff = 8.28721
binsize = 4.143605, bins = 5 25 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.28721
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) = 4.540 | 4.540 | 4.540 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2006.5068 0 -2006.5068 784.83808
57 0 -2024.5542 0 -2024.5542 -1093.2677
Loop time of 1.05225 on 1 procs for 57 steps with 604 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 =
-2006.50676789073 -2024.55255077231 -2024.55418778824
Force two-norm initial, final = 14.951168 0.092891243
Force max component initial, final = 4.3455188 0.012801773
Final line search alpha, max atom move = 1.0000000 0.012801773
Iterations, force evaluations = 57 104
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.0177 | 1.0177 | 1.0177 | 0.0 | 96.72
Neigh | 0.012841 | 0.012841 | 0.012841 | 0.0 | 1.22
Comm | 0.01197 | 0.01197 | 0.01197 | 0.0 | 1.14
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.009707 | | | 0.92
Nlocal: 604.000 ave 604 max 604 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4624.00 ave 4624 max 4624 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 84164.0 ave 84164 max 84164 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 84164
Ave neighs/atom = 139.34437
Neighbor list builds = 1
Dangerous builds = 0
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.28721
ghost atom cutoff = 8.28721
binsize = 4.143605, bins = 5 25 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.28721
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up cg style minimization ...
Unit style : metal
Current step : 57
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 4.541 | 4.541 | 4.541 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
57 0 -2024.5542 0 -2024.5542 -1093.2677 10097.38
60 0 -2024.5684 0 -2024.5684 34.384511 10083.114
Loop time of 0.049474 on 1 procs for 3 steps with 604 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 =
-2024.55418778824 -2024.56810340039 -2024.56839530636
Force two-norm initial, final = 14.599567 0.67636558
Force max component initial, final = 13.487203 0.66809506
Final line search alpha, max atom move = 0.00040538746 0.00027083736
Iterations, force evaluations = 3 4
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.047358 | 0.047358 | 0.047358 | 0.0 | 95.72
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00051712 | 0.00051712 | 0.00051712 | 0.0 | 1.05
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.001599 | | | 3.23
Nlocal: 604.000 ave 604 max 604 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4732.00 ave 4732 max 4732 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 84168.0 ave 84168 max 84168 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 84168
Ave neighs/atom = 139.35099
Neighbor list builds = 0
Dangerous builds = 0
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.28721
ghost atom cutoff = 8.28721
binsize = 4.143605, bins = 5 25 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.28721
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) = 4.679 | 4.679 | 4.679 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2024.5684 0 -2024.5684 34.384511
Loop time of 7.418e-06 on 1 procs for 0 steps with 604 atoms
148.3% 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 | | 7.418e-06 | | |100.00
Nlocal: 604.000 ave 604 max 604 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4732.00 ave 4732 max 4732 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0.00000 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 84156.0 ave 84156 max 84156 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 84156
Ave neighs/atom = 139.33113
Neighbor list builds = 0
Dangerous builds = 0
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.28721
ghost atom cutoff = 8.28721
binsize = 4.143605, bins = 5 25 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.28721
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) = 4.679 | 4.679 | 4.679 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 -2024.5684 -2024.5684 17.615945 99.948385 5.7268124 34.384511 34.384511 -2.0257765 106.24852 -1.0692107 2.6858199 499.22174
Loop time of 8.229e-06 on 1 procs for 0 steps with 604 atoms
194.4% 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 | | 8.229e-06 | | |100.00
Nlocal: 604.000 ave 604 max 604 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4732.00 ave 4732 max 4732 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 42078.0 ave 42078 max 42078 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 84156.0 ave 84156 max 84156 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 84156
Ave neighs/atom = 139.33113
Neighbor list builds = 0
Dangerous builds = 0
604
-2024.56839527992 eV
2.68581987299597 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:01