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 = 2.8552583 2.8552583 2.8552583 Created orthogonal box = (0.0000000 -30.351812 0.0000000) to (30.351812 30.351812 2.8552583) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0290016 4.0290016 2.8552583 Created 226 atoms using lattice units in orthogonal box = (0.0000000 -30.351812 0.0000000) to (30.351812 30.351812 2.8552583) create_atoms CPU = 0.001 seconds 226 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0290016 4.0290016 2.8552583 Created 227 atoms using lattice units in orthogonal box = (0.0000000 -30.351812 0.0000000) to (30.351812 30.351812 2.8552583) create_atoms CPU = 0.000 seconds 227 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 16 1 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 453 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_942420706858_005#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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.480 | 4.480 | 4.480 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1676.8406 0 -1676.8406 152843 54 0 -1864.7078 0 -1864.7078 5546.7438 Loop time of 0.406747 on 1 procs for 54 steps with 453 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1676.84064883559 -1864.7059726903 -1864.70776117567 Force two-norm initial, final = 310.19203 0.13180211 Force max component initial, final = 88.963765 0.039571355 Final line search alpha, max atom move = 1.0000000 0.039571355 Iterations, force evaluations = 54 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39386 | 0.39386 | 0.39386 | 0.0 | 96.83 Neigh | 0.0047157 | 0.0047157 | 0.0047157 | 0.0 | 1.16 Comm | 0.0049772 | 0.0049772 | 0.0049772 | 0.0 | 1.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003192 | | | 0.78 Nlocal: 453.000 ave 453 max 453 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5307.00 ave 5307 max 5307 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: 77326.0 ave 77326 max 77326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77326 Ave neighs/atom = 170.69757 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.481 | 4.481 | 4.481 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -1864.7078 0 -1864.7078 5546.7438 5260.7134 60 0 -1864.7916 0 -1864.7916 46.950525 5277.5206 Loop time of 0.0349805 on 1 procs for 6 steps with 453 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 = -1864.70776117567 -1864.79145953117 -1864.79159893276 Force two-norm initial, final = 40.210024 0.50454097 Force max component initial, final = 38.542254 0.44568648 Final line search alpha, max atom move = 0.0010604076 0.00047260935 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.03326 | 0.03326 | 0.03326 | 0.0 | 95.08 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032219 | 0.00032219 | 0.00032219 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001398 | | | 4.00 Nlocal: 453.000 ave 453 max 453 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5307.00 ave 5307 max 5307 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: 77226.0 ave 77226 max 77226 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77226 Ave neighs/atom = 170.47682 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.619 | 4.619 | 4.619 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1864.7916 0 -1864.7916 46.950525 Loop time of 1.956e-06 on 1 procs for 0 steps with 453 atoms 153.4% 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 | | 1.956e-06 | | |100.00 Nlocal: 453.000 ave 453 max 453 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5317.00 ave 5317 max 5317 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: 77126.0 ave 77126 max 77126 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77126 Ave neighs/atom = 170.25607 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 8 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.619 | 4.619 | 4.619 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 -1864.7916 -1864.7916 30.360841 60.985622 2.8502875 46.950525 46.950525 42.115973 135.93232 -37.196717 2.2452165 115.84537 Loop time of 1.793e-06 on 1 procs for 0 steps with 453 atoms 223.1% 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 | | 1.793e-06 | | |100.00 Nlocal: 453.000 ave 453 max 453 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5317.00 ave 5317 max 5317 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38563.0 ave 38563 max 38563 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 77126.0 ave 77126 max 77126 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77126 Ave neighs/atom = 170.25607 Neighbor list builds = 0 Dangerous builds = 0 453 -1864.79159893276 eV 2.24521651364448 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00