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 = 2.8669658 2.8669658 2.8669658 Created orthogonal box = (0.0000000 -30.071858 0.0000000) to (36.826842 30.071858 7.0226033) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6870527 4.3736714 4.6817355 Created 662 atoms using lattice units in orthogonal box = (0.0000000 -30.071858 0.0000000) to (36.826842 30.071858 7.0226033) create_atoms CPU = 0.001 seconds 662 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6870527 4.3736714 4.6817355 Created 662 atoms using lattice units in orthogonal box = (0.0000000 -30.071858 0.0000000) to (36.826842 30.071858 7.0226033) create_atoms CPU = 0.001 seconds 662 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 16 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 32 atoms, new total = 1292 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.466 | 5.466 | 5.466 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5103.5987 0 -5103.5987 5055.8149 114 0 -5178.3365 0 -5178.3365 -72507.985 Loop time of 1.96873 on 1 procs for 114 steps with 1292 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 = -5103.59867127657 -5178.33290783811 -5178.33649532466 Force two-norm initial, final = 48.838242 0.17809555 Force max component initial, final = 9.7932499 0.064468744 Final line search alpha, max atom move = 0.93556046 0.060314407 Iterations, force evaluations = 114 214 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9345 | 1.9345 | 1.9345 | 0.0 | 98.26 Neigh | 0.012304 | 0.012304 | 0.012304 | 0.0 | 0.62 Comm | 0.010422 | 0.010422 | 0.010422 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01147 | | | 0.58 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5932.00 ave 5932 max 5932 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: 207222.0 ave 207222 max 207222 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207222 Ave neighs/atom = 160.38854 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 114 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.466 | 5.466 | 5.466 Mbytes Step Temp E_pair E_mol TotEng Press Volume 114 0 -5178.3365 0 -5178.3365 -72507.985 15554.386 272 0 -5216.4671 0 -5216.4671 -15385.006 14164.97 Loop time of 1.71403 on 1 procs for 158 steps with 1292 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 = -5178.33649532467 -5216.46320944431 -5216.46714540207 Force two-norm initial, final = 963.53083 5.6141616 Force max component initial, final = 697.49424 2.2928213 Final line search alpha, max atom move = 0.00011511927 0.00026394790 Iterations, force evaluations = 158 176 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6515 | 1.6515 | 1.6515 | 0.0 | 96.35 Neigh | 0.012052 | 0.012052 | 0.012052 | 0.0 | 0.70 Comm | 0.0078921 | 0.0078921 | 0.0078921 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04257 | | | 2.48 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6014.00 ave 6014 max 6014 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: 209648.0 ave 209648 max 209648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 209648 Ave neighs/atom = 162.26625 Neighbor list builds = 1 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.605 | 5.605 | 5.605 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5216.4671 0 -5216.4671 -15385.006 Loop time of 1.648e-06 on 1 procs for 0 steps with 1292 atoms 182.0% 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 | | 1.648e-06 | | |100.00 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6098.00 ave 6098 max 6098 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: 212284.0 ave 212284 max 212284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212284 Ave neighs/atom = 164.30650 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.605 | 5.605 | 5.605 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 -5216.4671 -5216.4671 35.205315 60.143716 6.6898622 -15385.006 -15385.006 -247.91834 -46033.854 126.75457 2.2862789 6601.3088 Loop time of 1.78e-06 on 1 procs for 0 steps with 1292 atoms 168.5% 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 | | 1.78e-06 | | |100.00 Nlocal: 1292.00 ave 1292 max 1292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6098.00 ave 6098 max 6098 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 106142.0 ave 106142 max 106142 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 212284.0 ave 212284 max 212284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212284 Ave neighs/atom = 164.30650 Neighbor list builds = 0 Dangerous builds = 0 1292 -5216.46714540207 eV 2.28627893839054 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04