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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -39.370357 0.0000000) to (19.287457 39.370357 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1433219 4.7244428 5.7504086 Created 600 atoms using lattice units in orthogonal box = (0.0000000 -39.370357 0.0000000) to (19.287457 39.370357 8.6256130) create_atoms CPU = 0.001 seconds 600 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1433219 4.7244428 5.7504086 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -39.370357 0.0000000) to (19.287457 39.370357 8.6256130) create_atoms CPU = 0.001 seconds 612 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 7 26 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1200 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 7 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.965 | 4.965 | 4.965 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5146.1998 0 -5146.1998 58108.477 15 0 -5314.3455 0 -5314.3455 14983.141 Loop time of 1.35254 on 1 procs for 15 steps with 1200 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 = -5146.19982106247 -5314.34214801159 -5314.34545309206 Force two-norm initial, final = 282.29638 0.21604014 Force max component initial, final = 40.736694 0.019079867 Final line search alpha, max atom move = 1.0000000 0.019079867 Iterations, force evaluations = 15 28 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3486 | 1.3486 | 1.3486 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015525 | 0.0015525 | 0.0015525 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002356 | | | 0.17 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4309.00 ave 4309 max 4309 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: 103728.0 ave 103728 max 103728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103728 Ave neighs/atom = 86.440000 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 7 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 15 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.965 | 4.965 | 4.965 Mbytes Step Temp E_pair E_mol TotEng Press Volume 15 0 -5314.3455 0 -5314.3455 14983.141 13099.788 28 0 -5315.7605 0 -5315.7605 72.156111 13203.425 Loop time of 0.728955 on 1 procs for 13 steps with 1200 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 = -5314.34545309206 -5315.760362434 -5315.76045510421 Force two-norm initial, final = 273.00879 1.4751085 Force max component initial, final = 262.14100 0.88239956 Final line search alpha, max atom move = 0.0010934057 0.00096482071 Iterations, force evaluations = 13 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.72413 | 0.72413 | 0.72413 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00065589 | 0.00065589 | 0.00065589 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004168 | | | 0.57 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4309.00 ave 4309 max 4309 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: 103056.0 ave 103056 max 103056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 103056 Ave neighs/atom = 85.880000 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 7 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.103 | 5.103 | 5.103 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5315.7605 0 -5315.7605 72.156111 Loop time of 2.179e-06 on 1 procs for 0 steps with 1200 atoms 183.6% 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 | | 2.179e-06 | | |100.00 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4309.00 ave 4309 max 4309 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: 102672.0 ave 102672 max 102672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102672 Ave neighs/atom = 85.560000 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 7 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.103 | 5.103 | 5.103 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 -5315.7605 -5315.7605 19.243186 79.667004 8.6125378 72.156111 72.156111 106.82946 78.056049 31.58282 2.2579046 723.68645 Loop time of 2.284e-06 on 1 procs for 0 steps with 1200 atoms 175.1% 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 | | 2.284e-06 | | |100.00 Nlocal: 1200.00 ave 1200 max 1200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4309.00 ave 4309 max 4309 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51336.0 ave 51336 max 51336 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 102672.0 ave 102672 max 102672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102672 Ave neighs/atom = 85.560000 Neighbor list builds = 0 Dangerous builds = 0 1200 -5315.76045510421 eV 2.25790456317525 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02