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 = 3.5213918 3.5213918 3.5213918 Created orthogonal box = (0.0000000 -41.665669 0.0000000) to (51.029815 41.665669 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8319788 5.3570146 5.7504087 Created 1663 atoms using lattice units in orthogonal box = (0.0000000 -41.665669 0.0000000) to (51.029815 41.665669 8.6256130) create_atoms CPU = 0.003 seconds 1663 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8319788 5.3570146 5.7504087 Created 1687 atoms using lattice units in orthogonal box = (0.0000000 -41.665669 0.0000000) to (51.029815 41.665669 8.6256130) create_atoms CPU = 0.003 seconds 1687 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 ghost atom cutoff = 6 binsize = 3, bins = 18 28 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 3347 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_700541006254_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 ghost atom cutoff = 6 binsize = 3, bins = 18 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.616 | 5.616 | 5.616 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13869.917 0 -13869.917 105234.78 118 0 -14821.266 0 -14821.266 4247.1489 Loop time of 22.9434 on 1 procs for 118 steps with 3347 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13869.916661014 -14821.2531820142 -14821.2661104633 Force two-norm initial, final = 998.17900 0.41255816 Force max component initial, final = 91.754647 0.11883860 Final line search alpha, max atom move = 0.40636085 0.048291354 Iterations, force evaluations = 118 206 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.77 | 22.77 | 22.77 | 0.0 | 99.25 Neigh | 0.1122 | 0.1122 | 0.1122 | 0.0 | 0.49 Comm | 0.022964 | 0.022964 | 0.022964 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03784 | | | 0.16 Nlocal: 3347.00 ave 3347 max 3347 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7997.00 ave 7997 max 7997 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: 260486.0 ave 260486 max 260486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 260486 Ave neighs/atom = 77.826710 Neighbor list builds = 5 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 ghost atom cutoff = 6 binsize = 3, bins = 18 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 118 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.618 | 5.618 | 5.618 Mbytes Step Temp E_pair E_mol TotEng Press Volume 118 0 -14821.266 0 -14821.266 4247.1489 36679.408 123 0 -14821.822 0 -14821.822 -153.24135 36766.525 Loop time of 0.719729 on 1 procs for 5 steps with 3347 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 = -14821.2661104633 -14821.8204373143 -14821.822194022 Force two-norm initial, final = 264.38236 6.4749171 Force max component initial, final = 258.36756 4.6929841 Final line search alpha, max atom move = 7.6864260e-05 0.00036072275 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.71591 | 0.71591 | 0.71591 | 0.0 | 99.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048214 | 0.00048214 | 0.00048214 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003342 | | | 0.46 Nlocal: 3347.00 ave 3347 max 3347 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7993.00 ave 7993 max 7993 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: 260462.0 ave 260462 max 260462 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 260462 Ave neighs/atom = 77.819540 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 ghost atom cutoff = 6 binsize = 3, bins = 18 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.756 | 5.756 | 5.756 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14821.822 0 -14821.822 -153.24135 Loop time of 2.077e-06 on 1 procs for 0 steps with 3347 atoms 192.6% 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 | | 2.077e-06 | | |100.00 Nlocal: 3347.00 ave 3347 max 3347 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7997.00 ave 7997 max 7997 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: 260262.0 ave 260262 max 260262 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 260262 Ave neighs/atom = 77.759785 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 ghost atom cutoff = 6 binsize = 3, bins = 18 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.756 | 5.756 | 5.756 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 -14821.822 -14821.822 51.021131 83.684721 8.6110544 -153.24135 -153.24135 -174.45028 -81.112554 -204.16121 2.2425885 1575.3053 Loop time of 2.735e-06 on 1 procs for 0 steps with 3347 atoms 255.9% 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 | | 2.735e-06 | | |100.00 Nlocal: 3347.00 ave 3347 max 3347 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7997.00 ave 7997 max 7997 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130131.0 ave 130131 max 130131 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 260262.0 ave 260262 max 260262 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 260262 Ave neighs/atom = 77.759785 Neighbor list builds = 0 Dangerous builds = 0 3347 -14821.822194022 eV 2.24258851150783 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:24