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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -47.926958 0.0000000) to (23.963479 47.926958 3.1465590) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1316343 4.1316343 3.1465590 Created 232 atoms using lattice units in orthogonal box = (0.0000000 -47.926958 0.0000000) to (23.963479 47.926958 3.1465590) create_atoms CPU = 0.001 seconds 232 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1316343 4.1316343 3.1465590 Created 234 atoms using lattice units in orthogonal box = (0.0000000 -47.926958 0.0000000) to (23.963479 47.926958 3.1465590) create_atoms CPU = 0.000 seconds 234 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 34 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 464 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.449 | 4.449 | 4.449 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3108.6365 0 -3108.6365 25649.863 17 0 -4951.1162 0 -4951.1162 20087.279 Loop time of 1.42733 on 1 procs for 17 steps with 464 atoms 98.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3108.63652786489 -4951.11600574967 -4951.11619099154 Force two-norm initial, final = 25.498662 1231.6258 Force max component initial, final = 5.1919253 353.65225 Final line search alpha, max atom move = 1.3201099e-07 4.6685982e-05 Iterations, force evaluations = 17 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4207 | 1.4207 | 1.4207 | 0.0 | 99.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0037353 | 0.0037353 | 0.0037353 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002918 | | | 0.20 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3406.00 ave 3406 max 3406 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: 26816.0 ave 26816 max 26816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26816 Ave neighs/atom = 57.793103 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 17 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.449 | 4.449 | 4.449 Mbytes Step Temp E_pair E_mol TotEng Press Volume 17 0 -4951.1162 0 -4951.1162 20087.279 7227.6249 18 0 -4951.1171 0 -4951.1171 20071.555 7227.6262 Loop time of 0.0966556 on 1 procs for 1 steps with 464 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 = -4951.11619099154 -4951.11619099154 -4951.11707437943 Force two-norm initial, final = 1242.6383 934.06288 Force max component initial, final = 353.65225 264.77989 Final line search alpha, max atom move = 1.2080804e-07 3.1987539e-05 Iterations, force evaluations = 1 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.095506 | 0.095506 | 0.095506 | 0.0 | 98.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021313 | 0.00021313 | 0.00021313 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009365 | | | 0.97 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3411.00 ave 3411 max 3411 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: 26856.0 ave 26856 max 26856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26856 Ave neighs/atom = 57.879310 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.587 | 4.587 | 4.587 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4951.1171 0 -4951.1171 20071.555 Loop time of 1.575e-06 on 1 procs for 0 steps with 464 atoms 190.5% 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 | | 1.575e-06 | | |100.00 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3411.00 ave 3411 max 3411 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: 26856.0 ave 26856 max 26856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26856 Ave neighs/atom = 57.879310 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 9 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.587 | 4.587 | 4.587 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 -4951.1171 -4951.1171 23.96348 95.853924 3.1465591 20071.555 20071.555 18758.302 28654.755 12801.609 0.0056866421 376.23385 Loop time of 1.48e-06 on 1 procs for 0 steps with 464 atoms 135.1% 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 | | 1.48e-06 | | |100.00 Nlocal: 464.000 ave 464 max 464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3411.00 ave 3411 max 3411 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13428.0 ave 13428 max 13428 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26856.0 ave 26856 max 26856 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26856 Ave neighs/atom = 57.879310 Neighbor list builds = 0 Dangerous builds = 0 464 -4951.11707437943 eV 0.00568664207664772 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01