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 = 3.6203867 3.6203867 3.6203867 Created orthogonal box = (0.0000000 -69.265696 0.0000000) to (39.988478 69.265696 6.2706937) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8999394 5.2987380 6.2706937 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -69.265696 0.0000000) to (39.988478 69.265696 6.2706937) create_atoms CPU = 0.003 seconds 1466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8999394 5.2987380 6.2706937 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -69.265696 0.0000000) to (39.988478 69.265696 6.2706937) create_atoms CPU = 0.003 seconds 1466 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 ghost atom cutoff = 6 binsize = 3, bins = 14 47 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 2906 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_390178379548_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 ghost atom cutoff = 6 binsize = 3, bins = 14 47 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.778 | 5.778 | 5.778 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10209.603 0 -10209.603 3421.6748 49 0 -10259.357 0 -10259.357 -5540.9138 Loop time of 3.91373 on 1 procs for 49 steps with 2906 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10209.6025492915 -10259.3489846812 -10259.3567288852 Force two-norm initial, final = 58.484521 0.25244798 Force max component initial, final = 9.6400257 0.043178598 Final line search alpha, max atom move = 1.0000000 0.043178598 Iterations, force evaluations = 49 81 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.873 | 3.873 | 3.873 | 0.0 | 98.96 Neigh | 0.017725 | 0.017725 | 0.017725 | 0.0 | 0.45 Comm | 0.0099654 | 0.0099654 | 0.0099654 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01302 | | | 0.33 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9376.00 ave 9376 max 9376 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: 224888.0 ave 224888 max 224888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 224888 Ave neighs/atom = 77.387474 Neighbor list builds = 1 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 ghost atom cutoff = 6 binsize = 3, bins = 14 47 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.778 | 5.778 | 5.778 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -10259.357 0 -10259.357 -5540.9138 34737.508 52 0 -10259.49 0 -10259.49 -1720.3381 34643.729 Loop time of 0.288802 on 1 procs for 3 steps with 2906 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 = -10259.3567288852 -10259.4885852412 -10259.4895209873 Force two-norm initial, final = 135.39939 0.27646327 Force max component initial, final = 105.10333 0.046648733 Final line search alpha, max atom move = 0.00015776490 7.3595328e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28557 | 0.28557 | 0.28557 | 0.0 | 98.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00046476 | 0.00046476 | 0.00046476 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002767 | | | 0.96 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9388.00 ave 9388 max 9388 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: 225000.0 ave 225000 max 225000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225000 Ave neighs/atom = 77.426015 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 ghost atom cutoff = 6 binsize = 3, bins = 14 47 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.916 | 5.916 | 5.916 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10259.49 0 -10259.49 -1720.3381 Loop time of 2.326e-06 on 1 procs for 0 steps with 2906 atoms 172.0% 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 | | 2.326e-06 | | |100.00 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9388.00 ave 9388 max 9388 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: 225028.0 ave 225028 max 225028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225028 Ave neighs/atom = 77.435650 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 ghost atom cutoff = 6 binsize = 3, bins = 14 47 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.916 | 5.916 | 5.916 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 -10259.49 -10259.49 39.91891 138.53139 6.2646637 -1720.3381 -1720.3381 -2.1536215 -5157.2685 -1.5923276 2.3062164 1109.5103 Loop time of 2.65e-06 on 1 procs for 0 steps with 2906 atoms 226.4% 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 | | 2.65e-06 | | |100.00 Nlocal: 2906.00 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9388.00 ave 9388 max 9388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 112514.0 ave 112514 max 112514 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 225028.0 ave 225028 max 225028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 225028 Ave neighs/atom = 77.435650 Neighbor list builds = 0 Dangerous builds = 0 2906 -10259.4895209873 eV 2.30621635832902 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04