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 = 4.0612135 4.0612135 4.0612135 Created orthogonal box = (0.0000000 -57.146339 0.0000000) to (13.469521 57.146339 5.7434232) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1225097 6.9268290 5.7434232 Created 264 atoms using lattice units in orthogonal box = (0.0000000 -57.146339 0.0000000) to (13.469521 57.146339 5.7434232) create_atoms CPU = 0.003 seconds 264 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1225097 6.9268290 5.7434232 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -57.146339 0.0000000) to (13.469521 57.146339 5.7434232) create_atoms CPU = 0.002 seconds 266 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 3 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 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 524 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_411898953661_004#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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 3 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 4.950 | 4.950 | 4.950 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1383.7078 0 -1383.7078 5017.1354 61 0 -1408.2697 0 -1408.2697 -1946.3289 Loop time of 1.82289 on 1 procs for 61 steps with 524 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 = -1383.70776431691 -1408.26838866366 -1408.26972748612 Force two-norm initial, final = 44.862970 0.11518407 Force max component initial, final = 15.698296 0.011913562 Final line search alpha, max atom move = 1.0000000 0.011913562 Iterations, force evaluations = 61 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7817 | 1.7817 | 1.7817 | 0.0 | 97.74 Neigh | 0.016395 | 0.016395 | 0.016395 | 0.0 | 0.90 Comm | 0.01476 | 0.01476 | 0.01476 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01004 | | | 0.55 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5890.00 ave 5890 max 5890 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: 117564.0 ave 117564 max 117564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117564 Ave neighs/atom = 224.35878 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 3 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 4.950 | 4.950 | 4.950 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -1408.2697 0 -1408.2697 -1946.3289 8841.8143 71 0 -1408.5361 0 -1408.5361 -43.081554 8818.0187 Loop time of 0.196017 on 1 procs for 10 steps with 524 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 = -1408.26972748612 -1408.53605511636 -1408.53613586736 Force two-norm initial, final = 52.044168 0.52749534 Force max component initial, final = 46.043247 0.34058496 Final line search alpha, max atom move = 0.0013270823 0.00045198427 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19001 | 0.19001 | 0.19001 | 0.0 | 96.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013984 | 0.0013984 | 0.0013984 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004612 | | | 2.35 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5899.00 ave 5899 max 5899 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: 117600.0 ave 117600 max 117600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117600 Ave neighs/atom = 224.42748 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 3 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 5.088 | 5.088 | 5.088 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1408.5361 0 -1408.5361 -43.081554 Loop time of 6.575e-06 on 1 procs for 0 steps with 524 atoms 167.3% 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 | | 6.575e-06 | | |100.00 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5935.00 ave 5935 max 5935 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: 117488.0 ave 117488 max 117488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117488 Ave neighs/atom = 224.21374 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 3 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 5.088 | 5.088 | 5.088 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 -1408.5361 -1408.5361 13.34727 114.87791 5.7509826 -43.081554 -43.081554 -61.320413 -19.420098 -48.504152 2.645985 476.18701 Loop time of 6.535e-06 on 1 procs for 0 steps with 524 atoms 290.7% 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 | | 6.535e-06 | | |100.00 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5935.00 ave 5935 max 5935 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58744.0 ave 58744 max 58744 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 117488.0 ave 117488 max 117488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 117488 Ave neighs/atom = 224.21374 Neighbor list builds = 0 Dangerous builds = 0 524 -1408.53613586736 eV 2.64598502122333 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02