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 = 3.6583664 3.6583664 3.6583664 Created orthogonal box = (0.0000000 -72.431959 0.0000000) to (44.355335 72.431959 8.9611309) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1295286 5.1737114 5.9740873 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -72.431959 0.0000000) to (44.355335 72.431959 8.9611309) create_atoms CPU = 0.003 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1295286 5.1737114 5.9740873 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -72.431959 0.0000000) to (44.355335 72.431959 8.9611309) create_atoms CPU = 0.003 seconds 2358 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 13 40 3 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 4710 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_807997826449_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 13 40 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 11.46 | 11.46 | 11.46 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -18316.179 0 -18316.179 35197.721 1329 0 -19083.336 0 -19083.336 -49919.901 Loop time of 82.9211 on 1 procs for 1329 steps with 4710 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -18316.1790434303 -19083.3204254088 -19083.3358305327 Force two-norm initial, final = 431.70578 0.35923337 Force max component initial, final = 59.517115 0.035628620 Final line search alpha, max atom move = 0.58375103 0.020798244 Iterations, force evaluations = 1329 2615 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 81.032 | 81.032 | 81.032 | 0.0 | 97.72 Neigh | 0.94212 | 0.94212 | 0.94212 | 0.0 | 1.14 Comm | 0.38733 | 0.38733 | 0.38733 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.5596 | | | 0.67 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13263.0 ave 13263 max 13263 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: 660218.0 ave 660218 max 660218 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 660218 Ave neighs/atom = 140.17367 Neighbor list builds = 22 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 13 40 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1329 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.46 | 11.46 | 11.46 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1329 0 -19083.336 0 -19083.336 -49919.901 57579.636 1382 0 -19202.393 0 -19202.393 9.223549 55877.361 Loop time of 1.97829 on 1 procs for 53 steps with 4710 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 = -19083.3358305327 -19202.3816653057 -19202.3926091112 Force two-norm initial, final = 4264.2796 29.399089 Force max component initial, final = 3331.0646 20.279959 Final line search alpha, max atom move = 0.00059497094 0.012065987 Iterations, force evaluations = 53 55 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.695 | 1.695 | 1.695 | 0.0 | 85.68 Neigh | 0.22617 | 0.22617 | 0.22617 | 0.0 | 11.43 Comm | 0.0082102 | 0.0082102 | 0.0082102 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04887 | | | 2.47 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13089.0 ave 13089 max 13089 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: 663524.0 ave 663524 max 663524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 663524 Ave neighs/atom = 140.87558 Neighbor list builds = 5 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 39 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 10.96 | 10.96 | 10.96 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19202.393 0 -19202.393 9.223549 Loop time of 2.225e-06 on 1 procs for 0 steps with 4710 atoms 179.8% 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 | | 2.225e-06 | | |100.00 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13012.0 ave 13012 max 13012 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: 654048.0 ave 654048 max 654048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 654048 Ave neighs/atom = 138.86369 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 39 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 10.96 | 10.96 | 10.96 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 -19202.393 -19202.393 43.027855 139.21612 9.3281744 9.223549 9.223549 564.08608 -544.03934 7.6239079 2.2150398 4947.9932 Loop time of 2.7e-06 on 1 procs for 0 steps with 4710 atoms 333.3% 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 | | 2.7e-06 | | |100.00 Nlocal: 4710.00 ave 4710 max 4710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13012.0 ave 13012 max 13012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 327024.0 ave 327024 max 327024 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 654048.0 ave 654048 max 654048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 654048 Ave neighs/atom = 138.86369 Neighbor list builds = 0 Dangerous builds = 0 4710 -19202.3926091112 eV 2.21503980270228 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:25