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 = 4.0501996 4.0501996 4.0501996 Created orthogonal box = (0.0000000 -77.484881 0.0000000) to (44.735917 77.484881 7.0151515) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6003812 5.9278051 7.0151515 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -77.484881 0.0000000) to (44.735917 77.484881 7.0151515) create_atoms CPU = 0.003 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6003812 5.9278051 7.0151515 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -77.484881 0.0000000) to (44.735917 77.484881 7.0151515) create_atoms CPU = 0.003 seconds 1466 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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 11 37 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 8.403928746393108 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2926 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_060567868558_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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928746393108 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) = 6.601 | 6.601 | 6.601 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10317.507 0 -10317.507 7200.9745 107 0 -10463.023 0 -10463.023 4234.9079 Loop time of 4.49766 on 1 procs for 107 steps with 2926 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10317.506930569 -10463.0152363147 -10463.0228336888 Force two-norm initial, final = 138.60974 0.17695055 Force max component initial, final = 36.246524 0.034635114 Final line search alpha, max atom move = 1.0000000 0.034635114 Iterations, force evaluations = 107 183 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2989 | 4.2989 | 4.2989 | 0.0 | 95.58 Neigh | 0.14134 | 0.14134 | 0.14134 | 0.0 | 3.14 Comm | 0.02814 | 0.02814 | 0.02814 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02932 | | | 0.65 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11911.0 ave 11911 max 11911 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: 409924.0 ave 409924 max 409924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 409924 Ave neighs/atom = 140.09706 Neighbor list builds = 5 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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928746393108 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 107 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.601 | 6.601 | 6.601 Mbytes Step Temp E_pair E_mol TotEng Press Volume 107 0 -10463.023 0 -10463.023 4234.9079 48634.042 113 0 -10463.554 0 -10463.554 -230.00574 48919.272 Loop time of 0.18105 on 1 procs for 6 steps with 2926 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 = -10463.0228336888 -10463.5495960173 -10463.5537371021 Force two-norm initial, final = 237.28612 14.200945 Force max component initial, final = 195.37089 10.241415 Final line search alpha, max atom move = 5.6614295e-05 0.00057981048 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17562 | 0.17562 | 0.17562 | 0.0 | 97.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00078942 | 0.00078942 | 0.00078942 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004641 | | | 2.56 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11915.0 ave 11915 max 11915 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: 409944.0 ave 409944 max 409944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 409944 Ave neighs/atom = 140.10390 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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928746393108 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) = 6.740 | 6.740 | 6.740 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10463.554 0 -10463.554 -230.00574 Loop time of 2.713e-06 on 1 procs for 0 steps with 2926 atoms 184.3% 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 | | 2.713e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11891.0 ave 11891 max 11891 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: 409628.0 ave 409628 max 409628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 409628 Ave neighs/atom = 139.99590 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 = 8.4039287 ghost atom cutoff = 8.4039287 binsize = 4.2019644, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.403928746393108 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) = 6.740 | 6.740 | 6.740 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 -10463.554 -10463.554 44.748456 155.83839 7.0149966 -230.00574 -230.00574 -335.51508 -34.192198 -320.30993 2.5960914 1207.3118 Loop time of 2.587e-06 on 1 procs for 0 steps with 2926 atoms 270.6% 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 | | 2.587e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11891.0 ave 11891 max 11891 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 204814.0 ave 204814 max 204814 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 409628.0 ave 409628 max 409628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 409628 Ave neighs/atom = 139.99590 Neighbor list builds = 0 Dangerous builds = 0 2926 -10463.5537371021 eV 2.59609144637621 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05