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 = 3.6063026 3.6063026 3.6063026 Created orthogonal box = (0.0000000 -51.508304 0.0000000) to (36.421871 51.508304 5.1000820) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7132346 4.5448503 5.1000820 Created 813 atoms using lattice units in orthogonal box = (0.0000000 -51.508304 0.0000000) to (36.421871 51.508304 5.1000820) create_atoms CPU = 0.002 seconds 813 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7132346 4.5448503 5.1000820 Created 821 atoms using lattice units in orthogonal box = (0.0000000 -51.508304 0.0000000) to (36.421871 51.508304 5.1000820) create_atoms CPU = 0.001 seconds 821 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 7 18 1 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1634 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_147603128437_004#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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 7 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 12.65 | 12.65 | 12.65 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6431.2883 0 -6431.2883 52703.621 81 0 -6836.6417 0 -6836.6417 7609.4719 Loop time of 7.23642 on 1 procs for 81 steps with 1634 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6431.28832525248 -6836.63545926471 -6836.64173635198 Force two-norm initial, final = 429.53817 0.35586366 Force max component initial, final = 111.31068 0.032436490 Final line search alpha, max atom move = 0.51427521 0.016681283 Iterations, force evaluations = 81 140 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.0419 | 7.0419 | 7.0419 | 0.0 | 97.31 Neigh | 0.1438 | 0.1438 | 0.1438 | 0.0 | 1.99 Comm | 0.033037 | 0.033037 | 0.033037 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01769 | | | 0.24 Nlocal: 1634.00 ave 1634 max 1634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17481.0 ave 17481 max 17481 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: 1.01171e+06 ave 1.01171e+06 max 1.01171e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1011710 Ave neighs/atom = 619.16157 Neighbor list builds = 3 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 7 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.65 | 12.65 | 12.65 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -6836.6417 0 -6836.6417 7609.4719 19135.801 87 0 -6836.9702 0 -6836.9702 -2.1711636 19219.963 Loop time of 0.427007 on 1 procs for 6 steps with 1634 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 = -6836.64173635193 -6836.96506247135 -6836.97021582494 Force two-norm initial, final = 167.07453 0.97369965 Force max component initial, final = 135.31171 0.60859944 Final line search alpha, max atom move = 7.0787088e-05 4.3080982e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.42003 | 0.42003 | 0.42003 | 0.0 | 98.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013368 | 0.0013368 | 0.0013368 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005639 | | | 1.32 Nlocal: 1634.00 ave 1634 max 1634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17496.0 ave 17496 max 17496 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: 1.01152e+06 ave 1.01152e+06 max 1.01152e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1011524 Ave neighs/atom = 619.04774 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 7 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 12.16 | 12.16 | 12.16 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6836.9702 0 -6836.9702 -2.1711636 Loop time of 3.687e-06 on 1 procs for 0 steps with 1634 atoms 135.6% 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 | | 3.687e-06 | | |100.00 Nlocal: 1634.00 ave 1634 max 1634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17496.0 ave 17496 max 17496 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: 1.00835e+06 ave 1.00835e+06 max 1.00835e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1008352 Ave neighs/atom = 617.10649 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 7 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 12.16 | 12.16 | 12.16 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 -6836.9702 -6836.9702 36.397575 103.5619 5.0989422 -2.1711636 -2.1711636 -50.699019 -0.49166552 44.677193 2.3728563 990.08003 Loop time of 2.967e-06 on 1 procs for 0 steps with 1634 atoms 269.6% 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 | | 2.967e-06 | | |100.00 Nlocal: 1634.00 ave 1634 max 1634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17496.0 ave 17496 max 17496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 504176.0 ave 504176 max 504176 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.00835e+06 ave 1.00835e+06 max 1.00835e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1008352 Ave neighs/atom = 617.10649 Neighbor list builds = 0 Dangerous builds = 0 1634 -6836.97021582494 eV 2.37285632999608 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08