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 = 2.8169555 2.8169555 2.8169555 Created orthogonal box = (0.0000000 -32.851064 0.0000000) to (11.614605 32.851064 3.9837767) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7824845 4.8310389 3.9837767 Created 136 atoms using lattice units in orthogonal box = (0.0000000 -32.851064 0.0000000) to (11.614605 32.851064 3.9837767) create_atoms CPU = 0.002 seconds 136 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7824845 4.8310389 3.9837767 Created 138 atoms using lattice units in orthogonal box = (0.0000000 -32.851064 0.0000000) to (11.614605 32.851064 3.9837767) create_atoms CPU = 0.001 seconds 138 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 = 3 17 1 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 2 atoms, new total = 272 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_922363340570_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 ghost atom cutoff = 8 binsize = 4, bins = 3 17 1 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) = 4.457 | 4.457 | 4.457 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -651.54561 0 -651.54561 310249.77 157 0 -1086.746 0 -1086.746 87270.938 Loop time of 1.98135 on 1 procs for 157 steps with 272 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 = -651.54561185618 -1086.74501957264 -1086.74600781749 Force two-norm initial, final = 1195.2496 0.096866759 Force max component initial, final = 398.10604 0.017692383 Final line search alpha, max atom move = 1.0000000 0.017692383 Iterations, force evaluations = 157 297 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9071 | 1.9071 | 1.9071 | 0.0 | 96.25 Neigh | 0.024394 | 0.024394 | 0.024394 | 0.0 | 1.23 Comm | 0.030697 | 0.030697 | 0.030697 | 0.0 | 1.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01918 | | | 0.97 Nlocal: 272.000 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4053.00 ave 4053 max 4053 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: 49640.0 ave 49640 max 49640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49640 Ave neighs/atom = 182.50000 Neighbor list builds = 3 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 = 3 17 1 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 : 157 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.456 | 4.456 | 4.456 Mbytes Step Temp E_pair E_mol TotEng Press Volume 157 0 -1086.746 0 -1086.746 87270.938 3040.0371 317 0 -1093.7905 0 -1093.7905 425.95671 3188.5115 Loop time of 1.48584 on 1 procs for 160 steps with 272 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 = -1086.7460078175 -1093.78997390677 -1093.79047088147 Force two-norm initial, final = 304.94174 2.0773104 Force max component initial, final = 217.13725 1.2815206 Final line search alpha, max atom move = 0.00061241703 0.00078482506 Iterations, force evaluations = 160 211 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4096 | 1.4096 | 1.4096 | 0.0 | 94.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.018917 | 0.018917 | 0.018917 | 0.0 | 1.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05729 | | | 3.86 Nlocal: 272.000 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3971.00 ave 3971 max 3971 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: 49772.0 ave 49772 max 49772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49772 Ave neighs/atom = 182.98529 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 = 3 17 2 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) = 4.578 | 4.578 | 4.578 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1093.7905 0 -1093.7905 425.95671 Loop time of 6.375e-06 on 1 procs for 0 steps with 272 atoms 172.5% 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 | | 6.375e-06 | | |100.00 Nlocal: 272.000 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3335.00 ave 3335 max 3335 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: 48278.0 ave 48278 max 48278 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48278 Ave neighs/atom = 177.49265 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 = 3 17 2 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) = 4.578 | 4.578 | 4.578 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 -1093.7905 -1093.7905 11.834029 65.185677 4.1333596 425.95671 425.95671 285.46142 638.88209 353.52663 2.2962249 1012.3251 Loop time of 6.756e-06 on 1 procs for 0 steps with 272 atoms 251.6% 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 | | 6.756e-06 | | |100.00 Nlocal: 272.000 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3335.00 ave 3335 max 3335 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24139.0 ave 24139 max 24139 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 48278.0 ave 48278 max 48278 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48278 Ave neighs/atom = 177.49265 Neighbor list builds = 0 Dangerous builds = 0 272 -1093.79047088146 eV 2.29622487794745 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04