LAMMPS (7 Aug 2019)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
using 1 OpenMP thread(s) per MPI task
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 3.62843 3.62843 3.62843
Created orthogonal box = (0 -43.5448 0) to (15.3941 43.5448 5.13137)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 5.13137 6.04738 5.13137
Created 292 atoms
create_atoms CPU = 0.000235081 secs
292 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 5.13137 6.04738 5.13137
Created 292 atoms
create_atoms CPU = 0.000123978 secs
292 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 = 7.54989
ghost atom cutoff = 7.54989
binsize = 3.77495, bins = 5 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 7.54989
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Deleted 16 atoms, new total = 568
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 7.54989
ghost atom cutoff = 7.54989
binsize = 3.77495, bins = 5 24 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 7.54989
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) = 4.537 | 4.537 | 4.537 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2364.5899 0 -2364.5899 -2669.5698
64 0 -2375.2967 0 -2375.2967 -13375.206
Loop time of 0.187986 on 1 procs for 64 steps with 568 atoms
95.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2364.58987745 -2375.2943392 -2375.296671
Force two-norm initial, final = 9.26765 0.151371
Force max component initial, final = 2.89401 0.0204131
Final line search alpha, max atom move = 1 0.0204131
Iterations, force evaluations = 64 120
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.18326 | 0.18326 | 0.18326 | 0.0 | 97.49
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0029621 | 0.0029621 | 0.0029621 | 0.0 | 1.58
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.001764 | | | 0.94
Nlocal: 568 ave 568 max 568 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4404 ave 4404 max 4404 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: 78720 ave 78720 max 78720 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 78720
Ave neighs/atom = 138.592
Neighbor list builds = 0
Dangerous builds = 0
WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168)
Setting up cg style minimization ...
Unit style : metal
Current step : 64
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 4.537 | 4.537 | 4.537 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
64 0 -2375.2967 0 -2375.2967 -13375.206 6879.4638
94 0 -2376.8934 0 -2376.8934 3127.2675 6772.2207
Loop time of 0.064996 on 1 procs for 30 steps with 568 atoms
92.3% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-2375.296671 -2376.89300904 -2376.89340264
Force two-norm initial, final = 119.286 2.66696
Force max component initial, final = 118.726 1.81662
Final line search alpha, max atom move = 0.00306188 0.00556228
Iterations, force evaluations = 30 31
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.061237 | 0.061237 | 0.061237 | 0.0 | 94.22
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00080252 | 0.00080252 | 0.00080252 | 0.0 | 1.23
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.002957 | | | 4.55
Nlocal: 568 ave 568 max 568 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4348 ave 4348 max 4348 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: 80488 ave 80488 max 80488 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 80488
Ave neighs/atom = 141.704
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 = 7.54989
ghost atom cutoff = 7.54989
binsize = 3.77495, bins = 4 24 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 7.54989
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/newton
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 4.675 | 4.675 | 4.675 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -2376.8934 0 -2376.8934 3127.2675
Loop time of 9.53674e-07 on 1 procs for 0 steps with 568 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 | | 9.537e-07 | | |100.00
Nlocal: 568 ave 568 max 568 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4460 ave 4460 max 4460 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: 83032 ave 83032 max 83032 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 83032
Ave neighs/atom = 146.183
Neighbor list builds = 0
Dangerous builds = 0
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 4.675 | 4.675 | 4.675 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 -2376.8934 -2376.8934 14.943149 87.089554 5.2038277 3127.2675 3127.2675 417.18782 8545.6696 418.94501 2.3592362 529.79834
Loop time of 9.53674e-07 on 1 procs for 0 steps with 568 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 | | 9.537e-07 | | |100.00
Nlocal: 568 ave 568 max 568 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4460 ave 4460 max 4460 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 41516 ave 41516 max 41516 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 83032 ave 83032 max 83032 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 83032
Ave neighs/atom = 146.183
Neighbor list builds = 0
Dangerous builds = 0
568
-2376.89326721706 eV
2.3592361677369 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:00