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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -49.552060 0.0000000) to (30.344316 49.552060 7.7074639) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8942445 4.7953606 5.1383093 Created 744 atoms using lattice units in orthogonal box = (0.0000000 -49.552060 0.0000000) to (30.344316 49.552060 7.7074639) create_atoms CPU = 0.002 seconds 744 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8942445 4.7953606 5.1383093 Created 750 atoms using lattice units in orthogonal box = (0.0000000 -49.552060 0.0000000) to (30.344316 49.552060 7.7074639) create_atoms CPU = 0.001 seconds 750 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 35 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1494 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 35 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.601 | 4.601 | 4.601 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9976.9058 0 -9976.9058 37393.017 15 0 -13392.735 0 -13392.735 22351.343 Loop time of 4.14094 on 1 procs for 15 steps with 1494 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 = -9976.90579155997 -13392.7333968565 -13392.7350886799 Force two-norm initial, final = 47.987002 4082.9953 Force max component initial, final = 8.0400738 978.45854 Final line search alpha, max atom move = 4.8020858e-08 4.6986418e-05 Iterations, force evaluations = 15 114 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.128 | 4.128 | 4.128 | 0.0 | 99.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0056761 | 0.0056761 | 0.0056761 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007231 | | | 0.17 Nlocal: 1494.00 ave 1494 max 1494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4268.00 ave 4268 max 4268 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: 86604.0 ave 86604 max 86604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86604 Ave neighs/atom = 57.967871 Neighbor list builds = 0 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 35 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 15 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.601 | 4.601 | 4.601 Mbytes Step Temp E_pair E_mol TotEng Press Volume 15 0 -13392.735 0 -13392.735 22351.343 23178.245 51 0 -15535.701 0 -15535.701 -1292.0405 23440.711 Loop time of 9.394 on 1 procs for 36 steps with 1494 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 = -13392.7350886798 -15535.6970279897 -15535.7010277872 Force two-norm initial, final = 4122.2086 879.59984 Force max component initial, final = 978.45854 163.66945 Final line search alpha, max atom move = 4.6283791e-08 7.5752425e-06 Iterations, force evaluations = 36 258 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.3171 | 9.3171 | 9.3171 | 0.0 | 99.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.010352 | 0.010352 | 0.010352 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06658 | | | 0.71 Nlocal: 1494.00 ave 1494 max 1494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4268.00 ave 4268 max 4268 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: 86544.0 ave 86544 max 86544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86544 Ave neighs/atom = 57.927711 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 35 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.739 | 4.739 | 4.739 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15535.701 0 -15535.701 -1292.0405 Loop time of 2.106e-06 on 1 procs for 0 steps with 1494 atoms 189.9% 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 | | 2.106e-06 | | |100.00 Nlocal: 1494.00 ave 1494 max 1494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4268.00 ave 4268 max 4268 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: 86508.0 ave 86508 max 86508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86508 Ave neighs/atom = 57.903614 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 35 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.739 | 4.739 | 4.739 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 -15535.701 -15535.701 30.430107 99.658348 7.7295394 -1292.0405 -1292.0405 -5887.7708 1740.697 270.95243 0.0056873196 1116.4765 Loop time of 2.563e-06 on 1 procs for 0 steps with 1494 atoms 234.1% 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 | | 2.563e-06 | | |100.00 Nlocal: 1494.00 ave 1494 max 1494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4268.00 ave 4268 max 4268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43254.0 ave 43254 max 43254 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 86508.0 ave 86508 max 86508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86508 Ave neighs/atom = 57.903614 Neighbor list builds = 0 Dangerous builds = 0 1494 -15535.7010277872 eV 0.00568731961750096 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13