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 = 3.3024436 3.3024436 3.3024436 Created orthogonal box = (0.0000000 -66.213787 0.0000000) to (38.228548 66.213787 5.7200000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1351781 5.2707492 5.7200000 Created 804 atoms using lattice units in orthogonal box = (0.0000000 -66.213787 0.0000000) to (38.228548 66.213787 5.7200000) create_atoms CPU = 0.002 seconds 804 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1351781 5.2707492 5.7200000 Created 806 atoms using lattice units in orthogonal box = (0.0000000 -66.213787 0.0000000) to (38.228548 66.213787 5.7200000) create_atoms CPU = 0.002 seconds 806 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 12 41 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1608 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_072689718616_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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 12 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.725 | 4.725 | 4.725 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11456.848 0 -11456.848 37916.454 70 0 -11971.163 0 -11971.163 5116.5131 Loop time of 4.59299 on 1 procs for 70 steps with 1608 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11456.8475790603 -11971.1525394456 -11971.1625711614 Force two-norm initial, final = 465.15592 0.34303685 Force max component initial, final = 130.55991 0.066164326 Final line search alpha, max atom move = 0.51332784 0.033963991 Iterations, force evaluations = 70 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.5564 | 4.5564 | 4.5564 | 0.0 | 99.20 Neigh | 0.015355 | 0.015355 | 0.015355 | 0.0 | 0.33 Comm | 0.0098936 | 0.0098936 | 0.0098936 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01137 | | | 0.25 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6262.00 ave 6262 max 6262 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: 98548.0 ave 98548 max 98548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98548 Ave neighs/atom = 61.286070 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 12 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.725 | 4.725 | 4.725 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -11971.163 0 -11971.163 5116.5131 28957.58 72 0 -11971.289 0 -11971.289 0.43541305 29033.223 Loop time of 0.327613 on 1 procs for 2 steps with 1608 atoms 69.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11971.1625711614 -11971.286855441 -11971.2892118253 Force two-norm initial, final = 161.70723 0.96263545 Force max component initial, final = 103.28809 0.68225790 Final line search alpha, max atom move = 8.6681817e-05 5.9139354e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32514 | 0.32514 | 0.32514 | 0.0 | 99.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040351 | 0.00040351 | 0.00040351 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002069 | | | 0.63 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6312.00 ave 6312 max 6312 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: 97844.0 ave 97844 max 97844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 97844 Ave neighs/atom = 60.848259 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 12 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.863 | 4.863 | 4.863 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11971.289 0 -11971.289 0.43541305 Loop time of 2.101e-06 on 1 procs for 0 steps with 1608 atoms 190.4% 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 | | 2.101e-06 | | |100.00 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6310.00 ave 6310 max 6310 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: 96136.0 ave 96136 max 96136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96136 Ave neighs/atom = 59.786070 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 12 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.863 | 4.863 | 4.863 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 -11971.289 -11971.289 38.244723 132.58013 5.7259199 0.43541305 0.43541305 7.3692459 31.625847 -37.688853 2.6328623 1000.0211 Loop time of 2.43e-06 on 1 procs for 0 steps with 1608 atoms 246.9% 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 | | 2.43e-06 | | |100.00 Nlocal: 1608.00 ave 1608 max 1608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6310.00 ave 6310 max 6310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 48068.0 ave 48068 max 48068 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 96136.0 ave 96136 max 96136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96136 Ave neighs/atom = 59.786070 Neighbor list builds = 0 Dangerous builds = 0 1608 -11971.2892118253 eV 2.63286227896476 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05