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 -53.175371 0.0000000) to (37.598175 53.175371 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9365540 5.1306170 4.9800000 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -53.175371 0.0000000) to (37.598175 53.175371 4.9800000) create_atoms CPU = 0.003 seconds 916 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9365540 5.1306170 4.9800000 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -53.175371 0.0000000) to (37.598175 53.175371 4.9800000) 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 13 35 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 13 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.164 | 5.164 | 5.164 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7982.1022 0 -7982.1022 15364.853 79 0 -8060.4829 0 -8060.4829 -1954.2878 Loop time of 9.07004 on 1 procs for 79 steps with 1816 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 = -7982.10218607669 -8060.4749548791 -8060.48290153835 Force two-norm initial, final = 75.431325 0.30207393 Force max component initial, final = 13.861671 0.037056728 Final line search alpha, max atom move = 1.0000000 0.037056728 Iterations, force evaluations = 79 148 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.0177 | 9.0177 | 9.0177 | 0.0 | 99.42 Neigh | 0.021549 | 0.021549 | 0.021549 | 0.0 | 0.24 Comm | 0.015963 | 0.015963 | 0.015963 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01485 | | | 0.16 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7662.00 ave 7662 max 7662 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: 156264.0 ave 156264 max 156264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156264 Ave neighs/atom = 86.048458 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 13 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.164 | 5.164 | 5.164 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -8060.4829 0 -8060.4829 -1954.2878 19912.997 81 0 -8060.5065 0 -8060.5065 355.5855 19888.187 Loop time of 0.308046 on 1 procs for 2 steps with 1816 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8060.48290153836 -8060.50619763162 -8060.50652473207 Force two-norm initial, final = 49.170278 0.30824503 Force max component initial, final = 43.120283 0.044614706 Final line search alpha, max atom move = 0.00026052678 1.1623326e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30602 | 0.30602 | 0.30602 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041059 | 0.00041059 | 0.00041059 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001613 | | | 0.52 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7648.00 ave 7648 max 7648 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: 156224.0 ave 156224 max 156224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156224 Ave neighs/atom = 86.026432 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 13 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.302 | 5.302 | 5.302 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8060.5065 0 -8060.5065 355.5855 Loop time of 1.86e-06 on 1 procs for 0 steps with 1816 atoms 215.1% 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 | | 1.86e-06 | | |100.00 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7655.00 ave 7655 max 7655 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: 156232.0 ave 156232 max 156232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156232 Ave neighs/atom = 86.030837 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 13 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.302 | 5.302 | 5.302 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 -8060.5065 -8060.5065 37.563983 106.35074 4.9783225 355.5855 355.5855 -0.10359787 1070.453 -3.5929146 2.329093 772.90117 Loop time of 2.171e-06 on 1 procs for 0 steps with 1816 atoms 184.2% 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 | | 2.171e-06 | | |100.00 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7655.00 ave 7655 max 7655 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78116.0 ave 78116 max 78116 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 156232.0 ave 156232 max 156232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156232 Ave neighs/atom = 86.030837 Neighbor list builds = 0 Dangerous builds = 0 1816 -8060.50652473207 eV 2.32909296801689 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09