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 -46.692524 0.0000000) to (33.014083 46.692524 5.0346005) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1421550 5.9718442 5.0346005 Created 695 atoms using lattice units in orthogonal box = (0.0000000 -46.692524 0.0000000) to (33.014083 46.692524 5.0346005) create_atoms CPU = 0.006 seconds 695 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1421550 5.9718442 5.0346005 Created 695 atoms using lattice units in orthogonal box = (0.0000000 -46.692524 0.0000000) to (33.014083 46.692524 5.0346005) create_atoms CPU = 0.005 seconds 695 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 = 9 24 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 31 atoms, new total = 1359 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_803527979660_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 = 9 24 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) = 5.494 | 5.494 | 5.494 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5933.6126 0 -5933.6126 -10201.413 76 0 -5958.2738 0 -5958.2738 -3491.8385 Loop time of 3.85021 on 1 procs for 76 steps with 1359 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 = -5933.61262840978 -5958.26933121985 -5958.27375772203 Force two-norm initial, final = 21.299519 0.33055015 Force max component initial, final = 4.3102487 0.10608657 Final line search alpha, max atom move = 1.0000000 0.10608657 Iterations, force evaluations = 76 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8002 | 3.8002 | 3.8002 | 0.0 | 98.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.026502 | 0.026502 | 0.026502 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02354 | | | 0.61 Nlocal: 1359.00 ave 1359 max 1359 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7941.00 ave 7941 max 7941 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: 236466.0 ave 236466 max 236466 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236466 Ave neighs/atom = 174.00000 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 24 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 : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.494 | 5.494 | 5.494 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -5958.2738 0 -5958.2738 -3491.8385 15521.783 82 0 -5958.6241 0 -5958.6241 -2629.5985 15510.415 Loop time of 0.214522 on 1 procs for 6 steps with 1359 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 = -5958.27375772201 -5958.62398161469 -5958.62413391779 Force two-norm initial, final = 102.52319 0.72483266 Force max component initial, final = 80.334142 0.36921541 Final line search alpha, max atom move = 0.00061845141 0.00022834179 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20833 | 0.20833 | 0.20833 | 0.0 | 97.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013852 | 0.0013852 | 0.0013852 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004811 | | | 2.24 Nlocal: 1359.00 ave 1359 max 1359 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7949.00 ave 7949 max 7949 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: 236934.0 ave 236934 max 236934 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236934 Ave neighs/atom = 174.34437 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 = 9 24 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) = 5.632 | 5.632 | 5.632 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5958.6241 0 -5958.6241 -2629.5985 Loop time of 6.535e-06 on 1 procs for 0 steps with 1359 atoms 183.6% 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 | | 6.535e-06 | | |100.00 Nlocal: 1359.00 ave 1359 max 1359 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7949.00 ave 7949 max 7949 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: 237028.0 ave 237028 max 237028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237028 Ave neighs/atom = 174.41354 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 = 9 24 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) = 5.632 | 5.632 | 5.632 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 -5958.6241 -5958.6241 33.158516 93.385048 5.0089996 -2629.5985 -2629.5985 -38.305629 -7828.8466 -21.643246 2.3428917 959.10193 Loop time of 6.645e-06 on 1 procs for 0 steps with 1359 atoms 285.9% 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 | | 6.645e-06 | | |100.00 Nlocal: 1359.00 ave 1359 max 1359 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7949.00 ave 7949 max 7949 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 118514.0 ave 118514 max 118514 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 237028.0 ave 237028 max 237028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237028 Ave neighs/atom = 174.41354 Neighbor list builds = 0 Dangerous builds = 0 1359 -5958.62413391779 eV 2.34289169057304 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04