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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -54.526392 0.0000000) to (38.555982 54.526392 5.1068645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0877866 5.2613185 5.1068645 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -54.526392 0.0000000) to (38.555982 54.526392 5.1068645) create_atoms CPU = 0.002 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0877866 5.2613185 5.1068645 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -54.526392 0.0000000) to (38.555982 54.526392 5.1068645) 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 12 33 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 6.8 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_260546967793_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 33 2 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) = 5.563 | 5.563 | 5.563 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7341.7415 0 -7341.7415 35078.482 319 0 -7721.1742 0 -7721.1742 -3723.9549 Loop time of 85.1439 on 1 procs for 319 steps with 1816 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 = -7341.74145311136 -7721.16653118055 -7721.17422997618 Force two-norm initial, final = 477.76372 0.28298899 Force max component initial, final = 99.922956 0.045273584 Final line search alpha, max atom move = 1.0000000 0.045273584 Iterations, force evaluations = 319 582 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 84.838 | 84.838 | 84.838 | 0.0 | 99.64 Neigh | 0.17013 | 0.17013 | 0.17013 | 0.0 | 0.20 Comm | 0.072398 | 0.072398 | 0.072398 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06384 | | | 0.07 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8286.00 ave 8286 max 8286 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: 207916.0 ave 207916 max 207916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207916 Ave neighs/atom = 114.49119 Neighbor list builds = 12 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 33 2 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 : 319 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.562 | 5.562 | 5.562 Mbytes Step Temp E_pair E_mol TotEng Press Volume 319 0 -7721.1742 0 -7721.1742 -3723.9549 21472.512 346 0 -7732.5473 0 -7732.5473 31.500997 21408.055 Loop time of 4.79451 on 1 procs for 27 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 = -7721.17422997619 -7732.54641355428 -7732.54733259814 Force two-norm initial, final = 674.62613 6.7099171 Force max component initial, final = 483.96470 4.4383340 Final line search alpha, max atom move = 0.0016697128 0.0074107429 Iterations, force evaluations = 27 29 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7665 | 4.7665 | 4.7665 | 0.0 | 99.42 Neigh | 0.013135 | 0.013135 | 0.013135 | 0.0 | 0.27 Comm | 0.002337 | 0.002337 | 0.002337 | 0.0 | 0.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01251 | | | 0.26 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8166.00 ave 8166 max 8166 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: 205968.0 ave 205968 max 205968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205968 Ave neighs/atom = 113.41850 Neighbor list builds = 1 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 32 2 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) = 5.697 | 5.697 | 5.697 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7732.5473 0 -7732.5473 31.500997 Loop time of 2.499e-06 on 1 procs for 0 steps with 1816 atoms 160.1% 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 | | 2.499e-06 | | |100.00 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8156.00 ave 8156 max 8156 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: 205800.0 ave 205800 max 205800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205800 Ave neighs/atom = 113.32599 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 32 2 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) = 5.697 | 5.697 | 5.697 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 -7732.5473 -7732.5473 39.546312 108.10681 5.0074677 31.500997 31.500997 85.019376 329.28309 -319.79948 2.3831796 3477.3943 Loop time of 2.813e-06 on 1 procs for 0 steps with 1816 atoms 248.8% 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 | | 2.813e-06 | | |100.00 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8156.00 ave 8156 max 8156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 102900.0 ave 102900 max 102900 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 205800.0 ave 205800 max 205800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205800 Ave neighs/atom = 113.32599 Neighbor list builds = 0 Dangerous builds = 0 1816 -7732.54733259815 eV 2.38317962653976 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:30