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 = 3.6056636 3.6056636 3.6056636 Created orthogonal box = (0.0000000 -56.322266 0.0000000) to (28.161133 56.322266 3.6056636) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0782371 5.0782371 3.6056636 Created 487 atoms using lattice units in orthogonal box = (0.0000000 -56.322266 0.0000000) to (28.161133 56.322266 3.6056636) create_atoms CPU = 0.002 seconds 487 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0782371 5.0782371 3.6056636 Created 489 atoms using lattice units in orthogonal box = (0.0000000 -56.322266 0.0000000) to (28.161133 56.322266 3.6056636) create_atoms CPU = 0.002 seconds 489 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 8 30 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 7.673367000244601 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 976 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_960699513424_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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 5.031 | 5.031 | 5.031 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 214743.63 0 214743.63 97138261 128 0 -4075.6409 0 -4075.6409 3644.3345 Loop time of 4.35971 on 1 procs for 128 steps with 976 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 = 214743.634448514 -4075.63747756734 -4075.64094504041 Force two-norm initial, final = 1473863.1 0.23719639 Force max component initial, final = 533257.95 0.069158592 Final line search alpha, max atom move = 1.0000000 0.069158592 Iterations, force evaluations = 128 238 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2361 | 4.2361 | 4.2361 | 0.0 | 97.17 Neigh | 0.042492 | 0.042492 | 0.042492 | 0.0 | 0.97 Comm | 0.048684 | 0.048684 | 0.048684 | 0.0 | 1.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03238 | | | 0.74 Nlocal: 976.000 ave 976 max 976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8440.00 ave 8440 max 8440 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: 160918.0 ave 160918 max 160918 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160918 Ave neighs/atom = 164.87500 Neighbor list builds = 2 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 128 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.031 | 5.031 | 5.031 Mbytes Step Temp E_pair E_mol TotEng Press Volume 128 0 -4075.6409 0 -4075.6409 3644.3345 11437.877 154 0 -4077.1761 0 -4077.1761 -6.2140649 11471.513 Loop time of 0.536628 on 1 procs for 26 steps with 976 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 = -4075.64094504042 -4077.17421732793 -4077.17609592643 Force two-norm initial, final = 105.71794 1.8630072 Force max component initial, final = 104.02534 0.78616667 Final line search alpha, max atom move = 0.00042915236 0.00033738528 Iterations, force evaluations = 26 27 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49349 | 0.49349 | 0.49349 | 0.0 | 91.96 Neigh | 0.020948 | 0.020948 | 0.020948 | 0.0 | 3.90 Comm | 0.0053854 | 0.0053854 | 0.0053854 | 0.0 | 1.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0168 | | | 3.13 Nlocal: 976.000 ave 976 max 976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8461.00 ave 8461 max 8461 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: 155328.0 ave 155328 max 155328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 155328 Ave neighs/atom = 159.14754 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 8 30 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 5.169 | 5.169 | 5.169 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4077.1761 0 -4077.1761 -6.2140649 Loop time of 6.224e-06 on 1 procs for 0 steps with 976 atoms 160.7% 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 | | 6.224e-06 | | |100.00 Nlocal: 976.000 ave 976 max 976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8489.00 ave 8489 max 8489 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: 155374.0 ave 155374 max 155374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 155374 Ave neighs/atom = 159.19467 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 8 30 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 5.169 | 5.169 | 5.169 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 -4077.1761 -4077.1761 27.836087 111.41286 3.6989394 -6.2140649 -6.2140649 47.649953 46.348798 -112.64095 2.3220882 175.00186 Loop time of 7.488e-06 on 1 procs for 0 steps with 976 atoms 267.1% 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 | | 7.488e-06 | | |100.00 Nlocal: 976.000 ave 976 max 976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8489.00 ave 8489 max 8489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 77687.0 ave 77687 max 77687 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 155374.0 ave 155374 max 155374 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 155374 Ave neighs/atom = 159.19467 Neighbor list builds = 0 Dangerous builds = 0 976 -4077.17609592643 eV 2.32208821856814 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05