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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -35.687464 0.0000000) to (25.234848 35.687464 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8963138 5.3264872 4.3599177 Created 268 atoms using lattice units in orthogonal box = (0.0000000 -35.687464 0.0000000) to (25.234848 35.687464 4.3599177) create_atoms CPU = 0.002 seconds 268 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8963138 5.3264872 4.3599177 Created 270 atoms using lattice units in orthogonal box = (0.0000000 -35.687464 0.0000000) to (25.234848 35.687464 4.3599177) create_atoms CPU = 0.001 seconds 270 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 22 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 538 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.235 | 5.235 | 5.235 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2884.2968 0 -2884.2968 256715.6 257 0 -3488.2436 0 -3488.2436 12823.982 Loop time of 137.667 on 1 procs for 257 steps with 538 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 = -2884.29680337956 -3488.24021798673 -3488.24364467943 Force two-norm initial, final = 1094.0360 0.28307946 Force max component initial, final = 352.80606 0.069737757 Final line search alpha, max atom move = 1.0000000 0.069737757 Iterations, force evaluations = 257 496 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 137.4 | 137.4 | 137.4 | 0.0 | 99.80 Neigh | 0.21819 | 0.21819 | 0.21819 | 0.0 | 0.16 Comm | 0.02825 | 0.02825 | 0.02825 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02441 | | | 0.02 Nlocal: 538.000 ave 538 max 538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3346.00 ave 3346 max 3346 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: 41192.0 ave 41192 max 41192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41192 Ave neighs/atom = 76.565056 Neighbor list builds = 6 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 257 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.235 | 5.235 | 5.235 Mbytes Step Temp E_pair E_mol TotEng Press Volume 257 0 -3488.2436 0 -3488.2436 12823.982 7852.8025 265 0 -3488.8228 0 -3488.8228 -25.325958 7898.3036 Loop time of 3.01593 on 1 procs for 8 steps with 538 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 = -3488.24364467943 -3488.82273758777 -3488.82282656246 Force two-norm initial, final = 150.08311 1.0142747 Force max component initial, final = 123.18210 0.49725187 Final line search alpha, max atom move = 0.0011605680 0.00057709460 Iterations, force evaluations = 8 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0126 | 3.0126 | 3.0126 | 0.0 | 99.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005786 | 0.0005786 | 0.0005786 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002704 | | | 0.09 Nlocal: 538.000 ave 538 max 538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3346.00 ave 3346 max 3346 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: 41240.0 ave 41240 max 41240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 41240 Ave neighs/atom = 76.654275 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.373 | 5.373 | 5.373 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3488.8228 0 -3488.8228 -25.325958 Loop time of 3.708e-06 on 1 procs for 0 steps with 538 atoms 161.8% 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 | | 3.708e-06 | | |100.00 Nlocal: 538.000 ave 538 max 538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3342.00 ave 3342 max 3342 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: 40828.0 ave 40828 max 40828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40828 Ave neighs/atom = 75.888476 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.373 | 5.373 | 5.373 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 -3488.8228 -3488.8228 25.352637 71.778841 4.3402449 -25.325958 -25.325958 -101.33872 58.907684 -33.546838 2.5022173 2053.327 Loop time of 3.681e-06 on 1 procs for 0 steps with 538 atoms 163.0% 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 | | 3.681e-06 | | |100.00 Nlocal: 538.000 ave 538 max 538 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3342.00 ave 3342 max 3342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 20414.0 ave 20414 max 20414 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 40828.0 ave 40828 max 40828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 40828 Ave neighs/atom = 75.888476 Neighbor list builds = 0 Dangerous builds = 0 538 -3488.82282656246 eV 2.50221734612989 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:02:22