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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -46.580901 0.0000000) to (23.289006 46.580901 2.8886457) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.2246316 3.2246316 2.8886457 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -46.580901 0.0000000) to (23.289006 46.580901 2.8886457) create_atoms CPU = 0.002 seconds 261 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.2246316 3.2246316 2.8886457 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -46.580901 0.0000000) to (23.289006 46.580901 2.8886457) create_atoms CPU = 0.001 seconds 261 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 35 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 2 atoms, new total = 520 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.844 | 4.844 | 4.844 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2120.8243 0 -2120.8243 26644 30 0 -2164.6016 0 -2164.6016 3317.6784 Loop time of 5.71417 on 1 procs for 30 steps with 520 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 = -2120.82430623774 -2164.59962423104 -2164.60162127359 Force two-norm initial, final = 78.134311 0.15833137 Force max component initial, final = 26.792958 0.033015531 Final line search alpha, max atom move = 1.0000000 0.033015531 Iterations, force evaluations = 30 52 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.7042 | 5.7042 | 5.7042 | 0.0 | 99.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.005259 | 0.005259 | 0.005259 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004754 | | | 0.08 Nlocal: 520.000 ave 520 max 520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3710.00 ave 3710 max 3710 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: 30012.0 ave 30012 max 30012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30012 Ave neighs/atom = 57.715385 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 30 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.844 | 4.844 | 4.844 Mbytes Step Temp E_pair E_mol TotEng Press Volume 30 0 -2164.6016 0 -2164.6016 3317.6784 6267.3378 31 0 -2164.602 0 -2164.602 2765.5727 6269.3475 Loop time of 0.330656 on 1 procs for 1 steps with 520 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 = -2164.60162127359 -2164.60162127359 -2164.60201061313 Force two-norm initial, final = 3.0247880 1.3486085 Force max component initial, final = 2.8948924 1.2878565 Final line search alpha, max atom move = 0.00034543599 0.00044487198 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32965 | 0.32965 | 0.32965 | 0.0 | 99.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026628 | 0.00026628 | 0.00026628 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007358 | | | 0.22 Nlocal: 520.000 ave 520 max 520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3710.00 ave 3710 max 3710 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: 30028.0 ave 30028 max 30028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30028 Ave neighs/atom = 57.746154 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.982 | 4.982 | 4.982 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2164.602 0 -2164.602 2765.5727 Loop time of 6.335e-06 on 1 procs for 0 steps with 520 atoms 173.6% 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 | | 6.335e-06 | | |100.00 Nlocal: 520.000 ave 520 max 520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3710.00 ave 3710 max 3710 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: 30028.0 ave 30028 max 30028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30028 Ave neighs/atom = 57.746154 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.982 | 4.982 | 4.982 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 -2164.602 -2164.602 23.29072 93.161801 2.8893593 2765.5727 2765.5727 -329.14514 8531.954 93.909287 2.3779864 197.82969 Loop time of 9.803e-06 on 1 procs for 0 steps with 520 atoms 173.4% 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 | | 9.803e-06 | | |100.00 Nlocal: 520.000 ave 520 max 520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3710.00 ave 3710 max 3710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 15014.0 ave 15014 max 15014 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 30028.0 ave 30028 max 30028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30028 Ave neighs/atom = 57.746154 Neighbor list builds = 0 Dangerous builds = 0 520 -2164.60201061313 eV 2.37798637255415 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06