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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -42.753327 0.0000000) to (52.361918 42.753327 8.8507796) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9842192 5.4968563 5.9005197 Created 1663 atoms using lattice units in orthogonal box = (0.0000000 -42.753327 0.0000000) to (52.361918 42.753327 8.8507796) create_atoms CPU = 0.003 seconds 1663 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9842192 5.4968563 5.9005197 Created 1687 atoms using lattice units in orthogonal box = (0.0000000 -42.753327 0.0000000) to (52.361918 42.753327 8.8507796) create_atoms CPU = 0.003 seconds 1687 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 ghost atom cutoff = 7 binsize = 3.5, bins = 15 25 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3350 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_122936827583_001#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 ghost atom cutoff = 7 binsize = 3.5, bins = 15 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.519 | 6.519 | 6.519 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11107.57 0 -11107.57 68777.619 110 0 -11807.161 0 -11807.161 1963.8556 Loop time of 37.8737 on 1 procs for 110 steps with 3350 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 = -11107.5698538731 -11807.149705496 -11807.1606311346 Force two-norm initial, final = 534.64808 0.34436708 Force max component initial, final = 64.228934 0.10829902 Final line search alpha, max atom move = 0.53963053 0.058441455 Iterations, force evaluations = 110 199 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 37.656 | 37.656 | 37.656 | 0.0 | 99.43 Neigh | 0.15534 | 0.15534 | 0.15534 | 0.0 | 0.41 Comm | 0.024739 | 0.024739 | 0.024739 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03719 | | | 0.10 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9423.00 ave 9423 max 9423 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: 442036.0 ave 442036 max 442036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 442036 Ave neighs/atom = 131.95104 Neighbor list builds = 5 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 ghost atom cutoff = 7 binsize = 3.5, bins = 15 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 110 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.519 | 6.519 | 6.519 Mbytes Step Temp E_pair E_mol TotEng Press Volume 110 0 -11807.161 0 -11807.161 1963.8556 39627.528 112 0 -11807.221 0 -11807.221 3.9224996 39690.29 Loop time of 0.881463 on 1 procs for 2 steps with 3350 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 = -11807.1606311345 -11807.2135863553 -11807.2206031974 Force two-norm initial, final = 93.151544 2.2224597 Force max component initial, final = 80.741325 1.5424247 Final line search alpha, max atom move = 5.8470590e-05 9.0186483e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.87898 | 0.87898 | 0.87898 | 0.0 | 99.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037217 | 0.00037217 | 0.00037217 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002113 | | | 0.24 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9418.00 ave 9418 max 9418 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: 442096.0 ave 442096 max 442096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 442096 Ave neighs/atom = 131.96896 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 ghost atom cutoff = 7 binsize = 3.5, bins = 15 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.657 | 6.657 | 6.657 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11807.221 0 -11807.221 3.9224996 Loop time of 2.288e-06 on 1 procs for 0 steps with 3350 atoms 218.5% 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 | | 2.288e-06 | | |100.00 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9418.00 ave 9418 max 9418 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: 441998.0 ave 441998 max 441998 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 441998 Ave neighs/atom = 131.93970 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 ghost atom cutoff = 7 binsize = 3.5, bins = 15 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.657 | 6.657 | 6.657 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 -11807.221 -11807.221 52.361474 85.626574 8.8524573 3.9224996 3.9224996 62.262474 11.46224 -61.957215 2.2941554 2143.5076 Loop time of 4.663e-06 on 1 procs for 0 steps with 3350 atoms 235.9% 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 | | 4.663e-06 | | |100.00 Nlocal: 3350.00 ave 3350 max 3350 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9418.00 ave 9418 max 9418 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 220999.0 ave 220999 max 220999 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 441998.0 ave 441998 max 441998 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 441998 Ave neighs/atom = 131.93970 Neighbor list builds = 0 Dangerous builds = 0 3350 -11807.2206031974 eV 2.29415537806148 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:39