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 = 3.7004755 3.7004755 3.7004755 Created orthogonal box = (0.0000000 -47.389209 0.0000000) to (33.509231 47.389209 5.2332627) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7210883 6.3570891 5.2332627 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -47.389209 0.0000000) to (33.509231 47.389209 5.2332627) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7210883 6.3570891 5.2332627 Created 660 atoms using lattice units in orthogonal box = (0.0000000 -47.389209 0.0000000) to (33.509231 47.389209 5.2332627) create_atoms CPU = 0.001 seconds 660 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 9 25 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 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1316 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_466808877130_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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 5.081 | 5.081 | 5.081 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4992.9505 0 -4992.9505 61493.671 564 0 -5329.4463 0 -5329.4463 -101972.59 Loop time of 11.0089 on 1 procs for 564 steps with 1316 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 = -4992.95054110171 -5329.44154102373 -5329.44625344816 Force two-norm initial, final = 336.29077 0.30817784 Force max component initial, final = 91.779605 0.087933407 Final line search alpha, max atom move = 1.0000000 0.087933407 Iterations, force evaluations = 564 1060 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.663 | 10.663 | 10.663 | 0.0 | 96.85 Neigh | 0.20539 | 0.20539 | 0.20539 | 0.0 | 1.87 Comm | 0.077951 | 0.077951 | 0.077951 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06299 | | | 0.57 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7684.00 ave 7684 max 7684 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: 209038.0 ave 209038 max 209038 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 209038 Ave neighs/atom = 158.84347 Neighbor list builds = 17 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 564 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.463 | 5.463 | 5.463 Mbytes Step Temp E_pair E_mol TotEng Press Volume 564 0 -5329.4463 0 -5329.4463 -101972.59 16620.591 623 0 -5383.8285 0 -5383.8285 -42.286029 15338.849 Loop time of 0.671253 on 1 procs for 59 steps with 1316 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 = -5329.44625344814 -5383.82604676001 -5383.82851289536 Force two-norm initial, final = 1897.6014 5.1510625 Force max component initial, final = 1420.9272 2.3212534 Final line search alpha, max atom move = 0.00010778627 0.00025019926 Iterations, force evaluations = 59 63 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.63723 | 0.63723 | 0.63723 | 0.0 | 94.93 Neigh | 0.011986 | 0.011986 | 0.011986 | 0.0 | 1.79 Comm | 0.0037642 | 0.0037642 | 0.0037642 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01827 | | | 2.72 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8021.00 ave 8021 max 8021 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: 218330.0 ave 218330 max 218330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 218330 Ave neighs/atom = 165.90426 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 5.605 | 5.605 | 5.605 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5383.8285 0 -5383.8285 -42.286029 Loop time of 1.62e-06 on 1 procs for 0 steps with 1316 atoms 123.5% 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 | | 1.62e-06 | | |100.00 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8215.00 ave 8215 max 8215 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: 219888.0 ave 219888 max 219888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 219888 Ave neighs/atom = 167.08815 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 5.605 | 5.605 | 5.605 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 -5383.8285 -5383.8285 32.842251 94.340021 4.9506689 -42.286029 -42.286029 -237.63401 97.418263 13.357662 2.2328551 1835.4285 Loop time of 1.866e-06 on 1 procs for 0 steps with 1316 atoms 160.8% 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 | | 1.866e-06 | | |100.00 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8215.00 ave 8215 max 8215 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 109944.0 ave 109944 max 109944 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 219888.0 ave 219888 max 219888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 219888 Ave neighs/atom = 167.08815 Neighbor list builds = 0 Dangerous builds = 0 1316 -5383.82851289536 eV 2.232855114138 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12