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 -45.76 0) to (5.72 45.76 4.0446508)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 5.72 5.72 4.0446508
Created 64 atoms
using lattice units in orthogonal box = (0 -45.76 0) to (5.72 45.76 4.0446508)
create_atoms CPU = 0.001 seconds
64 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 5.72 5.72 4.0446508
Created 66 atoms
using lattice units in orthogonal box = (0 -45.76 0) to (5.72 45.76 4.0446508)
create_atoms CPU = 0.001 seconds
66 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 = 2 27 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 2 atoms, new total = 128
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 = 2 27 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) = 4.395 | 4.395 | 4.395 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -430.08 0 -430.08 -0.00035483941
1 0 -430.08 0 -430.08 -0.00035483939
Loop time of 0.0359445 on 1 procs for 1 steps with 128 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 =
-430.080000016137 -430.080000016137 -430.080000016137
Force two-norm initial, final = 3.8443275e-08 1.1288143e-08
Force max component initial, final = 1.6741502e-08 4.46862e-09
Final line search alpha, max atom move = 1 4.46862e-09
Iterations, force evaluations = 1 2
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.035572 | 0.035572 | 0.035572 | 0.0 | 98.96
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00014379 | 0.00014379 | 0.00014379 | 0.0 | 0.40
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0002291 | | | 0.64
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1988 ave 1988 max 1988 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: 9984 ave 9984 max 9984 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9984
Ave neighs/atom = 78
Neighbor list builds = 0
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 = 2 27 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 : 1
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 4.395 | 4.395 | 4.395 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
1 0 -430.08 0 -430.08 -0.00035483938 2117.352
2 0 -430.08 0 -430.08 1.4027816e-06 2117.352
Loop time of 0.0363544 on 1 procs for 1 steps with 128 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 =
-430.080000016137 -430.080000016137 -430.080000016135
Force two-norm initial, final = 8.1435694e-07 4.4510408e-08
Force max component initial, final = 5.1601442e-07 3.3156002e-08
Final line search alpha, max atom move = 1 3.3156002e-08
Iterations, force evaluations = 1 2
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.035803 | 0.035803 | 0.035803 | 0.0 | 98.48
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0001339 | 0.0001339 | 0.0001339 | 0.0 | 0.37
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0004173 | | | 1.15
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1988 ave 1988 max 1988 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: 9984 ave 9984 max 9984 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9984
Ave neighs/atom = 78
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 = 2 27 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) = 4.557 | 4.557 | 4.557 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -430.08 0 -430.08 1.4027894e-06
Loop time of 9.361e-06 on 1 procs for 0 steps with 128 atoms
138.9% 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 | | 9.361e-06 | | |100.00
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1988 ave 1988 max 1988 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: 9984 ave 9984 max 9984 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9984
Ave neighs/atom = 78
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 = 2 27 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) = 4.557 | 4.557 | 4.557 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 -430.08 -430.08 5.72 91.52 4.0446508 1.4027894e-06 1.4027894e-06 1.5862852e-05 -2.5088767e-05 1.3434283e-05 2.86 8.4027461e-17
Loop time of 6.605e-06 on 1 procs for 0 steps with 128 atoms
227.1% 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 | | 6.605e-06 | | |100.00
Nlocal: 128 ave 128 max 128 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1988 ave 1988 max 1988 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 4992 ave 4992 max 4992 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 9984 ave 9984 max 9984 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 9984
Ave neighs/atom = 78
Neighbor list builds = 0
Dangerous builds = 0
128
-430.080000016134 eV
2.85999999220265 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:00