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 = 2.8603420 2.8603420 2.8603420 Created orthogonal box = (0.0000000 -50.526574 0.0000000) to (29.169879 50.526574 4.9542577) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4876738 4.5341794 4.9542577 Created 626 atoms using lattice units in orthogonal box = (0.0000000 -50.526574 0.0000000) to (29.169879 50.526574 4.9542577) create_atoms CPU = 0.001 seconds 626 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4876738 4.5341794 4.9542577 Created 626 atoms using lattice units in orthogonal box = (0.0000000 -50.526574 0.0000000) to (29.169879 50.526574 4.9542577) create_atoms CPU = 0.001 seconds 626 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 26 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1248 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_820335782779_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.459 | 5.459 | 5.459 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5265.9421 0 -5265.9421 15202.618 188 0 -5454.1711 0 -5454.1711 -6522.5292 Loop time of 3.25426 on 1 procs for 188 steps with 1248 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 = -5265.9421414978 -5454.16627872991 -5454.17113857093 Force two-norm initial, final = 57.357087 0.30068261 Force max component initial, final = 8.3485063 0.069906512 Final line search alpha, max atom move = 0.86970687 0.060798174 Iterations, force evaluations = 188 318 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1501 | 3.1501 | 3.1501 | 0.0 | 96.80 Neigh | 0.062626 | 0.062626 | 0.062626 | 0.0 | 1.92 Comm | 0.022339 | 0.022339 | 0.022339 | 0.0 | 0.69 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01921 | | | 0.59 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7762.00 ave 7762 max 7762 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: 203232.0 ave 203232 max 203232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203232 Ave neighs/atom = 162.84615 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 188 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.457 | 5.457 | 5.457 Mbytes Step Temp E_pair E_mol TotEng Press Volume 188 0 -5454.1711 0 -5454.1711 -6522.5292 14603.706 195 0 -5454.683 0 -5454.683 -13327.638 14648.248 Loop time of 0.098775 on 1 procs for 7 steps with 1248 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 = -5454.17113857093 -5454.68298725615 -5454.68302324314 Force two-norm initial, final = 179.36059 0.73501950 Force max component initial, final = 178.10107 0.22675517 Final line search alpha, max atom move = 0.00082967420 0.00018813291 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.095703 | 0.095703 | 0.095703 | 0.0 | 96.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00055332 | 0.00055332 | 0.00055332 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002519 | | | 2.55 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7632.00 ave 7632 max 7632 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: 202736.0 ave 202736 max 202736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202736 Ave neighs/atom = 162.44872 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.595 | 5.595 | 5.595 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5454.683 0 -5454.683 -13327.638 Loop time of 1.58e-06 on 1 procs for 0 steps with 1248 atoms 189.9% 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 | | 1.58e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7611.00 ave 7611 max 7611 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: 201124.0 ave 201124 max 201124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201124 Ave neighs/atom = 161.15705 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.595 | 5.595 | 5.595 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 -5454.683 -5454.683 29.092047 101.05315 4.9826634 -13327.638 -13327.638 -21.129838 -39936.84 -24.943928 2.3828688 6592.8804 Loop time of 1.506e-06 on 1 procs for 0 steps with 1248 atoms 199.2% 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 | | 1.506e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7611.00 ave 7611 max 7611 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100562.0 ave 100562 max 100562 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 201124.0 ave 201124 max 201124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201124 Ave neighs/atom = 161.15705 Neighbor list builds = 0 Dangerous builds = 0 1248 -5454.68302324314 eV 2.38286877995064 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03