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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -54.660802 0.0000000) to (38.651023 54.660802 5.1194531) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1027932 5.2742879 5.1194531 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -54.660802 0.0000000) to (38.651023 54.660802 5.1194531) create_atoms CPU = 0.002 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1027932 5.2742879 5.1194531 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -54.660802 0.0000000) to (38.651023 54.660802 5.1194531) create_atoms CPU = 0.002 seconds 916 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 12 32 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1816 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_262519520678_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 12 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.565 | 5.565 | 5.565 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6010.4199 0 -6010.4199 70941.742 81 0 -6415.1888 0 -6415.1888 -2421.654 Loop time of 18.002 on 1 procs for 81 steps with 1816 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6010.41986106025 -6415.1832011776 -6415.18883622125 Force two-norm initial, final = 1059.3309 0.20201545 Force max component initial, final = 246.41377 0.022981900 Final line search alpha, max atom move = 1.0000000 0.022981900 Iterations, force evaluations = 81 148 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.934 | 17.934 | 17.934 | 0.0 | 99.62 Neigh | 0.03061 | 0.03061 | 0.03061 | 0.0 | 0.17 Comm | 0.019622 | 0.019622 | 0.019622 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01779 | | | 0.10 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8584.00 ave 8584 max 8584 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: 240784.0 ave 240784 max 240784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240784 Ave neighs/atom = 132.59031 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 12 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.560 | 5.560 | 5.560 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -6415.1888 0 -6415.1888 -2421.654 21631.696 84 0 -6415.2586 0 -6415.2586 117.50961 21591.648 Loop time of 0.616772 on 1 procs for 3 steps with 1816 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 = -6415.18883622125 -6415.2559310609 -6415.25855983759 Force two-norm initial, final = 65.909453 2.8084440 Force max component initial, final = 55.168263 1.8943234 Final line search alpha, max atom move = 0.00016651187 0.00031542732 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.61436 | 0.61436 | 0.61436 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003787 | 0.0003787 | 0.0003787 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002036 | | | 0.33 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7956.00 ave 7956 max 7956 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: 241104.0 ave 241104 max 241104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241104 Ave neighs/atom = 132.76652 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 12 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.698 | 5.698 | 5.698 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6415.2586 0 -6415.2586 117.50961 Loop time of 2.522e-06 on 1 procs for 0 steps with 1816 atoms 158.6% 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 | | 2.522e-06 | | |100.00 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7956.00 ave 7956 max 7956 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: 241096.0 ave 241096 max 241096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241096 Ave neighs/atom = 132.76211 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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 12 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.698 | 5.698 | 5.698 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 -6415.2586 -6415.2586 38.575012 109.46712 5.113238 117.50961 117.50961 84.740659 140.75259 127.03558 2.3330678 696.02027 Loop time of 2.868e-06 on 1 procs for 0 steps with 1816 atoms 209.2% 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 | | 2.868e-06 | | |100.00 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7956.00 ave 7956 max 7956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 120548.0 ave 120548 max 120548 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 241096.0 ave 241096 max 241096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 241096 Ave neighs/atom = 132.76211 Neighbor list builds = 0 Dangerous builds = 0 1816 -6415.25855983759 eV 2.33306782487723 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19