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 = 3.5200135 3.5200135 3.5200135 Created orthogonal box = (0.0000000 -41.652882 0.0000000) to (51.009842 41.652882 8.6222370) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8296962 5.3549179 5.7481580 Created 1690 atoms using lattice units in orthogonal box = (0.0000000 -41.652882 0.0000000) to (51.009842 41.652882 8.6222370) create_atoms CPU = 0.002 seconds 1690 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8296962 5.3549179 5.7481580 Created 1690 atoms using lattice units in orthogonal box = (0.0000000 -41.652882 0.0000000) to (51.009842 41.652882 8.6222370) create_atoms CPU = 0.002 seconds 1690 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 20 3 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 68 atoms, new total = 3312 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_871937946490_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.876 | 7.876 | 7.876 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14589.421 0 -14589.421 464.52884 47 0 -14669.235 0 -14669.235 -17654.622 Loop time of 2.73262 on 1 procs for 47 steps with 3312 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14589.4212544778 -14669.2219905162 -14669.2347275751 Force two-norm initial, final = 33.479709 0.35533295 Force max component initial, final = 3.1411419 0.027219484 Final line search alpha, max atom move = 1.0000000 0.027219484 Iterations, force evaluations = 47 83 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6708 | 2.6708 | 2.6708 | 0.0 | 97.74 Neigh | 0.038647 | 0.038647 | 0.038647 | 0.0 | 1.41 Comm | 0.009925 | 0.009925 | 0.009925 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01321 | | | 0.48 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12377.0 ave 12377 max 12377 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: 739498.0 ave 739498 max 739498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 739498 Ave neighs/atom = 223.27838 Neighbor list builds = 1 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.889 | 7.889 | 7.889 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -14669.235 0 -14669.235 -17654.622 36639.453 52 0 -14670.353 0 -14670.353 -5727.3294 36387.914 Loop time of 0.247155 on 1 procs for 5 steps with 3312 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 = -14669.2347275751 -14670.3533845794 -14670.3534182961 Force two-norm initial, final = 457.93403 0.45996293 Force max component initial, final = 324.03142 0.090492900 Final line search alpha, max atom move = 0.00078226021 7.0788995e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24256 | 0.24256 | 0.24256 | 0.0 | 98.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069237 | 0.00069237 | 0.00069237 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003899 | | | 1.58 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12624.0 ave 12624 max 12624 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: 740268.0 ave 740268 max 740268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 740268 Ave neighs/atom = 223.51087 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 8.027 | 8.027 | 8.027 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14670.353 0 -14670.353 -5727.3294 Loop time of 1.687e-06 on 1 procs for 0 steps with 3312 atoms 118.6% 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 | | 1.687e-06 | | |100.00 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12636.0 ave 12636 max 12636 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: 740954.0 ave 740954 max 740954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 740954 Ave neighs/atom = 223.71800 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 8.027 | 8.027 | 8.027 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 -14670.353 -14670.353 50.837309 83.305763 8.5921048 -5727.3294 -5727.3294 -2.9474935 -17183.011 3.9705193 2.3249423 1595.4733 Loop time of 2.357e-06 on 1 procs for 0 steps with 3312 atoms 254.6% 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 | | 2.357e-06 | | |100.00 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12636.0 ave 12636 max 12636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 370477.0 ave 370477 max 370477 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 740954.0 ave 740954 max 740954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 740954 Ave neighs/atom = 223.71800 Neighbor list builds = 0 Dangerous builds = 0 3312 -14580.0636556936 eV 2.3249422809483 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03