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 = 3.6110509 3.6110509 3.6110509 Created orthogonal box = (0.0000000 -62.545236 0.0000000) to (25.533986 62.545236 8.8452321) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1281566 5.4205871 5.8968214 Created 1193 atoms using lattice units in orthogonal box = (0.0000000 -62.545236 0.0000000) to (25.533986 62.545236 8.8452321) create_atoms CPU = 0.002 seconds 1193 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1281566 5.4205871 5.8968214 Created 1201 atoms using lattice units in orthogonal box = (0.0000000 -62.545236 0.0000000) to (25.533986 62.545236 8.8452321) create_atoms CPU = 0.002 seconds 1201 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 25 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 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2394 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_984358344196_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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 12.47 | 12.47 | 12.47 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9781.2376 0 -9781.2376 14875.735 85 0 -9921.7014 0 -9921.7014 -666.17872 Loop time of 5.51363 on 1 procs for 85 steps with 2394 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9781.23764761399 -9921.69238440601 -9921.70141475778 Force two-norm initial, final = 110.54572 0.40991707 Force max component initial, final = 34.036040 0.028495490 Final line search alpha, max atom move = 1.0000000 0.028495490 Iterations, force evaluations = 85 149 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2932 | 5.2932 | 5.2932 | 0.0 | 96.00 Neigh | 0.16236 | 0.16236 | 0.16236 | 0.0 | 2.94 Comm | 0.034552 | 0.034552 | 0.034552 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02348 | | | 0.43 Nlocal: 2394.00 ave 2394 max 2394 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14416.0 ave 14416 max 14416 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: 908836.0 ave 908836 max 908836 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 908836 Ave neighs/atom = 379.63074 Neighbor list builds = 3 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.47 | 12.47 | 12.47 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -9921.7014 0 -9921.7014 -666.17872 28252.188 88 0 -9921.8049 0 -9921.8049 28.215649 28240.729 Loop time of 0.220937 on 1 procs for 3 steps with 2394 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9921.70141475776 -9921.80450053444 -9921.80487342261 Force two-norm initial, final = 100.13809 0.97069899 Force max component initial, final = 85.970917 0.56421594 Final line search alpha, max atom move = 0.00020081875 0.00011330514 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21631 | 0.21631 | 0.21631 | 0.0 | 97.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00079273 | 0.00079273 | 0.00079273 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003833 | | | 1.73 Nlocal: 2394.00 ave 2394 max 2394 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14371.0 ave 14371 max 14371 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: 909404.0 ave 909404 max 909404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 909404 Ave neighs/atom = 379.86800 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 11.98 | 11.98 | 11.98 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9921.8049 0 -9921.8049 28.215649 Loop time of 2.303e-06 on 1 procs for 0 steps with 2394 atoms 173.7% 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 | | 2.303e-06 | | |100.00 Nlocal: 2394.00 ave 2394 max 2394 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14413.0 ave 14413 max 14413 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: 909252.0 ave 909252 max 909252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 909252 Ave neighs/atom = 379.80451 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 11.98 | 11.98 | 11.98 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 -9921.8049 -9921.8049 25.492655 125.25607 8.8442714 28.215649 28.215649 31.957756 28.395005 24.294186 2.3838223 1288.5091 Loop time of 2.717e-06 on 1 procs for 0 steps with 2394 atoms 257.6% 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 | | 2.717e-06 | | |100.00 Nlocal: 2394.00 ave 2394 max 2394 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14413.0 ave 14413 max 14413 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 454626.0 ave 454626 max 454626 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 909252.0 ave 909252 max 909252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 909252 Ave neighs/atom = 379.80451 Neighbor list builds = 0 Dangerous builds = 0 2394 -9921.80487342261 eV 2.38382231724287 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06