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 = 3.5181211 3.5181211 3.5181211
Created orthogonal box = (0.0000000 -46.673151 0.0000000) to (16.501451 46.673151 4.9753746)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 6.0005275 5.3037672 4.9753746
Created 350 atoms
using lattice units in orthogonal box = (0.0000000 -46.673151 0.0000000) to (16.501451 46.673151 4.9753746)
create_atoms CPU = 0.001 seconds
350 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 6.0005275 5.3037672 4.9753746
Created 358 atoms
using lattice units in orthogonal box = (0.0000000 -46.673151 0.0000000) to (16.501451 46.673151 4.9753746)
create_atoms CPU = 0.001 seconds
358 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 = 9.6
ghost atom cutoff = 9.6
binsize = 4.8, bins = 4 20 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 9.6
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Deleted 4 atoms, new total = 704
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_306032198193_000#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 = 9.6
ghost atom cutoff = 9.6
binsize = 4.8, bins = 4 20 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 9.6
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) = 5.406 | 5.406 | 5.406 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -3070.1449 0 -3070.1449 6935.4958
36 0 -3081.7031 0 -3081.7031 4457.6522
Loop time of 1.03855 on 1 procs for 36 steps with 704 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 =
-3070.14489749683 -3081.70081420198 -3081.70310947164
Force two-norm initial, final = 22.871502 0.11911256
Force max component initial, final = 3.7630777 0.012185051
Final line search alpha, max atom move = 1.0000000 0.012185051
Iterations, force evaluations = 36 70
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.0293 | 1.0293 | 1.0293 | 0.0 | 99.11
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0054382 | 0.0054382 | 0.0054382 | 0.0 | 0.52
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.003805 | | | 0.37
Nlocal: 704.000 ave 704 max 704 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8088.00 ave 8088 max 8088 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: 226500.0 ave 226500 max 226500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 226500
Ave neighs/atom = 321.73295
Neighbor list builds = 0
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 = 9.6
ghost atom cutoff = 9.6
binsize = 4.8, bins = 4 20 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 9.6
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up cg style minimization ...
Unit style : metal
Current step : 36
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 5.409 | 5.409 | 5.409 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
36 0 -3081.7031 0 -3081.7031 4457.6522 7663.8153
42 0 -3081.8352 0 -3081.8352 -14.589922 7684.3097
Loop time of 0.133676 on 1 procs for 6 steps with 704 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 =
-3081.70310947164 -3081.83523866011 -3081.83524469767
Force two-norm initial, final = 54.796315 0.22959778
Force max component initial, final = 53.112629 0.12763022
Final line search alpha, max atom move = 0.0029679219 0.00037879653
Iterations, force evaluations = 6 8
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.13053 | 0.13053 | 0.13053 | 0.0 | 97.65
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00057359 | 0.00057359 | 0.00057359 | 0.0 | 0.43
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.002573 | | | 1.93
Nlocal: 704.000 ave 704 max 704 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 8013.00 ave 8013 max 8013 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: 228768.0 ave 228768 max 228768 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 228768
Ave neighs/atom = 324.95455
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 = 9.6
ghost atom cutoff = 9.6
binsize = 4.8, bins = 4 20 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 9.6
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) = 5.546 | 5.546 | 5.546 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -3081.8352 0 -3081.8352 -14.589922
Loop time of 2.403e-06 on 1 procs for 0 steps with 704 atoms
166.5% 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 | | 2.403e-06 | | |100.00
Nlocal: 704.000 ave 704 max 704 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7908.00 ave 7908 max 7908 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: 225568.0 ave 225568 max 225568 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 225568
Ave neighs/atom = 320.40909
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 = 9.6
ghost atom cutoff = 9.6
binsize = 4.8, bins = 4 20 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 9.6
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) = 5.546 | 5.546 | 5.546 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 -3081.8352 -3081.8352 16.497323 93.811066 4.9652064 -14.589922 -14.589922 -26.604211 -12.227895 -4.9376582 2.3482326 202.38657
Loop time of 2.595e-06 on 1 procs for 0 steps with 704 atoms
231.2% 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 | | 2.595e-06 | | |100.00
Nlocal: 704.000 ave 704 max 704 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7908.00 ave 7908 max 7908 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 112784.0 ave 112784 max 112784 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 225568.0 ave 225568 max 225568 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 225568
Ave neighs/atom = 320.40909
Neighbor list builds = 0
Dangerous builds = 0
704
-3081.83524469767 eV
2.34823263609103 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:01