LAMMPS (30 Jul 2021) 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 = 3.6583664 3.6583664 3.6583664 Created orthogonal box = (0.0000000 -69.988670 0.0000000) to (40.407977 69.988670 6.3364764) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9618327 5.3543245 6.3364764 Created 1463 atoms using lattice units in orthogonal box = (0.0000000 -69.988670 0.0000000) to (40.407977 69.988670 6.3364764) create_atoms CPU = 0.003 seconds 1463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9618327 5.3543245 6.3364764 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -69.988670 0.0000000) to (40.407977 69.988670 6.3364764) create_atoms CPU = 0.003 seconds 1465 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 39 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 2925 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_807997826449_000#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:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.211 | 6.211 | 6.211 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11251.555 0 -11251.555 38726.152 1168 0 -11871.418 0 -11871.418 -65560.459 Loop time of 47.2282 on 1 procs for 1168 steps with 2925 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 = -11251.5547037705 -11871.4066803928 -11871.4175746449 Force two-norm initial, final = 833.62530 0.37768956 Force max component initial, final = 282.08797 0.10080323 Final line search alpha, max atom move = 0.64640581 0.065159792 Iterations, force evaluations = 1168 2286 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 46.095 | 46.095 | 46.095 | 0.0 | 97.60 Neigh | 0.50826 | 0.50826 | 0.50826 | 0.0 | 1.08 Comm | 0.31287 | 0.31287 | 0.31287 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.3116 | | | 0.66 Nlocal: 2925.00 ave 2925 max 2925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11565.0 ave 11565 max 11565 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 395574.0 ave 395574 max 395574 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 395574 Ave neighs/atom = 135.23897 Neighbor list builds = 21 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1168 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.591 | 6.591 | 6.591 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1168 0 -11871.418 0 -11871.418 -65560.459 35840.386 1199 0 -11911.443 0 -11911.443 -185.34983 34282.149 Loop time of 0.775261 on 1 procs for 31 steps with 2925 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11871.4175746448 -11911.4395464904 -11911.4425871626 Force two-norm initial, final = 2619.4854 10.914207 Force max component initial, final = 1775.3072 8.6064877 Final line search alpha, max atom move = 5.3042882e-05 0.00045651291 Iterations, force evaluations = 31 33 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.67511 | 0.67511 | 0.67511 | 0.0 | 87.08 Neigh | 0.07747 | 0.07747 | 0.07747 | 0.0 | 9.99 Comm | 0.0040397 | 0.0040397 | 0.0040397 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01864 | | | 2.40 Nlocal: 2925.00 ave 2925 max 2925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11738.0 ave 11738 max 11738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 412062.0 ave 412062 max 412062 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 412062 Ave neighs/atom = 140.87590 Neighbor list builds = 3 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.729 | 6.729 | 6.729 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11911.443 0 -11911.443 -185.34983 Loop time of 2.253e-06 on 1 procs for 0 steps with 2925 atoms 177.5% 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 | | 2.253e-06 | | |100.00 Nlocal: 2925.00 ave 2925 max 2925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11713.0 ave 11713 max 11713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 411964.0 ave 411964 max 411964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 411964 Ave neighs/atom = 140.84239 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.729 | 6.729 | 6.729 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 -11911.443 -11911.443 39.524808 136.52634 6.3530435 -185.34983 -185.34983 52.38303 -392.30783 -216.12468 2.2127541 9813.7976 Loop time of 2.54e-06 on 1 procs for 0 steps with 2925 atoms 196.9% 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 | | 2.54e-06 | | |100.00 Nlocal: 2925.00 ave 2925 max 2925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11713.0 ave 11713 max 11713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 205982.0 ave 205982 max 205982 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 411964.0 ave 411964 max 411964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 411964 Ave neighs/atom = 140.84239 Neighbor list builds = 0 Dangerous builds = 0 2925 -11911.4425871626 eV 2.2127540757263 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:48