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 = 3.56201 3.56201 3.56201
Created orthogonal box = (0 -40.3031 0) to (3.56201 40.3031 5.03744)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 3.56201 5.03744 5.03744
Created 66 atoms
create_atoms CPU = 0.000145912 secs
66 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 3.56201 5.03744 5.03744
Created 66 atoms
create_atoms CPU = 3.71933e-05 secs
66 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 = 7.18
ghost atom cutoff = 7.18
binsize = 3.59, bins = 1 23 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 7.18
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Deleted 0 atoms, new total = 132
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 = 7.18
ghost atom cutoff = 7.18
binsize = 3.59, bins = 1 23 2
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 7.18
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) = 4.451 | 4.451 | 4.451 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -421.50886 0 -421.50886 470554.69
29 0 -577.45948 0 -577.45948 79957.431
Loop time of 0.0190909 on 1 procs for 29 steps with 132 atoms
104.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-421.508862773 -577.459132875 -577.459482121
Force two-norm initial, final = 164.737 0.083218
Force max component initial, final = 41.8946 0.0144761
Final line search alpha, max atom move = 1 0.0144761
Iterations, force evaluations = 29 49
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.018174 | 0.018174 | 0.018174 | 0.0 | 95.20
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00070429 | 0.00070429 | 0.00070429 | 0.0 | 3.69
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0002124 | | | 1.11
Nlocal: 132 ave 132 max 132 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2788 ave 2788 max 2788 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: 18736 ave 18736 max 18736 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18736
Ave neighs/atom = 141.939
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 : 29
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 4.451 | 4.451 | 4.451 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
29 0 -577.45948 0 -577.45948 79957.431 1446.3483
199 0 -580.7911 0 -580.7911 -362.81989 1584.0354
Loop time of 0.0972381 on 1 procs for 170 steps with 132 atoms
102.8% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
-577.459482121 -580.791001216 -580.791098155
Force two-norm initial, final = 63.9836 0.928365
Force max component initial, final = 59.143 0.699862
Final line search alpha, max atom move = 0.002133 0.0014928
Iterations, force evaluations = 170 184
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.085285 | 0.085285 | 0.085285 | 0.0 | 87.71
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0031481 | 0.0031481 | 0.0031481 | 0.0 | 3.24
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.008805 | | | 9.05
Nlocal: 132 ave 132 max 132 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2788 ave 2788 max 2788 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: 18512 ave 18512 max 18512 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18512
Ave neighs/atom = 140.242
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 = 7.18
ghost atom cutoff = 7.18
binsize = 3.59, bins = 2 23 2
3 neighbor lists, perpetual/occasional/extra = 1 2 0
(1) pair kim, perpetual
attributes: full, newton off, cut 7.18
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) = 4.579 | 4.579 | 4.579 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -580.7911 0 -580.7911 -362.81989
Loop time of 1.19209e-06 on 1 procs for 0 steps with 132 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 | | 1.192e-06 | | |100.00
Nlocal: 132 ave 132 max 132 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2788 ave 2788 max 2788 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: 18088 ave 18088 max 18088 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18088
Ave neighs/atom = 137.03
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) = 4.579 | 4.579 | 4.579 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 -580.7911 -580.7911 4.0255954 80.606155 4.881649 -362.81989 -362.81989 238.32579 -2012.7707 685.98525 2.3992339 72.45466
Loop time of 1.90735e-06 on 1 procs for 0 steps with 132 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 | | 1.907e-06 | | |100.00
Nlocal: 132 ave 132 max 132 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2788 ave 2788 max 2788 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 9044 ave 9044 max 9044 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 18088 ave 18088 max 18088 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 18088
Ave neighs/atom = 137.03
Neighbor list builds = 0
Dangerous builds = 0
132
-580.79109815514 eV
2.39923391143098 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:00