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 = 3.6149251 3.6149251 3.6149251 Created orthogonal box = (0.0000000 -71.571865 0.0000000) to (43.828637 71.571865 8.8547219) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0686179 5.1122761 5.9031479 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -71.571865 0.0000000) to (43.828637 71.571865 8.8547219) create_atoms CPU = 0.009 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0686179 5.1122761 5.9031479 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -71.571865 0.0000000) to (43.828637 71.571865 8.8547219) create_atoms CPU = 0.009 seconds 2358 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 38 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 30 atoms, new total = 4680 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_469343973171_005#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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 38 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 11.55 | 11.55 | 11.55 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15871.451 0 -15871.451 34434.56 93 0 -16521.65 0 -16521.65 -2204.7691 Loop time of 11.4042 on 1 procs for 93 steps with 4680 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 = -15871.4512647839 -16521.6361538267 -16521.6499483433 Force two-norm initial, final = 1012.4500 0.41064107 Force max component initial, final = 187.98670 0.065393805 Final line search alpha, max atom move = 1.0000000 0.065393805 Iterations, force evaluations = 93 173 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.16 | 11.16 | 11.16 | 0.0 | 97.86 Neigh | 0.10625 | 0.10625 | 0.10625 | 0.0 | 0.93 Comm | 0.060568 | 0.060568 | 0.060568 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07753 | | | 0.68 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14466.0 ave 14466 max 14466 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: 662640.0 ave 662640 max 662640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 662640 Ave neighs/atom = 141.58974 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 38 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.54 | 11.54 | 11.54 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -16521.65 0 -16521.65 -2204.7691 55552.707 95 0 -16521.734 0 -16521.734 -2.2421161 55463.83 Loop time of 0.312122 on 1 procs for 2 steps with 4680 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 = -16521.6499483435 -16521.7215990517 -16521.7337506831 Force two-norm initial, final = 138.56387 5.9185022 Force max component initial, final = 102.48100 4.7766654 Final line search alpha, max atom move = 3.8365013e-05 0.00018325683 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30465 | 0.30465 | 0.30465 | 0.0 | 97.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016025 | 0.0016025 | 0.0016025 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005874 | | | 1.88 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13858.0 ave 13858 max 13858 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: 659472.0 ave 659472 max 659472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 659472 Ave neighs/atom = 140.91282 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 11.06 | 11.06 | 11.06 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -16521.734 0 -16521.734 -2.2421161 Loop time of 6.094e-06 on 1 procs for 0 steps with 4680 atoms 180.5% 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 | | 6.094e-06 | | |100.00 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13863.0 ave 13863 max 13863 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: 659940.0 ave 659940 max 659940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 659940 Ave neighs/atom = 141.01282 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 11.06 | 11.06 | 11.06 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 -16521.734 -16521.734 43.797381 143.18999 8.8440064 -2.2421161 -2.2421161 -137.88452 39.08942 92.068748 2.274655 1753.8041 Loop time of 8.69e-06 on 1 procs for 0 steps with 4680 atoms 253.2% 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 | | 8.69e-06 | | |100.00 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13863.0 ave 13863 max 13863 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 329970.0 ave 329970 max 329970 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 659940.0 ave 659940 max 659940 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 659940 Ave neighs/atom = 141.01282 Neighbor list builds = 0 Dangerous builds = 0 4680 -16521.7571506831 eV 2.27465496998107 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13