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 -41.809931 0.0000000) to (29.564086 41.809931 5.1464468) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4794069 5.7013543 5.1464468 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -41.809931 0.0000000) to (29.564086 41.809931 5.1464468) create_atoms CPU = 0.003 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4794069 5.7013543 5.1464468 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -41.809931 0.0000000) to (29.564086 41.809931 5.1464468) create_atoms CPU = 0.003 seconds 532 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 = 7 18 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 12 atoms, new total = 1048 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 = 7 18 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) = 5.843 | 5.843 | 5.843 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3113.9075 0 -3113.9075 73700.028 48 0 -3424.4949 0 -3424.4949 -1823.5738 Loop time of 3.25473 on 1 procs for 48 steps with 1048 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 = -3113.90753288038 -3424.49190543287 -3424.49488655464 Force two-norm initial, final = 692.79475 0.13826790 Force max component initial, final = 169.23729 0.0088489625 Final line search alpha, max atom move = 1.0000000 0.0088489625 Iterations, force evaluations = 48 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1501 | 3.1501 | 3.1501 | 0.0 | 96.78 Neigh | 0.075362 | 0.075362 | 0.075362 | 0.0 | 2.32 Comm | 0.017195 | 0.017195 | 0.017195 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01209 | | | 0.37 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9056.00 ave 9056 max 9056 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: 331952.0 ave 331952 max 331952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 331952 Ave neighs/atom = 316.74809 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 = 7 18 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 : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.843 | 5.843 | 5.843 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -3424.4949 0 -3424.4949 -1823.5738 12722.762 51 0 -3424.5183 0 -3424.5183 -20.297638 12707.247 Loop time of 0.307852 on 1 procs for 3 steps with 1048 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3424.49488655463 -3424.51659470843 -3424.51829390519 Force two-norm initial, final = 29.834256 0.31935337 Force max component initial, final = 21.348521 0.18343845 Final line search alpha, max atom move = 0.00025398190 4.6590045e-05 Iterations, force evaluations = 3 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30167 | 0.30167 | 0.30167 | 0.0 | 97.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014931 | 0.0014931 | 0.0014931 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004693 | | | 1.52 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9056.00 ave 9056 max 9056 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: 331888.0 ave 331888 max 331888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 331888 Ave neighs/atom = 316.68702 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 = 7 18 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) = 5.981 | 5.981 | 5.981 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3424.5183 0 -3424.5183 -20.297638 Loop time of 6.194e-06 on 1 procs for 0 steps with 1048 atoms 177.6% 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 | | 6.194e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9056.00 ave 9056 max 9056 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: 331904.0 ave 331904 max 331904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 331904 Ave neighs/atom = 316.70229 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 = 7 18 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) = 5.981 | 5.981 | 5.981 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 -3424.5183 -3424.5183 29.510211 83.705552 5.1442834 -20.297638 -20.297638 -21.991156 -15.782885 -23.118873 2.3178004 496.06421 Loop time of 6.766e-06 on 1 procs for 0 steps with 1048 atoms 221.7% 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 | | 6.766e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9056.00 ave 9056 max 9056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 165952.0 ave 165952 max 165952 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 331904.0 ave 331904 max 331904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 331904 Ave neighs/atom = 316.70229 Neighbor list builds = 0 Dangerous builds = 0 1048 -3424.51829390519 eV 2.31780035293646 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04