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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -38.153146 0.0000000) to (31.149344 38.153146 7.7074639) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4499063 4.4119047 5.1383093 Created 590 atoms using lattice units in orthogonal box = (0.0000000 -38.153146 0.0000000) to (31.149344 38.153146 7.7074639) create_atoms CPU = 0.003 seconds 590 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4499063 4.4119047 5.1383093 Created 590 atoms using lattice units in orthogonal box = (0.0000000 -38.153146 0.0000000) to (31.149344 38.153146 7.7074639) create_atoms CPU = 0.002 seconds 590 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 27 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1176 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.538 | 4.538 | 4.538 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7866.235 0 -7866.235 26762.791 52 0 -7952.1925 0 -7952.1925 14497.283 Loop time of 5.09242 on 1 procs for 52 steps with 1176 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 = -7866.23496477574 -7952.18579237615 -7952.19246947239 Force two-norm initial, final = 44.404108 0.26972471 Force max component initial, final = 7.4442249 0.047481482 Final line search alpha, max atom move = 1.0000000 0.047481482 Iterations, force evaluations = 52 85 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.0623 | 5.0623 | 5.0623 | 0.0 | 99.41 Neigh | 0.011669 | 0.011669 | 0.011669 | 0.0 | 0.23 Comm | 0.0069908 | 0.0069908 | 0.0069908 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0115 | | | 0.23 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3463.00 ave 3463 max 3463 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: 67460.0 ave 67460 max 67460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67460 Ave neighs/atom = 57.363946 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.538 | 4.538 | 4.538 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -7952.1925 0 -7952.1925 14497.283 18319.802 56 0 -7952.3503 0 -7952.3503 7647.6013 18366.984 Loop time of 0.40995 on 1 procs for 4 steps with 1176 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 = -7952.19246947238 -7952.35011129467 -7952.35031660957 Force two-norm initial, final = 134.43745 0.30013988 Force max component initial, final = 122.75237 0.040801039 Final line search alpha, max atom move = 0.00020582957 8.3980603e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40709 | 0.40709 | 0.40709 | 0.0 | 99.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049078 | 0.00049078 | 0.00049078 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00237 | | | 0.58 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3449.00 ave 3449 max 3449 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: 67372.0 ave 67372 max 67372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67372 Ave neighs/atom = 57.289116 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.676 | 4.676 | 4.676 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7952.3503 0 -7952.3503 7647.6013 Loop time of 6.064e-06 on 1 procs for 0 steps with 1176 atoms 181.4% 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 | | 6.064e-06 | | |100.00 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3449.00 ave 3449 max 3449 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: 67364.0 ave 67364 max 67364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67364 Ave neighs/atom = 57.282313 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.676 | 4.676 | 4.676 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 -7952.3503 -7952.3503 31.149164 76.306293 7.7273591 7647.6013 7647.6013 -3.4080913 22947.844 -1.6315413 2.3579789 1341.9629 Loop time of 6.836e-06 on 1 procs for 0 steps with 1176 atoms 263.3% 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 | | 6.836e-06 | | |100.00 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3449.00 ave 3449 max 3449 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33682.0 ave 33682 max 33682 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 67364.0 ave 67364 max 67364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67364 Ave neighs/atom = 57.282313 Neighbor list builds = 0 Dangerous builds = 0 1176 -7952.35031660957 eV 2.35797894173971 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06