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 = 3.6533440 3.6533440 3.6533440 Created orthogonal box = (0.0000000 -68.931158 0.0000000) to (34.465579 68.931158 3.6533440) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0342980 5.0342980 3.6533440 Created 712 atoms using lattice units in orthogonal box = (0.0000000 -68.931158 0.0000000) to (34.465579 68.931158 3.6533440) create_atoms CPU = 0.004 seconds 712 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0342980 5.0342980 3.6533440 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -68.931158 0.0000000) to (34.465579 68.931158 3.6533440) create_atoms CPU = 0.003 seconds 714 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 8 32 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 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1424 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_673777079812_004#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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 5.954 | 5.954 | 5.954 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4303.7928 0 -4303.7928 34969.306 75 0 -4642.1544 0 -4642.1544 2043.3515 Loop time of 4.39843 on 1 procs for 75 steps with 1424 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 = -4303.79282137259 -4642.15088125524 -4642.1543864653 Force two-norm initial, final = 457.82416 0.22642409 Force max component initial, final = 126.49376 0.029718048 Final line search alpha, max atom move = 1.0000000 0.029718048 Iterations, force evaluations = 75 135 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2892 | 4.2892 | 4.2892 | 0.0 | 97.52 Neigh | 0.042315 | 0.042315 | 0.042315 | 0.0 | 0.96 Comm | 0.04284 | 0.04284 | 0.04284 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02407 | | | 0.55 Nlocal: 1424.00 ave 1424 max 1424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13156.0 ave 13156 max 13156 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: 319152.0 ave 319152 max 319152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 319152 Ave neighs/atom = 224.12360 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 8 32 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.954 | 5.954 | 5.954 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -4642.1544 0 -4642.1544 2043.3515 17358.881 80 0 -4642.2713 0 -4642.2713 116.85384 17384.669 Loop time of 0.227697 on 1 procs for 5 steps with 1424 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 = -4642.1543864653 -4642.27062014846 -4642.27133892031 Force two-norm initial, final = 61.914777 3.1309203 Force max component initial, final = 44.070093 3.0316546 Final line search alpha, max atom move = 0.00017240150 0.00052266179 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21962 | 0.21962 | 0.21962 | 0.0 | 96.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021317 | 0.0021317 | 0.0021317 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005941 | | | 2.61 Nlocal: 1424.00 ave 1424 max 1424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13072.0 ave 13072 max 13072 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: 318944.0 ave 318944 max 318944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 318944 Ave neighs/atom = 223.97753 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 6.092 | 6.092 | 6.092 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4642.2713 0 -4642.2713 116.85384 Loop time of 6.355e-06 on 1 procs for 0 steps with 1424 atoms 204.6% 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 | | 6.355e-06 | | |100.00 Nlocal: 1424.00 ave 1424 max 1424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13072.0 ave 13072 max 13072 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: 318920.0 ave 318920 max 318920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 318920 Ave neighs/atom = 223.96067 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 8 32 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 6.092 | 6.092 | 6.092 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 -4642.2713 -4642.2713 34.377997 137.88564 3.667472 116.85384 116.85384 4.6737176 65.409086 280.4787 2.2870685 370.1635 Loop time of 7.267e-06 on 1 procs for 0 steps with 1424 atoms 220.2% 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 | | 7.267e-06 | | |100.00 Nlocal: 1424.00 ave 1424 max 1424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13072.0 ave 13072 max 13072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 159460.0 ave 159460 max 159460 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 318920.0 ave 318920 max 318920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 318920 Ave neighs/atom = 223.96067 Neighbor list builds = 0 Dangerous builds = 0 1424 -4642.27133892031 eV 2.28706851905168 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05