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 -40.446508 0) to (4.0446508 40.446508 4.0446508)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 4.0446508 4.0446508 4.0446508
Created 40 atoms
using lattice units in orthogonal box = (0 -40.446508 0) to (4.0446508 40.446508 4.0446508)
create_atoms CPU = 0.001 seconds
40 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 4.0446508 4.0446508 4.0446508
Created 42 atoms
using lattice units in orthogonal box = (0 -40.446508 0) to (4.0446508 40.446508 4.0446508)
create_atoms CPU = 0.000 seconds
42 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 24 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 = 80
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 24 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) = 4.385 | 4.385 | 4.385 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -268.8 0 -268.8 -0.00036405818
1 0 -268.8 0 -268.8 -0.00036405821
Loop time of 0.0236093 on 1 procs for 1 steps with 80 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 =
-268.800000010084 -268.800000010084 -268.800000010084
Force two-norm initial, final = 4.8767206e-08 1.6397873e-08
Force max component initial, final = 2.4377502e-08 8.1872803e-09
Final line search alpha, max atom move = 1 8.1872803e-09
Iterations, force evaluations = 1 2
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.023223 | 0.023223 | 0.023223 | 0.0 | 98.37
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00015374 | 0.00015374 | 0.00015374 | 0.0 | 0.65
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0002321 | | | 0.98
Nlocal: 80 ave 80 max 80 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1823 ave 1823 max 1823 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: 6240 ave 6240 max 6240 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6240
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 24 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) = 4.385 | 4.385 | 4.385 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
1 0 -268.8 0 -268.8 -0.00036405821 1323.345
2 0 -268.8 0 -268.8 1.6656406e-06 1323.345
Loop time of 0.0236298 on 1 procs for 1 steps with 80 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 =
-268.800000010084 -268.800000010084 -268.800000010081
Force two-norm initial, final = 5.2228368e-07 3.2110121e-08
Force max component initial, final = 3.2956435e-07 2.11067e-08
Final line search alpha, max atom move = 1 2.11067e-08
Iterations, force evaluations = 1 2
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.02308 | 0.02308 | 0.02308 | 0.0 | 97.67
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00016189 | 0.00016189 | 0.00016189 | 0.0 | 0.69
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0003876 | | | 1.64
Nlocal: 80 ave 80 max 80 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1823 ave 1823 max 1823 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: 6240 ave 6240 max 6240 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6240
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 24 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) = 4.546 | 4.546 | 4.546 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -268.8 0 -268.8 1.6657514e-06
Loop time of 6.656e-06 on 1 procs for 0 steps with 80 atoms
165.3% 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 | | 6.656e-06 | | |100.00
Nlocal: 80 ave 80 max 80 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1823 ave 1823 max 1823 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: 6240 ave 6240 max 6240 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6240
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 24 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) = 4.546 | 4.546 | 4.546 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 -268.8 -268.8 4.0446508 80.893016 4.0446508 1.6657514e-06 1.6657514e-06 1.5275538e-05 -2.5553811e-05 1.5275527e-05 2.86 1.2192397e-16
Loop time of 6.294e-06 on 1 procs for 0 steps with 80 atoms
206.5% 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 | | 6.294e-06 | | |100.00
Nlocal: 80 ave 80 max 80 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 1823 ave 1823 max 1823 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3120 ave 3120 max 3120 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 6240 ave 6240 max 6240 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6240
Ave neighs/atom = 78
Neighbor list builds = 0
Dangerous builds = 0
80
-268.800000010081 eV
2.85999999228217 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:00