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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -46.564820 0.0000000) to (38.020017 46.564820 7.7074639) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6873993 4.4651198 5.1383093 Created 876 atoms using lattice units in orthogonal box = (0.0000000 -46.564820 0.0000000) to (38.020017 46.564820 7.7074639) create_atoms CPU = 0.001 seconds 876 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6873993 4.4651198 5.1383093 Created 878 atoms using lattice units in orthogonal box = (0.0000000 -46.564820 0.0000000) to (38.020017 46.564820 7.7074639) create_atoms CPU = 0.001 seconds 878 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 12 28 3 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1738 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_486450342170_001#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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.066 | 5.066 | 5.066 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10041.127 0 -10041.127 157859.49 222 0 -11763.546 0 -11763.546 -9265.6787 Loop time of 19.0699 on 1 procs for 222 steps with 1738 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 = -10041.1266428661 -11763.5361248675 -11763.545975693 Force two-norm initial, final = 1694.5878 0.60245385 Force max component initial, final = 494.28523 0.15226290 Final line search alpha, max atom move = 0.77666633 0.11825747 Iterations, force evaluations = 222 424 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.958 | 18.958 | 18.958 | 0.0 | 99.41 Neigh | 0.052452 | 0.052452 | 0.052452 | 0.0 | 0.28 Comm | 0.025072 | 0.025072 | 0.025072 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03456 | | | 0.18 Nlocal: 1738.00 ave 1738 max 1738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5904.00 ave 5904 max 5904 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: 115068.0 ave 115068 max 115068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 115068 Ave neighs/atom = 66.207135 Neighbor list builds = 5 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 12 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 222 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.078 | 5.078 | 5.078 Mbytes Step Temp E_pair E_mol TotEng Press Volume 222 0 -11763.546 0 -11763.546 -9265.6787 27290.515 225 0 -11763.861 0 -11763.861 -4.3692087 27193.21 Loop time of 0.269823 on 1 procs for 3 steps with 1738 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11763.545975693 -11763.8524125281 -11763.8612087345 Force two-norm initial, final = 278.34887 1.3362493 Force max component initial, final = 195.17349 1.0257157 Final line search alpha, max atom move = 4.1573680e-05 4.2642777e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26801 | 0.26801 | 0.26801 | 0.0 | 99.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027189 | 0.00027189 | 0.00027189 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001541 | | | 0.57 Nlocal: 1738.00 ave 1738 max 1738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5899.00 ave 5899 max 5899 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: 114588.0 ave 114588 max 114588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114588 Ave neighs/atom = 65.930955 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.216 | 5.216 | 5.216 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11763.861 0 -11763.861 -4.3692087 Loop time of 1.97e-06 on 1 procs for 0 steps with 1738 atoms 152.3% 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 | | 1.97e-06 | | |100.00 Nlocal: 1738.00 ave 1738 max 1738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5905.00 ave 5905 max 5905 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: 114884.0 ave 114884 max 114884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114884 Ave neighs/atom = 66.101266 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 12 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.216 | 5.216 | 5.216 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 -11763.861 -11763.861 37.941416 93.018324 7.7051026 -4.3692087 -4.3692087 25.194922 -60.361146 22.058598 2.4660356 1352.6381 Loop time of 1.741e-06 on 1 procs for 0 steps with 1738 atoms 172.3% 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 | | 1.741e-06 | | |100.00 Nlocal: 1738.00 ave 1738 max 1738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5905.00 ave 5905 max 5905 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57442.0 ave 57442 max 57442 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114884.0 ave 114884 max 114884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114884 Ave neighs/atom = 66.101266 Neighbor list builds = 0 Dangerous builds = 0 1738 -11763.8612087345 eV 2.46603556995671 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19