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 = 3.5200244 3.5200244 3.5200244 Created orthogonal box = (0.0000000 -38.563455 0.0000000) to (7.8710137 38.563455 8.6222635) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7226082 5.1413246 5.7481757 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -38.563455 0.0000000) to (7.8710137 38.563455 8.6222635) create_atoms CPU = 0.002 seconds 242 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7226082 5.1413246 5.7481757 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -38.563455 0.0000000) to (7.8710137 38.563455 8.6222635) create_atoms CPU = 0.001 seconds 242 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 2 19 3 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 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 472 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_532072268679_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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 2 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 4.996 | 4.996 | 4.996 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2081.8695 0 -2081.8695 -1760.3722 60 0 -2089.4691 0 -2089.4691 -16315.363 Loop time of 1.31055 on 1 procs for 60 steps with 472 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 = -2081.86948469472 -2089.46737205846 -2089.46906580624 Force two-norm initial, final = 9.4595690 0.12897490 Force max component initial, final = 2.0043982 0.011332398 Final line search alpha, max atom move = 1.0000000 0.011332398 Iterations, force evaluations = 60 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2894 | 1.2894 | 1.2894 | 0.0 | 98.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.012098 | 0.012098 | 0.012098 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009093 | | | 0.69 Nlocal: 472.000 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4888.00 ave 4888 max 4888 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: 104140.0 ave 104140 max 104140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104140 Ave neighs/atom = 220.63559 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 2 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.994 | 4.994 | 4.994 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -2089.4691 0 -2089.4691 -16315.363 5234.2914 65 0 -2089.6599 0 -2089.6599 -2964.4677 5194.0266 Loop time of 0.0852976 on 1 procs for 5 steps with 472 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 = -2089.46906580623 -2089.65879283791 -2089.65991233418 Force two-norm initial, final = 69.977994 1.6374857 Force max component initial, final = 52.232533 1.6144045 Final line search alpha, max atom move = 0.00021238060 0.00034286819 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.082281 | 0.082281 | 0.082281 | 0.0 | 96.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00067097 | 0.00067097 | 0.00067097 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002345 | | | 2.75 Nlocal: 472.000 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4720.00 ave 4720 max 4720 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: 104564.0 ave 104564 max 104564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104564 Ave neighs/atom = 221.53390 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 2 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.132 | 5.132 | 5.132 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2089.6599 0 -2089.6599 -2964.4677 Loop time of 6.555e-06 on 1 procs for 0 steps with 472 atoms 167.8% 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 | | 6.555e-06 | | |100.00 Nlocal: 472.000 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4720.00 ave 4720 max 4720 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: 104668.0 ave 104668 max 104668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104668 Ave neighs/atom = 221.75424 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 2 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.132 | 5.132 | 5.132 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 -2089.6599 -2089.6599 7.8358419 77.12691 8.5943408 -2964.4677 -2964.4677 -51.061058 -9338.717 496.37492 2.2094254 287.52135 Loop time of 7.247e-06 on 1 procs for 0 steps with 472 atoms 276.0% 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 | | 7.247e-06 | | |100.00 Nlocal: 472.000 ave 472 max 472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4720.00 ave 4720 max 4720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52334.0 ave 52334 max 52334 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 104668.0 ave 104668 max 104668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104668 Ave neighs/atom = 221.75424 Neighbor list builds = 0 Dangerous builds = 0 472 -2076.79253068458 eV 2.20942541299409 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01