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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -44.038330 0.0000000) to (20.758189 44.038330 5.0346005) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1053498 6.0439880 5.0346005 Created 412 atoms using lattice units in orthogonal box = (0.0000000 -44.038330 0.0000000) to (20.758189 44.038330 5.0346005) create_atoms CPU = 0.004 seconds 412 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1053498 6.0439880 5.0346005 Created 412 atoms using lattice units in orthogonal box = (0.0000000 -44.038330 0.0000000) to (20.758189 44.038330 5.0346005) create_atoms CPU = 0.003 seconds 412 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 23 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 808 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_820335782779_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.985 | 4.985 | 4.985 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3509.9305 0 -3509.9305 4110.1522 86 0 -3543.0501 0 -3543.0501 -3170.441 Loop time of 2.63389 on 1 procs for 86 steps with 808 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 = -3509.93049326418 -3543.04722896178 -3543.05014525837 Force two-norm initial, final = 40.522705 0.24252069 Force max component initial, final = 9.6640040 0.039405026 Final line search alpha, max atom move = 1.0000000 0.039405026 Iterations, force evaluations = 86 163 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5747 | 2.5747 | 2.5747 | 0.0 | 97.75 Neigh | 0.018155 | 0.018155 | 0.018155 | 0.0 | 0.69 Comm | 0.022565 | 0.022565 | 0.022565 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01842 | | | 0.70 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5888.00 ave 5888 max 5888 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: 141192.0 ave 141192 max 141192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141192 Ave neighs/atom = 174.74257 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 86 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.985 | 4.985 | 4.985 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -3543.0501 0 -3543.0501 -3170.441 9204.8203 90 0 -3543.1222 0 -3543.1222 -2293.1626 9200.0978 Loop time of 0.0984027 on 1 procs for 4 steps with 808 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 = -3543.05014525838 -3543.12199238738 -3543.12218535732 Force two-norm initial, final = 34.654916 0.39360986 Force max component initial, final = 28.600965 0.16762392 Final line search alpha, max atom move = 0.00075227682 0.00012609959 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.095309 | 0.095309 | 0.095309 | 0.0 | 96.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00071246 | 0.00071246 | 0.00071246 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002381 | | | 2.42 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5880.00 ave 5880 max 5880 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: 141160.0 ave 141160 max 141160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141160 Ave neighs/atom = 174.70297 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.123 | 5.123 | 5.123 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3543.1222 0 -3543.1222 -2293.1626 Loop time of 6.465e-06 on 1 procs for 0 steps with 808 atoms 154.7% 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 | | 6.465e-06 | | |100.00 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5880.00 ave 5880 max 5880 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: 141136.0 ave 141136 max 141136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141136 Ave neighs/atom = 174.67327 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.123 | 5.123 | 5.123 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 -3543.1222 -3543.1222 20.813247 88.076659 5.0187063 -2293.1626 -2293.1626 22.428019 -6931.0151 29.099174 2.4072707 544.58261 Loop time of 6.736e-06 on 1 procs for 0 steps with 808 atoms 282.1% 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 | | 6.736e-06 | | |100.00 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5880.00 ave 5880 max 5880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70568.0 ave 70568 max 70568 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 141136.0 ave 141136 max 141136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141136 Ave neighs/atom = 174.67327 Neighbor list builds = 0 Dangerous builds = 0 808 -3543.12218535732 eV 2.40727069240199 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03