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 = 3.5200244 3.5200244 3.5200244 Created orthogonal box = (0.0000000 -40.750748 0.0000000) to (28.812641 40.750748 4.9780662) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5905124 6.0816758 4.9780662 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -40.750748 0.0000000) to (28.812641 40.750748 4.9780662) create_atoms CPU = 0.001 seconds 538 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5905124 6.0816758 4.9780662 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -40.750748 0.0000000) to (28.812641 40.750748 4.9780662) create_atoms CPU = 0.001 seconds 538 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 7 20 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 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 1066 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_532072268679_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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.440 | 5.440 | 5.440 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4697.0771 0 -4697.0771 12570.368 62 0 -4731.1566 0 -4731.1566 -5505.2016 Loop time of 1.18675 on 1 procs for 62 steps with 1066 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 = -4697.07713281677 -4731.15206608435 -4731.15662965965 Force two-norm initial, final = 50.248240 0.23669266 Force max component initial, final = 16.933458 0.022419406 Final line search alpha, max atom move = 1.0000000 0.022419406 Iterations, force evaluations = 62 105 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1461 | 1.1461 | 1.1461 | 0.0 | 96.57 Neigh | 0.02759 | 0.02759 | 0.02759 | 0.0 | 2.32 Comm | 0.0073248 | 0.0073248 | 0.0073248 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005735 | | | 0.48 Nlocal: 1066.00 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8051.00 ave 8051 max 8051 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: 237664.0 ave 237664 max 237664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237664 Ave neighs/atom = 222.94934 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.440 | 5.440 | 5.440 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -4731.1566 0 -4731.1566 -5505.2016 11689.86 66 0 -4731.272 0 -4731.272 -369.23878 11655.963 Loop time of 0.0670255 on 1 procs for 4 steps with 1066 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 = -4731.15662965965 -4731.26978972257 -4731.27201830504 Force two-norm initial, final = 75.758220 4.0720605 Force max component initial, final = 71.699353 3.9434669 Final line search alpha, max atom move = 0.00011139326 0.00043927563 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.065222 | 0.065222 | 0.065222 | 0.0 | 97.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034122 | 0.00034122 | 0.00034122 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001462 | | | 2.18 Nlocal: 1066.00 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8033.00 ave 8033 max 8033 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: 237796.0 ave 237796 max 237796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237796 Ave neighs/atom = 223.07317 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.578 | 5.578 | 5.578 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4731.272 0 -4731.272 -369.23878 Loop time of 1.757e-06 on 1 procs for 0 steps with 1066 atoms 113.8% 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 | | 1.757e-06 | | |100.00 Nlocal: 1066.00 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8042.00 ave 8042 max 8042 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: 237936.0 ave 237936 max 237936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237936 Ave neighs/atom = 223.20450 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.578 | 5.578 | 5.578 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 -4731.272 -4731.272 28.722928 81.501496 4.9791349 -369.23878 -369.23878 -540.36352 -432.32922 -135.02361 2.3010606 511.06843 Loop time of 1.955e-06 on 1 procs for 0 steps with 1066 atoms 255.8% 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 | | 1.955e-06 | | |100.00 Nlocal: 1066.00 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8042.00 ave 8042 max 8042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 118968.0 ave 118968 max 118968 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 237936.0 ave 237936 max 237936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237936 Ave neighs/atom = 223.20450 Neighbor list builds = 0 Dangerous builds = 0 1066 -4702.21136398624 eV 2.3010605692911 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01