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 -37.371138 0.0000000) to (22.885055 37.371138 6.9001037) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1609191 4.2467202 4.6000691 Created 526 atoms using lattice units in orthogonal box = (0.0000000 -37.371138 0.0000000) to (22.885055 37.371138 6.9001037) create_atoms CPU = 0.001 seconds 526 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1609191 4.2467202 4.6000691 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -37.371138 0.0000000) to (22.885055 37.371138 6.9001037) create_atoms CPU = 0.001 seconds 532 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 = 6 19 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 1048 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 = 6 19 2 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) = 5.050 | 5.050 | 5.050 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3826.2456 0 -3826.2456 78182.57 304 0 -4187.4661 0 -4187.4661 74022.918 Loop time of 5.58366 on 1 procs for 304 steps with 1048 atoms 97.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3826.24555997701 -4187.46230069502 -4187.46607551315 Force two-norm initial, final = 498.54235 0.25071638 Force max component initial, final = 92.601667 0.061579753 Final line search alpha, max atom move = 0.73300043 0.045137986 Iterations, force evaluations = 304 601 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.4633 | 5.4633 | 5.4633 | 0.0 | 97.84 Neigh | 0.047684 | 0.047684 | 0.047684 | 0.0 | 0.85 Comm | 0.040144 | 0.040144 | 0.040144 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03256 | | | 0.58 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6176.00 ave 6176 max 6176 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: 189670.0 ave 189670 max 189670 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189670 Ave neighs/atom = 180.98282 Neighbor list builds = 4 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 = 6 19 2 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 : 304 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.050 | 5.050 | 5.050 Mbytes Step Temp E_pair E_mol TotEng Press Volume 304 0 -4187.4661 0 -4187.4661 74022.918 11802.497 333 0 -4197.3929 0 -4197.3929 854.61691 12176.739 Loop time of 0.283782 on 1 procs for 29 steps with 1048 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 = -4187.46607551316 -4197.38909924744 -4197.39291841864 Force two-norm initial, final = 951.48535 14.476600 Force max component initial, final = 639.42531 11.641426 Final line search alpha, max atom move = 0.00011462752 0.0013344277 Iterations, force evaluations = 29 31 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2746 | 0.2746 | 0.2746 | 0.0 | 96.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015475 | 0.0015475 | 0.0015475 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007639 | | | 2.69 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6164.00 ave 6164 max 6164 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: 189960.0 ave 189960 max 189960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189960 Ave neighs/atom = 181.25954 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 = 6 19 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) = 5.187 | 5.187 | 5.187 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4197.3929 0 -4197.3929 854.61691 Loop time of 1.943e-06 on 1 procs for 0 steps with 1048 atoms 154.4% 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 | | 1.943e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6106.00 ave 6106 max 6106 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: 186814.0 ave 186814 max 186814 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186814 Ave neighs/atom = 178.25763 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 = 6 19 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) = 5.187 | 5.187 | 5.187 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 -4197.3929 -4197.3929 23.010054 74.982468 7.0575443 854.61691 854.61691 228.42397 1536.6641 798.76262 2.2544226 5209.2082 Loop time of 2.308e-06 on 1 procs for 0 steps with 1048 atoms 260.0% 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 | | 2.308e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6106.00 ave 6106 max 6106 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 93407.0 ave 93407 max 93407 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 186814.0 ave 186814 max 186814 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186814 Ave neighs/atom = 178.25763 Neighbor list builds = 0 Dangerous builds = 0 1048 -4197.39291841864 eV 2.25442260907211 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06