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 -63.179465 0) to (31.589732 63.179465 4.0446508)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 5.6965091 5.6965091 4.0446508
Created 488 atoms
using lattice units in orthogonal box = (0 -63.179465 0) to (31.589732 63.179465 4.0446508)
create_atoms CPU = 0.002 seconds
488 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 5.6965091 5.6965091 4.0446508
Created 490 atoms
using lattice units in orthogonal box = (0 -63.179465 0) to (31.589732 63.179465 4.0446508)
create_atoms CPU = 0.002 seconds
490 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 = 10 38 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 = 978
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 = 10 38 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) = 4.595 | 4.595 | 4.595 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -3172.3142 0 -3172.3142 20988.73
75 0 -3280.3481 0 -3280.3481 3507.1009
Loop time of 11.413 on 1 procs for 75 steps with 978 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 =
-3172.31424283911 -3280.34497338255 -3280.34806487634
Force two-norm initial, final = 143.06409 0.14746152
Force max component initial, final = 29.798979 0.022733873
Final line search alpha, max atom move = 1 0.022733873
Iterations, force evaluations = 75 136
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 11.35 | 11.35 | 11.35 | 0.0 | 99.45
Neigh | 0.024952 | 0.024952 | 0.024952 | 0.0 | 0.22
Comm | 0.019836 | 0.019836 | 0.019836 | 0.0 | 0.17
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01818 | | | 0.16
Nlocal: 978 ave 978 max 978 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5992 ave 5992 max 5992 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: 76136 ave 76136 max 76136 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 76136
Ave neighs/atom = 77.848671
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 = 10 38 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 : 75
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
75 0 -3280.3481 0 -3280.3481 3507.1009 16144.809
81 0 -3280.5044 0 -3280.5044 -190.06164 16219.47
Loop time of 0.653598 on 1 procs for 6 steps with 978 atoms
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-3280.34806487635 -3280.50320270248 -3280.5044430243
Force two-norm initial, final = 68.79953 3.6873776
Force max component initial, final = 60.869647 3.014022
Final line search alpha, max atom move = 0.00022539355 0.00067934112
Iterations, force evaluations = 6 7
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.64889 | 0.64889 | 0.64889 | 0.0 | 99.28
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0010118 | 0.0010118 | 0.0010118 | 0.0 | 0.15
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.003696 | | | 0.57
Nlocal: 978 ave 978 max 978 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6005 ave 6005 max 6005 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: 76164 ave 76164 max 76164 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 76164
Ave neighs/atom = 77.877301
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 = 10 38 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) = 4.806 | 4.806 | 4.806 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -3280.5044 0 -3280.5044 -190.06164
Loop time of 5.873e-06 on 1 procs for 0 steps with 978 atoms
0.0% 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 | | 5.873e-06 | | |100.00
Nlocal: 978 ave 978 max 978 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6005 ave 6005 max 6005 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: 76100 ave 76100 max 76100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 76100
Ave neighs/atom = 77.811861
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 = 10 38 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) = 4.806 | 4.806 | 4.806 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 -3280.5044 -3280.5044 31.593731 127.05336 4.0406348 -190.06164 -190.06164 -193.91116 -78.841081 -297.43268 2.5597879 173.34125
Loop time of 6.806e-06 on 1 procs for 0 steps with 978 atoms
264.5% 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 | | 6.806e-06 | | |100.00
Nlocal: 978 ave 978 max 978 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 6005 ave 6005 max 6005 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 38050 ave 38050 max 38050 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 76100 ave 76100 max 76100 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 76100
Ave neighs/atom = 77.811861
Neighbor list builds = 0
Dangerous builds = 0
978
-3280.5044430243 eV
2.55978793586823 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:12