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 = 3.4986963 3.4986963 3.4986963
Created orthogonal box = (0.0000000 -56.850586 0.0000000) to (20.098480 56.850586 4.9479038)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 5.4814037 6.0292365 4.9479038
Created 530 atoms
using lattice units in orthogonal box = (0.0000000 -56.850586 0.0000000) to (20.098480 56.850586 4.9479038)
create_atoms CPU = 0.005 seconds
530 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 5.4814037 6.0292365 4.9479038
Created 530 atoms
using lattice units in orthogonal box = (0.0000000 -56.850586 0.0000000) to (20.098480 56.850586 4.9479038)
create_atoms CPU = 0.005 seconds
530 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 = 7.6
ghost atom cutoff = 7.6
binsize = 3.8, bins = 6 30 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 7.6
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Deleted 4 atoms, new total = 1056
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_715003088863_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 = 7.6
ghost atom cutoff = 7.6
binsize = 3.8, bins = 6 30 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 7.6
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) = 5.066 | 5.066 | 5.066 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -4299.7467 0 -4299.7467 13636.417
43 0 -4338.1464 0 -4338.1464 1787.7212
Loop time of 1.72191 on 1 procs for 43 steps with 1056 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 =
-4299.7466652357 -4338.14338026502 -4338.14635022103
Force two-norm initial, final = 47.781699 0.26337300
Force max component initial, final = 13.275778 0.035790703
Final line search alpha, max atom move = 1.0000000 0.035790703
Iterations, force evaluations = 43 80
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.6696 | 1.6696 | 1.6696 | 0.0 | 96.96
Neigh | 0.025908 | 0.025908 | 0.025908 | 0.0 | 1.50
Comm | 0.014793 | 0.014793 | 0.014793 | 0.0 | 0.86
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01158 | | | 0.67
Nlocal: 1056.00 ave 1056 max 1056 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7914.00 ave 7914 max 7914 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: 184732.0 ave 184732 max 184732 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 184732
Ave neighs/atom = 174.93561
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 = 7.6
ghost atom cutoff = 7.6
binsize = 3.8, bins = 6 30 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 7.6
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up cg style minimization ...
Unit style : metal
Current step : 43
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 5.066 | 5.066 | 5.066 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
43 0 -4338.1464 0 -4338.1464 1787.7212 11307.052
44 0 -4338.1472 0 -4338.1472 1317.0325 11311.536
Loop time of 0.0641757 on 1 procs for 1 steps with 1056 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 =
-4338.14635022104 -4338.14635022104 -4338.14719794611
Force two-norm initial, final = 6.0360682 0.39962295
Force max component initial, final = 4.7819158 0.26718329
Final line search alpha, max atom move = 0.00020912121 5.5873691e-05
Iterations, force evaluations = 1 2
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.062369 | 0.062369 | 0.062369 | 0.0 | 97.18
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00048081 | 0.00048081 | 0.00048081 | 0.0 | 0.75
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.001326 | | | 2.07
Nlocal: 1056.00 ave 1056 max 1056 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7914.00 ave 7914 max 7914 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: 184640.0 ave 184640 max 184640 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 184640
Ave neighs/atom = 174.84848
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 = 7.6
ghost atom cutoff = 7.6
binsize = 3.8, bins = 6 30 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 7.6
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) = 5.204 | 5.204 | 5.204 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -4338.1472 0 -4338.1472 1317.0325
Loop time of 6.385e-06 on 1 procs for 0 steps with 1056 atoms
187.9% 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 | | 6.385e-06 | | |100.00
Nlocal: 1056.00 ave 1056 max 1056 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7914.00 ave 7914 max 7914 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: 184632.0 ave 184632 max 184632 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 184632
Ave neighs/atom = 174.84091
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 = 7.6
ghost atom cutoff = 7.6
binsize = 3.8, bins = 6 30 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 7.6
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) = 5.204 | 5.204 | 5.204 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 -4338.1472 -4338.1472 20.101943 113.70117 4.9490133 1317.0325 1317.0325 -37.850608 3969.4265 19.521589 2.2741204 334.86631
Loop time of 7.067e-06 on 1 procs for 0 steps with 1056 atoms
283.0% 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 | | 7.067e-06 | | |100.00
Nlocal: 1056.00 ave 1056 max 1056 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7914.00 ave 7914 max 7914 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 92316.0 ave 92316 max 92316 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 184632.0 ave 184632 max 184632 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 184632
Ave neighs/atom = 174.84091
Neighbor list builds = 0
Dangerous builds = 0
1056
-4338.14719794611 eV
2.27412042772421 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:02