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 -50.029567 0) to (16.676522 50.029567 4.0446508)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 4.9048595 4.9048595 4.0446508
Created 204 atoms
using lattice units in orthogonal box = (0 -50.029567 0) to (16.676522 50.029567 4.0446508)
create_atoms CPU = 0.001 seconds
204 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 4.9048595 4.9048595 4.0446508
Created 206 atoms
using lattice units in orthogonal box = (0 -50.029567 0) to (16.676522 50.029567 4.0446508)
create_atoms CPU = 0.001 seconds
206 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 = 5 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 6.8
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Deleted 2 atoms, new total = 408
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 = 5 30 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) = 4.45 | 4.45 | 4.45 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1161.2797 0 -1161.2797 53449.014
66 0 -1365.8701 0 -1365.8701 4504.1624
Loop time of 4.27024 on 1 procs for 66 steps with 408 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 =
-1161.27974790443 -1365.86877994312 -1365.87006855425
Force two-norm initial, final = 339.74144 0.072974085
Force max component initial, final = 118.30917 0.010177607
Final line search alpha, max atom move = 1 0.010177607
Iterations, force evaluations = 66 111
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.2429 | 4.2429 | 4.2429 | 0.0 | 99.36
Neigh | 0.010248 | 0.010248 | 0.010248 | 0.0 | 0.24
Comm | 0.0085969 | 0.0085969 | 0.0085969 | 0.0 | 0.20
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.008539 | | | 0.20
Nlocal: 408 ave 408 max 408 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2956 ave 2956 max 2956 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: 31624 ave 31624 max 31624 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 31624
Ave neighs/atom = 77.509804
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 = 5 30 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 : 66
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 4.45 | 4.45 | 4.45 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
66 0 -1365.8701 0 -1365.8701 4504.1624 6749.0596
77 0 -1366.0382 0 -1366.0382 -38.870191 6787.3011
Loop time of 0.489889 on 1 procs for 11 steps with 408 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 =
-1365.87006855425 -1366.03811855461 -1366.03815643555
Force two-norm initial, final = 40.083905 0.37929875
Force max component initial, final = 37.561569 0.26717533
Final line search alpha, max atom move = 0.0045870432 0.0012255448
Iterations, force evaluations = 11 12
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.48031 | 0.48031 | 0.48031 | 0.0 | 98.04
Neigh | 0.0051951 | 0.0051951 | 0.0051951 | 0.0 | 1.06
Comm | 0.0011126 | 0.0011126 | 0.0011126 | 0.0 | 0.23
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.003271 | | | 0.67
Nlocal: 408 ave 408 max 408 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2964 ave 2964 max 2964 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: 31632 ave 31632 max 31632 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 31632
Ave neighs/atom = 77.529412
Neighbor list builds = 1
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 = 5 30 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) = 4.626 | 4.626 | 4.626 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1366.0382 0 -1366.0382 -38.870191
Loop time of 6.184e-06 on 1 procs for 0 steps with 408 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 | | 6.184e-06 | | |100.00
Nlocal: 408 ave 408 max 408 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2964 ave 2964 max 2964 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: 31648 ave 31648 max 31648 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 31648
Ave neighs/atom = 77.568627
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 = 5 30 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) = 4.626 | 4.626 | 4.626 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 -1366.0382 -1366.0382 16.656756 101.07529 4.0314538 -38.870191 -38.870191 -32.63089 -63.70857 -20.271113 2.6321257 237.00801
Loop time of 6.795e-06 on 1 procs for 0 steps with 408 atoms
279.6% 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 | | 6.795e-06 | | |100.00
Nlocal: 408 ave 408 max 408 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2964 ave 2964 max 2964 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 15824 ave 15824 max 15824 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 31648 ave 31648 max 31648 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 31648
Ave neighs/atom = 77.568627
Neighbor list builds = 0
Dangerous builds = 0
408
-1366.03815643555 eV
2.63212574756883 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:05