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 = 3.6390874 3.6390874 3.6390874 Created orthogonal box = (0.0000000 -63.030843 0.0000000) to (25.732234 63.030843 8.9139073) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1757361 5.4626730 5.9426049 Created 1196 atoms using lattice units in orthogonal box = (0.0000000 -63.030843 0.0000000) to (25.732234 63.030843 8.9139073) create_atoms CPU = 0.002 seconds 1196 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1757361 5.4626730 5.9426049 Created 1204 atoms using lattice units in orthogonal box = (0.0000000 -63.030843 0.0000000) to (25.732234 63.030843 8.9139073) create_atoms CPU = 0.002 seconds 1204 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 27 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2400 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_609260676108_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 7.790 | 7.790 | 7.790 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7336.9533 0 -7336.9533 56037.451 36 0 -7859.0612 0 -7859.0612 4113.518 Loop time of 2.0929 on 1 procs for 36 steps with 2400 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 = -7336.95329247301 -7859.05430029483 -7859.06122225647 Force two-norm initial, final = 1274.8223 0.21157820 Force max component initial, final = 358.10564 0.018151664 Final line search alpha, max atom move = 1.0000000 0.018151664 Iterations, force evaluations = 36 49 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9876 | 1.9876 | 1.9876 | 0.0 | 94.97 Neigh | 0.087205 | 0.087205 | 0.087205 | 0.0 | 4.17 Comm | 0.0098768 | 0.0098768 | 0.0098768 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008213 | | | 0.39 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12888.0 ave 12888 max 12888 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: 764010.0 ave 764010 max 764010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 764010 Ave neighs/atom = 318.33750 Neighbor list builds = 2 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 36 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.790 | 7.790 | 7.790 Mbytes Step Temp E_pair E_mol TotEng Press Volume 36 0 -7859.0612 0 -7859.0612 4113.518 28915.367 41 0 -7859.3282 0 -7859.3282 -12.592839 28998.367 Loop time of 0.323905 on 1 procs for 5 steps with 2400 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 = -7859.06122225647 -7859.32709687979 -7859.32820982622 Force two-norm initial, final = 157.17403 1.8021110 Force max component initial, final = 146.42335 1.4672358 Final line search alpha, max atom move = 7.9525409e-05 0.00011668252 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3184 | 0.3184 | 0.3184 | 0.0 | 98.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00088475 | 0.00088475 | 0.00088475 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004623 | | | 1.43 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12888.0 ave 12888 max 12888 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: 763604.0 ave 763604 max 763604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 763604 Ave neighs/atom = 318.16833 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 7.928 | 7.928 | 7.928 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7859.3282 0 -7859.3282 -12.592839 Loop time of 2.253e-06 on 1 procs for 0 steps with 2400 atoms 221.9% 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 | | 2.253e-06 | | |100.00 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12888.0 ave 12888 max 12888 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: 763142.0 ave 763142 max 763142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 763142 Ave neighs/atom = 317.97583 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 7.928 | 7.928 | 7.928 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 -7859.3282 -7859.3282 25.711307 126.55201 8.9121062 -12.592839 -12.592839 54.976944 -11.706217 -81.049244 2.3857017 798.37603 Loop time of 4.976e-06 on 1 procs for 0 steps with 2400 atoms 281.4% 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 | | 4.976e-06 | | |100.00 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12888.0 ave 12888 max 12888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 381571.0 ave 381571 max 381571 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 763142.0 ave 763142 max 763142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 763142 Ave neighs/atom = 317.97583 Neighbor list builds = 0 Dangerous builds = 0 2400 -7859.32820982622 eV 2.38570165597317 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03