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 = 4.0248454 4.0248454 4.0248454 Created orthogonal box = (0.0000000 -58.602633 0.0000000) to (29.301317 58.602633 4.0248454) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9756953 4.9756953 4.0248454 Created 424 atoms using lattice units in orthogonal box = (0.0000000 -58.602633 0.0000000) to (29.301317 58.602633 4.0248454) create_atoms CPU = 0.001 seconds 424 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9756953 4.9756953 4.0248454 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -58.602633 0.0000000) to (29.301317 58.602633 4.0248454) create_atoms CPU = 0.001 seconds 426 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 8 29 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 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 848 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_149316865608_005#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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 4.979 | 4.979 | 4.979 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2185.5841 0 -2185.5841 10259.181 71 0 -2237.1844 0 -2237.1844 4942.0478 Loop time of 1.12919 on 1 procs for 71 steps with 848 atoms 91.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2185.58408591964 -2237.18235607926 -2237.1844287837 Force two-norm initial, final = 91.936386 0.12097916 Force max component initial, final = 30.823483 0.021829855 Final line search alpha, max atom move = 1.0000000 0.021829855 Iterations, force evaluations = 71 136 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1059 | 1.1059 | 1.1059 | 0.0 | 97.94 Neigh | 0.0072808 | 0.0072808 | 0.0072808 | 0.0 | 0.64 Comm | 0.0086507 | 0.0086507 | 0.0086507 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00733 | | | 0.65 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6732.00 ave 6732 max 6732 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: 118456.0 ave 118456 max 118456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118456 Ave neighs/atom = 139.68868 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 8 29 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.979 | 4.979 | 4.979 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -2237.1844 0 -2237.1844 4942.0478 13822.4 82 0 -2237.536 0 -2237.536 -25.142436 13905.934 Loop time of 0.108282 on 1 procs for 11 steps with 848 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 = -2237.18442878369 -2237.53598074041 -2237.53599047755 Force two-norm initial, final = 88.082746 0.47107323 Force max component initial, final = 81.694976 0.24618275 Final line search alpha, max atom move = 0.0041168828 0.0010135055 Iterations, force evaluations = 11 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.09684 | 0.09684 | 0.09684 | 0.0 | 89.43 Neigh | 0.0073902 | 0.0073902 | 0.0073902 | 0.0 | 6.82 Comm | 0.00082649 | 0.00082649 | 0.00082649 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003225 | | | 2.98 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6762.00 ave 6762 max 6762 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: 118456.0 ave 118456 max 118456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118456 Ave neighs/atom = 139.68868 Neighbor list builds = 1 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 7 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 5.116 | 5.116 | 5.116 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2237.536 0 -2237.536 -25.142436 Loop time of 1.802e-06 on 1 procs for 0 steps with 848 atoms 166.5% 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 | | 1.802e-06 | | |100.00 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6762.00 ave 6762 max 6762 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: 118460.0 ave 118460 max 118460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118460 Ave neighs/atom = 139.69340 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 7 29 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 5.116 | 5.116 | 5.116 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 -2237.536 -2237.536 29.268986 118.36003 4.0140928 -25.142436 -25.142436 -19.400306 -27.738756 -28.288245 2.5999384 486.46179 Loop time of 2.027e-06 on 1 procs for 0 steps with 848 atoms 197.3% 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 | | 2.027e-06 | | |100.00 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6762.00 ave 6762 max 6762 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59230.0 ave 59230 max 59230 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 118460.0 ave 118460 max 118460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118460 Ave neighs/atom = 139.69340 Neighbor list builds = 0 Dangerous builds = 0 848 -2211.47333536439 eV 2.5999384172963 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01