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 = 3.9412164 3.9412164 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 = 3.9412164 3.9412164 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) = 4.840 | 4.840 | 4.840 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2118.4621 0 -2118.4621 25299.7 29 0 -2161.9483 0 -2161.9483 6044.9421 Loop time of 4.95382 on 1 procs for 29 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 = -2118.46212437496 -2161.9479506741 -2161.94830676274 Force two-norm initial, final = 98.232808 0.36875416 Force max component initial, final = 43.719331 0.16973937 Final line search alpha, max atom move = 0.86454860 0.14674794 Iterations, force evaluations = 29 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.9454 | 4.9454 | 4.9454 | 0.0 | 99.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0041395 | 0.0041395 | 0.0041395 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004231 | | | 0.09 Nlocal: 520.000 ave 520 max 520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3268.00 ave 3268 max 3268 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: 30008.0 ave 30008 max 30008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 30008 Ave neighs/atom = 57.707692 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 : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.840 | 4.840 | 4.840 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -2161.9483 0 -2161.9483 6044.9421 6267.3378 31 0 -2161.956 0 -2161.956 5417.3271 6270.0965 Loop time of 0.413681 on 1 procs for 2 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 = -2161.94830676274 -2161.95523011803 -2161.95604324792 Force two-norm initial, final = 8.3425825 0.71877437 Force max component initial, final = 6.6324993 0.48961747 Final line search alpha, max atom move = 0.00043662381 0.00021377864 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41194 | 0.41194 | 0.41194 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034672 | 0.00034672 | 0.00034672 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001398 | | | 0.34 Nlocal: 520.000 ave 520 max 520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3283.00 ave 3283 max 3283 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: 29908.0 ave 29908 max 29908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29908 Ave neighs/atom = 57.515385 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) = 4.978 | 4.978 | 4.978 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2161.956 0 -2161.956 5417.3271 Loop time of 6.365e-06 on 1 procs for 0 steps with 520 atoms 188.5% 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 | | 6.365e-06 | | |100.00 Nlocal: 520.000 ave 520 max 520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3283.00 ave 3283 max 3283 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: 29908.0 ave 29908 max 29908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29908 Ave neighs/atom = 57.515385 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) = 4.978 | 4.978 | 4.978 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 -2161.956 -2161.956 23.264085 93.161801 2.893013 5417.3271 5417.3271 -124.97641 16470.214 -93.256781 2.2819128 269.92852 Loop time of 6.786e-06 on 1 procs for 0 steps with 520 atoms 294.7% 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 | | 6.786e-06 | | |100.00 Nlocal: 520.000 ave 520 max 520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3283.00 ave 3283 max 3283 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14954.0 ave 14954 max 14954 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29908.0 ave 29908 max 29908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29908 Ave neighs/atom = 57.515385 Neighbor list builds = 0 Dangerous builds = 0 520 -2161.95604324792 eV 2.28191281349746 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06