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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -39.480734 0.0000000) to (27.917095 39.480734 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7663332 5.2961960 4.3599177 Created 328 atoms using lattice units in orthogonal box = (0.0000000 -39.480734 0.0000000) to (27.917095 39.480734 4.3599177) create_atoms CPU = 0.001 seconds 328 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7663332 5.2961960 4.3599177 Created 330 atoms using lattice units in orthogonal box = (0.0000000 -39.480734 0.0000000) to (27.917095 39.480734 4.3599177) create_atoms CPU = 0.001 seconds 330 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 24 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 658 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.266 | 5.266 | 5.266 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3562.6587 0 -3562.6587 250111.04 92 0 -4260.8286 0 -4260.8286 12071.555 Loop time of 31.6795 on 1 procs for 92 steps with 658 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 = -3562.65865108959 -4260.82429254491 -4260.82855290156 Force two-norm initial, final = 1104.1656 0.31663484 Force max component initial, final = 262.64617 0.074001517 Final line search alpha, max atom move = 1.0000000 0.074001517 Iterations, force evaluations = 92 163 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 31.64 | 31.64 | 31.64 | 0.0 | 99.88 Neigh | 0.025413 | 0.025413 | 0.025413 | 0.0 | 0.08 Comm | 0.0071753 | 0.0071753 | 0.0071753 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006907 | | | 0.02 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3898.00 ave 3898 max 3898 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: 48016.0 ave 48016 max 48016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48016 Ave neighs/atom = 72.972644 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 92 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.651 | 5.651 | 5.651 Mbytes Step Temp E_pair E_mol TotEng Press Volume 92 0 -4260.8286 0 -4260.8286 12071.555 9610.8927 98 0 -4261.1748 0 -4261.1748 262.79891 9661.8349 Loop time of 1.56927 on 1 procs for 6 steps with 658 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 = -4260.82855290157 -4261.1731209227 -4261.17483625885 Force two-norm initial, final = 144.92247 3.0660765 Force max component initial, final = 129.95732 2.3356861 Final line search alpha, max atom move = 0.00021143489 0.00049384553 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5675 | 1.5675 | 1.5675 | 0.0 | 99.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028758 | 0.00028758 | 0.00028758 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001443 | | | 0.09 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4314.00 ave 4314 max 4314 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: 49512.0 ave 49512 max 49512 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49512 Ave neighs/atom = 75.246201 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.408 | 5.408 | 5.408 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4261.1748 0 -4261.1748 262.79891 Loop time of 2.046e-06 on 1 procs for 0 steps with 658 atoms 146.6% 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 | | 2.046e-06 | | |100.00 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4295.00 ave 4295 max 4295 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: 48804.0 ave 48804 max 48804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48804 Ave neighs/atom = 74.170213 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.408 | 5.408 | 5.408 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 -4261.1748 -4261.1748 27.882944 79.343659 4.3672572 262.79891 262.79891 104.11348 389.19049 295.09277 2.4574969 885.51944 Loop time of 1.947e-06 on 1 procs for 0 steps with 658 atoms 154.1% 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 | | 1.947e-06 | | |100.00 Nlocal: 658.000 ave 658 max 658 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4295.00 ave 4295 max 4295 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24402.0 ave 24402 max 24402 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 48804.0 ave 48804 max 48804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48804 Ave neighs/atom = 74.170213 Neighbor list builds = 0 Dangerous builds = 0 658 -4261.17483625885 eV 2.45749692785699 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:34