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 = 3.6149590 3.6149590 3.6149590 Created orthogonal box = (0.0000000 -38.597200 0.0000000) to (27.292342 38.597200 5.1123240) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2669431 6.0942947 5.1123240 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -38.597200 0.0000000) to (27.292342 38.597200 5.1123240) create_atoms CPU = 0.004 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2669431 6.0942947 5.1123240 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.597200 0.0000000) to (27.292342 38.597200 5.1123240) create_atoms CPU = 0.003 seconds 458 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 8 21 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 7.715751993501819 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 908 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_759493141826_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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 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) = 4.987 | 4.987 | 4.987 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3018.4589 0 -3018.4589 41144.428 68 0 -3201.5785 0 -3201.5785 8425.7393 Loop time of 2.19605 on 1 procs for 68 steps with 908 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 = -3018.45891698879 -3201.57532474999 -3201.57846883261 Force two-norm initial, final = 337.35980 0.17473546 Force max component initial, final = 102.40040 0.025595279 Final line search alpha, max atom move = 1.0000000 0.025595279 Iterations, force evaluations = 68 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.142 | 2.142 | 2.142 | 0.0 | 97.54 Neigh | 0.019929 | 0.019929 | 0.019929 | 0.0 | 0.91 Comm | 0.018546 | 0.018546 | 0.018546 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01553 | | | 0.71 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5929.00 ave 5929 max 5929 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: 153912.0 ave 153912 max 153912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 153912 Ave neighs/atom = 169.50661 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.987 | 4.987 | 4.987 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -3201.5785 0 -3201.5785 8425.7393 10770.726 75 0 -3201.847 0 -3201.847 -63.99634 10836.11 Loop time of 0.166019 on 1 procs for 7 steps with 908 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 = -3201.57846883261 -3201.84684918877 -3201.84695610019 Force two-norm initial, final = 107.89735 1.5648786 Force max component initial, final = 92.914894 1.2493841 Final line search alpha, max atom move = 0.00030539552 0.00038155631 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16039 | 0.16039 | 0.16039 | 0.0 | 96.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013203 | 0.0013203 | 0.0013203 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004307 | | | 2.59 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5896.00 ave 5896 max 5896 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: 154720.0 ave 154720 max 154720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154720 Ave neighs/atom = 170.39648 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 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) = 5.125 | 5.125 | 5.125 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3201.847 0 -3201.847 -63.99634 Loop time of 6.465e-06 on 1 procs for 0 steps with 908 atoms 201.1% 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 | | 6.465e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5888.00 ave 5888 max 5888 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: 154100.0 ave 154100 max 154100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154100 Ave neighs/atom = 169.71366 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 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) = 5.125 | 5.125 | 5.125 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 -3201.847 -3201.847 27.298187 77.64655 5.1123128 -63.99634 -63.99634 -184.76766 -96.731129 89.509763 2.387731 647.63635 Loop time of 7.377e-06 on 1 procs for 0 steps with 908 atoms 257.6% 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 | | 7.377e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5888.00 ave 5888 max 5888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 77050.0 ave 77050 max 77050 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 154100.0 ave 154100 max 154100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 154100 Ave neighs/atom = 169.71366 Neighbor list builds = 0 Dangerous builds = 0 908 -3201.84695610019 eV 2.38773096334222 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02