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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -54.502858 0.0000000) to (27.251429 54.502858 2.8886457) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9805458 3.9805458 2.8886457 Created 356 atoms using lattice units in orthogonal box = (0.0000000 -54.502858 0.0000000) to (27.251429 54.502858 2.8886457) create_atoms CPU = 0.002 seconds 356 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9805458 3.9805458 2.8886457 Created 357 atoms using lattice units in orthogonal box = (0.0000000 -54.502858 0.0000000) to (27.251429 54.502858 2.8886457) create_atoms CPU = 0.001 seconds 357 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 41 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 713 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.280 | 5.280 | 5.280 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2886.1075 0 -2886.1075 32869.55 39 0 -2966.8066 0 -2966.8066 6385.7394 Loop time of 8.74174 on 1 procs for 39 steps with 713 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 = -2886.10745285628 -2966.8041166049 -2966.80662894994 Force two-norm initial, final = 130.45805 0.17763411 Force max component initial, final = 54.152636 0.045631952 Final line search alpha, max atom move = 0.77077118 0.035171794 Iterations, force evaluations = 39 68 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.7274 | 8.7274 | 8.7274 | 0.0 | 99.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0074239 | 0.0074239 | 0.0074239 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006876 | | | 0.08 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4737.00 ave 4737 max 4737 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: 41228.0 ave 41228 max 41228 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41228 Ave neighs/atom = 57.823282 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.280 | 5.280 | 5.280 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -2966.8066 0 -2966.8066 6385.7394 8580.8996 47 0 -2967.0971 0 -2967.0971 307.1635 8607.4533 Loop time of 1.49866 on 1 procs for 8 steps with 713 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 = -2966.80662894994 -2967.09636464644 -2967.09705639545 Force two-norm initial, final = 92.290200 3.3046241 Force max component initial, final = 91.054937 2.6027972 Final line search alpha, max atom move = 0.00031857036 0.00082917406 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4929 | 1.4929 | 1.4929 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011517 | 0.0011517 | 0.0011517 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004631 | | | 0.31 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4742.00 ave 4742 max 4742 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: 41094.0 ave 41094 max 41094 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41094 Ave neighs/atom = 57.635344 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.418 | 5.418 | 5.418 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2967.0971 0 -2967.0971 307.1635 Loop time of 6.334e-06 on 1 procs for 0 steps with 713 atoms 173.7% 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 | | 6.334e-06 | | |100.00 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4742.00 ave 4742 max 4742 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: 41080.0 ave 41080 max 41080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41080 Ave neighs/atom = 57.615708 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 11 42 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 5.418 | 5.418 | 5.418 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 -2967.0971 -2967.0971 27.226675 109.72818 2.8811235 307.1635 307.1635 348.41074 487.69122 85.388529 2.3130664 302.92624 Loop time of 6.776e-06 on 1 procs for 0 steps with 713 atoms 280.4% 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 | | 6.776e-06 | | |100.00 Nlocal: 713.000 ave 713 max 713 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4742.00 ave 4742 max 4742 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20540.0 ave 20540 max 20540 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 41080.0 ave 41080 max 41080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41080 Ave neighs/atom = 57.615708 Neighbor list builds = 0 Dangerous builds = 0 713 -2967.09705639545 eV 2.31306636825625 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11