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 = 3.6583648 3.6583648 3.6583648 Created orthogonal box = (0.0000000 -37.308147 0.0000000) to (18.654074 37.308147 3.6583648) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3047862 4.3047862 3.6583648 Created 208 atoms using lattice units in orthogonal box = (0.0000000 -37.308147 0.0000000) to (18.654074 37.308147 3.6583648) create_atoms CPU = 0.001 seconds 208 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3047862 4.3047862 3.6583648 Created 210 atoms using lattice units in orthogonal box = (0.0000000 -37.308147 0.0000000) to (18.654074 37.308147 3.6583648) create_atoms CPU = 0.001 seconds 210 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 21 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 414 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_769582363439_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.461 | 4.461 | 4.461 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1325.2858 0 -1325.2858 159744.71 90 0 -1652.1182 0 -1652.1182 -2152.4851 Loop time of 1.17226 on 1 procs for 90 steps with 414 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 = -1325.28583735648 -1652.1167395408 -1652.11823038022 Force two-norm initial, final = 987.11224 0.10946109 Force max component initial, final = 348.71769 0.016539640 Final line search alpha, max atom move = 1.0000000 0.016539640 Iterations, force evaluations = 90 163 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1368 | 1.1368 | 1.1368 | 0.0 | 96.97 Neigh | 0.0070881 | 0.0070881 | 0.0070881 | 0.0 | 0.60 Comm | 0.016093 | 0.016093 | 0.016093 | 0.0 | 1.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0123 | | | 1.05 Nlocal: 414.000 ave 414 max 414 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4016.00 ave 4016 max 4016 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: 55996.0 ave 55996 max 55996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55996 Ave neighs/atom = 135.25604 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.461 | 4.461 | 4.461 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -1652.1182 0 -1652.1182 -2152.4851 5092.07 489 0 -1669.7952 0 -1669.7952 685.20957 4853.03 Loop time of 3.6142 on 1 procs for 399 steps with 414 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 = -1652.11823038021 -1669.79399046204 -1669.79517846056 Force two-norm initial, final = 90.428689 4.7882081 Force max component initial, final = 66.269235 3.4208941 Final line search alpha, max atom move = 0.00068332155 0.0023375707 Iterations, force evaluations = 399 450 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3526 | 3.3526 | 3.3526 | 0.0 | 92.76 Neigh | 0.072049 | 0.072049 | 0.072049 | 0.0 | 1.99 Comm | 0.043465 | 0.043465 | 0.043465 | 0.0 | 1.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1461 | | | 4.04 Nlocal: 414.000 ave 414 max 414 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4406.00 ave 4406 max 4406 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: 59420.0 ave 59420 max 59420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59420 Ave neighs/atom = 143.52657 Neighbor list builds = 8 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.602 | 4.602 | 4.602 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1669.7952 0 -1669.7952 685.20957 Loop time of 6.255e-06 on 1 procs for 0 steps with 414 atoms 175.9% 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 | | 6.255e-06 | | |100.00 Nlocal: 414.000 ave 414 max 414 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4411.00 ave 4411 max 4411 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: 59580.0 ave 59580 max 59580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59580 Ave neighs/atom = 143.91304 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.602 | 4.602 | 4.602 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 -1669.7952 -1669.7952 15.243236 80.219771 3.9687558 685.20957 685.20957 922.86995 474.09714 658.66163 2.2122063 466.42227 Loop time of 7.097e-06 on 1 procs for 0 steps with 414 atoms 239.5% 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 | | 7.097e-06 | | |100.00 Nlocal: 414.000 ave 414 max 414 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4411.00 ave 4411 max 4411 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29790.0 ave 29790 max 29790 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 59580.0 ave 59580 max 59580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59580 Ave neighs/atom = 143.91304 Neighbor list builds = 0 Dangerous builds = 0 414 -1669.79517846056 eV 2.2122062550469 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05