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 = 3.6385685 3.6385685 3.6385685 Created orthogonal box = (0.0000000 -39.858520 0.0000000) to (8.1360864 39.858520 8.9126361) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8816519 5.3144694 5.9417574 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -39.858520 0.0000000) to (8.1360864 39.858520 8.9126361) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8816519 5.3144694 5.9417574 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -39.858520 0.0000000) to (8.1360864 39.858520 8.9126361) 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 2 17 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 480 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_097471813275_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 2 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.027 | 5.027 | 5.027 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1455.2587 0 -1455.2587 109484.68 75 0 -1626.9166 0 -1626.9166 5500.3372 Loop time of 1.2779 on 1 procs for 75 steps with 480 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1455.25865172333 -1626.91504277849 -1626.91662732085 Force two-norm initial, final = 562.83837 0.11029639 Force max component initial, final = 155.85870 0.010689435 Final line search alpha, max atom move = 1.0000000 0.010689435 Iterations, force evaluations = 75 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2564 | 1.2564 | 1.2564 | 0.0 | 98.32 Neigh | 0.0096421 | 0.0096421 | 0.0096421 | 0.0 | 0.75 Comm | 0.0073053 | 0.0073053 | 0.0073053 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004582 | | | 0.36 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5750.00 ave 5750 max 5750 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: 152280.0 ave 152280 max 152280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 152280 Ave neighs/atom = 317.25000 Neighbor list builds = 1 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 2 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.027 | 5.027 | 5.027 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -1626.9166 0 -1626.9166 5500.3372 5780.5997 78 0 -1626.9549 0 -1626.9549 -2.6482589 5802.8378 Loop time of 0.0507457 on 1 procs for 3 steps with 480 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 = -1626.91662732085 -1626.95479593556 -1626.95486272219 Force two-norm initial, final = 34.397529 0.19474635 Force max component initial, final = 20.825903 0.10647072 Final line search alpha, max atom move = 0.0017117542 0.00018225170 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.049495 | 0.049495 | 0.049495 | 0.0 | 97.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025861 | 0.00025861 | 0.00025861 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009923 | | | 1.96 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5723.00 ave 5723 max 5723 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: 152340.0 ave 152340 max 152340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 152340 Ave neighs/atom = 317.37500 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 2 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.165 | 5.165 | 5.165 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1626.9549 0 -1626.9549 -2.6482589 Loop time of 1.966e-06 on 1 procs for 0 steps with 480 atoms 152.6% 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 | | 1.966e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5723.00 ave 5723 max 5723 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: 152264.0 ave 152264 max 152264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 152264 Ave neighs/atom = 317.21667 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 2 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.165 | 5.165 | 5.165 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 -1626.9549 -1626.9549 8.1447014 79.820428 8.9258835 -2.6482589 -2.6482589 -10.360537 29.434929 -27.019169 2.3271707 281.05707 Loop time of 2.592e-06 on 1 procs for 0 steps with 480 atoms 231.5% 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 | | 2.592e-06 | | |100.00 Nlocal: 480.000 ave 480 max 480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5723.00 ave 5723 max 5723 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 76132.0 ave 76132 max 76132 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 152264.0 ave 152264 max 152264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 152264 Ave neighs/atom = 317.21667 Neighbor list builds = 0 Dangerous builds = 0 480 -1626.95486272219 eV 2.32717068310765 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01