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 -49.2053 0) to (24.60265 49.2053 4.0446508)
1 by 1 by 1 MPI processor grid
Lattice spacing in x,y,z = 4.6545554 4.6545554 4.0446508
Created 296 atoms
using lattice units in orthogonal box = (0 -49.2053 0) to (24.60265 49.2053 4.0446508)
create_atoms CPU = 0.002 seconds
296 atoms in group upper
Displacing atoms ...
Lattice spacing in x,y,z = 4.6545554 4.6545554 4.0446508
Created 298 atoms
using lattice units in orthogonal box = (0 -49.2053 0) to (24.60265 49.2053 4.0446508)
create_atoms CPU = 0.001 seconds
298 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 = 8 29 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 = 592
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 = 8 29 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) = 4.497 | 4.497 | 4.497 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1873.83 0 -1873.83 27829.608
63 0 -1982.0665 0 -1982.0665 4089.9473
Loop time of 6.19168 on 1 procs for 63 steps with 592 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 =
-1873.82998810063 -1982.06486012081 -1982.0665358807
Force two-norm initial, final = 208.01726 0.092704959
Force max component initial, final = 57.367537 0.015775556
Final line search alpha, max atom move = 1 0.015775556
Iterations, force evaluations = 63 116
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.1611 | 6.1611 | 6.1611 | 0.0 | 99.51
Neigh | 0.0077907 | 0.0077907 | 0.0077907 | 0.0 | 0.13
Comm | 0.011723 | 0.011723 | 0.011723 | 0.0 | 0.19
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01103 | | | 0.18
Nlocal: 592 ave 592 max 592 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4082 ave 4082 max 4082 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: 45896 ave 45896 max 45896 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 45896
Ave neighs/atom = 77.527027
Neighbor list builds = 1
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 = 8 29 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 : 63
WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies
Per MPI rank memory allocation (min/avg/max) = 4.496 | 4.496 | 4.496 Mbytes
Step Temp E_pair E_mol TotEng Press Volume
63 0 -1982.0665 0 -1982.0665 4089.9473 9792.7531
72 0 -1982.2404 0 -1982.2404 14.013175 9842.7948
Loop time of 0.580013 on 1 procs for 9 steps with 592 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 =
-1982.0665358807 -1982.24011243144 -1982.24036117628
Force two-norm initial, final = 50.833513 0.24435581
Force max component initial, final = 46.052855 0.10714387
Final line search alpha, max atom move = 0.0010459406 0.00011206613
Iterations, force evaluations = 9 10
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.57546 | 0.57546 | 0.57546 | 0.0 | 99.21
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0009653 | 0.0009653 | 0.0009653 | 0.0 | 0.17
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.00359 | | | 0.62
Nlocal: 592 ave 592 max 592 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4105 ave 4105 max 4105 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: 46080 ave 46080 max 46080 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 46080
Ave neighs/atom = 77.837838
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 = 8 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) = 4.685 | 4.685 | 4.685 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -1982.2404 0 -1982.2404 14.013175
Loop time of 6.265e-06 on 1 procs for 0 steps with 592 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 | | 6.265e-06 | | |100.00
Nlocal: 592 ave 592 max 592 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4092 ave 4092 max 4092 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: 45928 ave 45928 max 45928 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 45928
Ave neighs/atom = 77.581081
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 = 8 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) = 4.685 | 4.685 | 4.685 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 -1982.2404 -1982.2404 24.599356 99.228521 4.0323497 14.013175 14.013175 13.64348 11.008573 17.387471 2.6089345 245.87724
Loop time of 6.655e-06 on 1 procs for 0 steps with 592 atoms
285.5% 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 | | 6.655e-06 | | |100.00
Nlocal: 592 ave 592 max 592 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4092 ave 4092 max 4092 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 22964 ave 22964 max 22964 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 45928 ave 45928 max 45928 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 45928
Ave neighs/atom = 77.581081
Neighbor list builds = 0
Dangerous builds = 0
592
-1982.24036117628 eV
2.6089344696456 Angstroms
This indicates that LAMMPS ran successfully
Total wall time: 0:00:07