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 = 3.6133157 3.6133157 3.6133157 Created orthogonal box = (0.0000000 -49.674878 0.0000000) to (13.519789 49.674878 8.8507797) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7941954 5.5194309 5.9005198 Created 503 atoms using lattice units in orthogonal box = (0.0000000 -49.674878 0.0000000) to (13.519789 49.674878 8.8507797) create_atoms CPU = 0.001 seconds 503 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7941954 5.5194309 5.9005198 Created 507 atoms using lattice units in orthogonal box = (0.0000000 -49.674878 0.0000000) to (13.519789 49.674878 8.8507797) create_atoms CPU = 0.001 seconds 507 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 ghost atom cutoff = 8 binsize = 4, bins = 4 25 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 1007 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_380272712420_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.076 | 5.076 | 5.076 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3463.5836 0 -3463.5836 29094.016 44 0 -3551.3386 0 -3551.3386 5351.8668 Loop time of 4.68606 on 1 procs for 44 steps with 1007 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 = -3463.5836347628 -3551.33661833543 -3551.33863336273 Force two-norm initial, final = 153.17906 0.14362678 Force max component initial, final = 36.016282 0.054462172 Final line search alpha, max atom move = 1.0000000 0.054462172 Iterations, force evaluations = 44 82 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6757 | 4.6757 | 4.6757 | 0.0 | 99.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0053569 | 0.0053569 | 0.0053569 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005015 | | | 0.11 Nlocal: 1007.00 ave 1007 max 1007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6222.00 ave 6222 max 6222 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: 177502.0 ave 177502 max 177502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177502 Ave neighs/atom = 176.26812 Neighbor list builds = 0 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 ghost atom cutoff = 8 binsize = 4, bins = 4 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.075 | 5.075 | 5.075 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -3551.3386 0 -3551.3386 5351.8668 11888.259 49 0 -3551.5028 0 -3551.5028 -297.56171 11935.592 Loop time of 0.393668 on 1 procs for 5 steps with 1007 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 = -3551.33863336273 -3551.50081392624 -3551.50278516283 Force two-norm initial, final = 80.045818 4.0564788 Force max component initial, final = 69.484626 2.8124747 Final line search alpha, max atom move = 0.00016227913 0.00045640595 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39192 | 0.39192 | 0.39192 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031634 | 0.00031634 | 0.00031634 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001431 | | | 0.36 Nlocal: 1007.00 ave 1007 max 1007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6016.00 ave 6016 max 6016 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: 177184.0 ave 177184 max 177184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177184 Ave neighs/atom = 175.95233 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 ghost atom cutoff = 8 binsize = 4, bins = 4 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.212 | 5.212 | 5.212 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3551.5028 0 -3551.5028 -297.56171 Loop time of 1.763e-06 on 1 procs for 0 steps with 1007 atoms 226.9% 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 | | 1.763e-06 | | |100.00 Nlocal: 1007.00 ave 1007 max 1007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5967.00 ave 5967 max 5967 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: 176982.0 ave 176982 max 176982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176982 Ave neighs/atom = 175.75174 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 ghost atom cutoff = 8 binsize = 4, bins = 4 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.212 | 5.212 | 5.212 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 -3551.5028 -3551.5028 13.53244 99.802785 8.8374135 -297.56171 -297.56171 -359.56573 -156.15646 -376.96295 2.2926254 425.84627 Loop time of 1.95e-06 on 1 procs for 0 steps with 1007 atoms 205.1% 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 | | 1.95e-06 | | |100.00 Nlocal: 1007.00 ave 1007 max 1007 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5967.00 ave 5967 max 5967 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 88491.0 ave 88491 max 88491 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 176982.0 ave 176982 max 176982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176982 Ave neighs/atom = 175.75174 Neighbor list builds = 0 Dangerous builds = 0 1007 -3551.50278516283 eV 2.29262540199879 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05