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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -40.858527 0.0000000) to (5.1068645 40.858527 3.6110985) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1068645 5.1068645 3.6110985 Created 66 atoms using lattice units in orthogonal box = (0.0000000 -40.858527 0.0000000) to (5.1068645 40.858527 3.6110985) create_atoms CPU = 0.001 seconds 66 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1068645 5.1068645 3.6110985 Created 66 atoms using lattice units in orthogonal box = (0.0000000 -40.858527 0.0000000) to (5.1068645 40.858527 3.6110985) create_atoms CPU = 0.001 seconds 66 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 2 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 124 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_110119204723_001#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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 2 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.406 | 4.406 | 4.406 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -520.16537 0 -520.16537 -13513.968 35 0 -524.9111 0 -524.9111 -49419.341 Loop time of 1.34758 on 1 procs for 35 steps with 124 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 = -520.165370815361 -524.910799716768 -524.911098597512 Force two-norm initial, final = 1.5653961 0.038761500 Force max component initial, final = 0.44798478 0.0054047120 Final line search alpha, max atom move = 1.0000000 0.0054047120 Iterations, force evaluations = 35 63 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3419 | 1.3419 | 1.3419 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0035535 | 0.0035535 | 0.0035535 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002155 | | | 0.16 Nlocal: 124.000 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2396.00 ave 2396 max 2396 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: 15928.0 ave 15928 max 15928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15928 Ave neighs/atom = 128.45161 Neighbor list builds = 0 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 2 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.406 | 4.406 | 4.406 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -524.9111 0 -524.9111 -49419.341 1506.9762 226 0 -527.25654 0 -527.25654 41839.586 1426.8211 Loop time of 6.98886 on 1 procs for 191 steps with 124 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 = -524.911098597512 -527.256260191193 -527.25654134419 Force two-norm initial, final = 52.932969 0.25517181 Force max component initial, final = 45.590813 0.25137500 Final line search alpha, max atom move = 0.0032866020 0.00082616957 Iterations, force evaluations = 191 191 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.9394 | 6.9394 | 6.9394 | 0.0 | 99.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.011598 | 0.011598 | 0.011598 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03789 | | | 0.54 Nlocal: 124.000 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2396.00 ave 2396 max 2396 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: 13640.0 ave 13640 max 13640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13640 Ave neighs/atom = 110.00000 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 2 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.558 | 4.558 | 4.558 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -527.25654 0 -527.25654 41839.586 Loop time of 6.445e-06 on 1 procs for 0 steps with 124 atoms 186.2% 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 | | 6.445e-06 | | |100.00 Nlocal: 124.000 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2900.00 ave 2900 max 2900 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: 14880.0 ave 14880 max 14880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 14880 Ave neighs/atom = 120.00000 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 2 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.558 | 4.558 | 4.558 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 -527.25654 -527.25654 5.9066705 81.717055 2.9560657 41839.586 41839.586 -23.826549 125773.65 -231.06685 2.4681276 0.00067171779 Loop time of 8.049e-06 on 1 procs for 0 steps with 124 atoms 248.5% 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 | | 8.049e-06 | | |100.00 Nlocal: 124.000 ave 124 max 124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2900.00 ave 2900 max 2900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 7440.00 ave 7440 max 7440 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 14880.0 ave 14880 max 14880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 14880 Ave neighs/atom = 120.00000 Neighbor list builds = 0 Dangerous builds = 0 124 -527.25654134419 eV 2.46812761867019 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08