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 -72.803714 0) to (51.48 72.803714 5.72)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 6.9911111 6.7410846 5.72
Created 1294 atoms
using lattice units in orthogonal box = (0 -72.803714 0) to (51.48 72.803714 5.72)
create_atoms CPU = 0.011 seconds
1294 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 6.9911111 6.7410846 5.72
Created 1298 atoms
using lattice units in orthogonal box = (0 -72.803714 0) to (51.48 72.803714 5.72)
create_atoms CPU = 0.010 seconds
1298 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 = 16 43 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 8 atoms, new total = 2584
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 = 16 43 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) = 5.701 | 5.701 | 5.701 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -8373.2573 0 -8373.2573 15956.875
81 0 -8665.9425 0 -8665.9425 98.202876
Loop time of 29.1961 on 1 procs for 81 steps with 2584 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 =
-8373.25727186957 -8665.93444819909 -8665.94245264755
Force two-norm initial, final = 323.32503 0.21073254
Force max component initial, final = 54.732982 0.019898645
Final line search alpha, max atom move = 1 0.019898645
Iterations, force evaluations = 81 139
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 29.058 | 29.058 | 29.058 | 0.0 | 99.53
Neigh | 0.065775 | 0.065775 | 0.065775 | 0.0 | 0.23
Comm | 0.033364 | 0.033364 | 0.033364 | 0.0 | 0.11
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.03851 | | | 0.13
Nlocal: 2584 ave 2584 max 2584 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9287 ave 9287 max 9287 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: 200632 ave 200632 max 200632 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 200632
Ave neighs/atom = 77.643963
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 = 16 43 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 : 81
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 5.708 | 5.708 | 5.708 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
81 0 -8665.9425 0 -8665.9425 98.202876 42876.378
83 0 -8665.9669 0 -8665.9669 167.57935 42872.716
Loop time of 0.810748 on 1 procs for 2 steps with 2584 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 =
-8665.94245264755 -8665.96417733745 -8665.96694863306
Force two-norm initial, final = 29.248788 9.0364899
Force max component initial, final = 26.215327 8.2415247
Final line search alpha, max atom move = 0.00011728943 0.00096664372
Iterations, force evaluations = 2 3
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.80679 | 0.80679 | 0.80679 | 0.0 | 99.51
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00085707 | 0.00085707 | 0.00085707 | 0.0 | 0.11
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.003105 | | | 0.38
Nlocal: 2584 ave 2584 max 2584 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9897 ave 9897 max 9897 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: 200416 ave 200416 max 200416 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 200416
Ave neighs/atom = 77.560372
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 = 16 43 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) = 5.971 | 5.971 | 5.971 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -8665.9669 0 -8665.9669 167.57935
Loop time of 6.305e-06 on 1 procs for 0 steps with 2584 atoms
237.9% 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 | | 6.305e-06 | | |100.00
Nlocal: 2584 ave 2584 max 2584 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9897 ave 9897 max 9897 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: 200404 ave 200404 max 200404 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 200404
Ave neighs/atom = 77.555728
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 = 16 43 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) = 5.971 | 5.971 | 5.971 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 -8665.9669 -8665.9669 51.448825 145.77922 5.7162329 167.57935 167.57935 107.22547 308.3536 87.158962 2.6944985 1523.0947
Loop time of 7.256e-06 on 1 procs for 0 steps with 2584 atoms
261.9% 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 | | 7.256e-06 | | |100.00
Nlocal: 2584 ave 2584 max 2584 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9897 ave 9897 max 9897 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 100202 ave 100202 max 100202 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 200404 ave 200404 max 200404 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 200404
Ave neighs/atom = 77.555728
Neighbor list builds = 0
Dangerous builds = 0
2584
-8665.96694863306 eV
2.69449853278011 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:31