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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -37.598175 0.0000000) to (26.585925 37.598175 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0634565 5.9365540 4.9800000 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -37.598175 0.0000000) to (26.585925 37.598175 4.9800000) create_atoms CPU = 0.002 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0634565 5.9365540 4.9800000 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -37.598175 0.0000000) to (26.585925 37.598175 4.9800000) create_atoms CPU = 0.001 seconds 458 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 = 9 26 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 912 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_000553624872_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 9 26 2 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) = 4.563 | 4.563 | 4.563 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3406.1638 0 -3406.1638 132132.7 59 0 -4038.6271 0 -4038.6271 10737.865 Loop time of 3.3187 on 1 procs for 59 steps with 912 atoms 98.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3406.16382054427 -4038.62319530551 -4038.62708750747 Force two-norm initial, final = 844.48855 0.22788057 Force max component initial, final = 197.23357 0.037541775 Final line search alpha, max atom move = 1.0000000 0.037541775 Iterations, force evaluations = 59 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2947 | 3.2947 | 3.2947 | 0.0 | 99.28 Neigh | 0.011683 | 0.011683 | 0.011683 | 0.0 | 0.35 Comm | 0.0060364 | 0.0060364 | 0.0060364 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00628 | | | 0.19 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4086.00 ave 4086 max 4086 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: 71012.0 ave 71012 max 71012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71012 Ave neighs/atom = 77.864035 Neighbor list builds = 2 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 = 9 26 2 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 : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.569 | 4.569 | 4.569 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -4038.6271 0 -4038.6271 10737.865 9955.8392 65 0 -4038.9308 0 -4038.9308 101.35944 10012.314 Loop time of 0.252459 on 1 procs for 6 steps with 912 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 = -4038.62708750747 -4038.93062037153 -4038.93082353052 Force two-norm initial, final = 129.90059 1.4127781 Force max component initial, final = 114.90684 1.1528209 Final line search alpha, max atom move = 0.00036236876 0.00041774629 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25061 | 0.25061 | 0.25061 | 0.0 | 99.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030487 | 0.00030487 | 0.00030487 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001542 | | | 0.61 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4058.00 ave 4058 max 4058 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: 71056.0 ave 71056 max 71056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71056 Ave neighs/atom = 77.912281 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 = 9 26 2 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) = 4.706 | 4.706 | 4.706 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4038.9308 0 -4038.9308 101.35944 Loop time of 2.244e-06 on 1 procs for 0 steps with 912 atoms 178.3% 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 | | 2.244e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4051.00 ave 4051 max 4051 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: 70924.0 ave 70924 max 70924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70924 Ave neighs/atom = 77.767544 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 = 9 26 2 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) = 4.706 | 4.706 | 4.706 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 -4038.9308 -4038.9308 26.592352 75.574093 4.9820121 101.35944 101.35944 117.59656 185.40179 1.0799823 2.3347116 722.43773 Loop time of 2.221e-06 on 1 procs for 0 steps with 912 atoms 270.1% 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 | | 2.221e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4051.00 ave 4051 max 4051 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35462.0 ave 35462 max 35462 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 70924.0 ave 70924 max 70924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70924 Ave neighs/atom = 77.767544 Neighbor list builds = 0 Dangerous builds = 0 912 -4038.93082353052 eV 2.33471162387541 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03