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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -41.247507 0.0000000) to (20.623753 41.247507 4.0446508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7593277 4.7593277 4.0446508 Created 207 atoms using lattice units in orthogonal box = (0.0000000 -41.247507 0.0000000) to (20.623753 41.247507 4.0446508) create_atoms CPU = 0.001 seconds 207 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7593277 4.7593277 4.0446508 Created 209 atoms using lattice units in orthogonal box = (0.0000000 -41.247507 0.0000000) to (20.623753 41.247507 4.0446508) create_atoms CPU = 0.000 seconds 209 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 = 8 ghost atom cutoff = 8 binsize = 4, 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 412 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_793141037706_001#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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.457 | 4.457 | 4.457 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1344.4338 0 -1344.4338 11788.321 61 0 -1378.312 0 -1378.312 -2374.0345 Loop time of 3.78818 on 1 procs for 61 steps with 412 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1344.43377938677 -1378.31074219709 -1378.31195719896 Force two-norm initial, final = 80.992346 0.089108827 Force max component initial, final = 28.708491 0.010796756 Final line search alpha, max atom move = 1.0000000 0.010796756 Iterations, force evaluations = 61 111 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7775 | 3.7775 | 3.7775 | 0.0 | 99.72 Neigh | 0.0029046 | 0.0029046 | 0.0029046 | 0.0 | 0.08 Comm | 0.0041537 | 0.0041537 | 0.0041537 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003661 | | | 0.10 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3486.00 ave 3486 max 3486 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: 54488.0 ave 54488 max 54488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54488 Ave neighs/atom = 132.25243 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.457 | 4.457 | 4.457 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -1378.312 0 -1378.312 -2374.0345 6881.3942 66 0 -1378.3443 0 -1378.3443 -2.141918 6860.3169 Loop time of 0.27719 on 1 procs for 5 steps with 412 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 = -1378.31195719896 -1378.34418598659 -1378.34426846469 Force two-norm initial, final = 19.621576 0.12307391 Force max component initial, final = 16.619959 0.034777198 Final line search alpha, max atom move = 0.00086528329 3.0092128e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27591 | 0.27591 | 0.27591 | 0.0 | 99.54 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002335 | 0.0002335 | 0.0002335 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001044 | | | 0.38 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3540.00 ave 3540 max 3540 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: 54556.0 ave 54556 max 54556 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54556 Ave neighs/atom = 132.41748 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.595 | 4.595 | 4.595 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1378.3443 0 -1378.3443 -2.141918 Loop time of 1.906e-06 on 1 procs for 0 steps with 412 atoms 157.4% 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 | | 1.906e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3540.00 ave 3540 max 3540 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: 54536.0 ave 54536 max 54536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54536 Ave neighs/atom = 132.36893 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 6 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.595 | 4.595 | 4.595 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 -1378.3443 -1378.3443 20.610327 82.620424 4.0287644 -2.141918 -2.141918 -8.1166711 0.48889296 1.2020242 2.6222947 241.49323 Loop time of 1.915e-06 on 1 procs for 0 steps with 412 atoms 208.9% 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 | | 1.915e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3540.00 ave 3540 max 3540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27268.0 ave 27268 max 27268 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 54536.0 ave 54536 max 54536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54536 Ave neighs/atom = 132.36893 Neighbor list builds = 0 Dangerous builds = 0 412 -1378.34426846469 eV 2.62229465420758 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04