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 = 4.0320382 4.0320382 4.0320382 Created orthogonal box = (0.0000000 -52.261188 0.0000000) to (30.173011 52.261188 6.9836950) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4656452 6.2215700 6.9836950 Created 670 atoms using lattice units in orthogonal box = (0.0000000 -52.261188 0.0000000) to (30.173011 52.261188 6.9836950) create_atoms CPU = 0.001 seconds 670 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4656452 6.2215700 6.9836950 Created 674 atoms using lattice units in orthogonal box = (0.0000000 -52.261188 0.0000000) to (30.173011 52.261188 6.9836950) create_atoms CPU = 0.001 seconds 674 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 7 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 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1344 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_019873715786_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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 7 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.494 | 5.494 | 5.494 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4419.4827 0 -4419.4827 13458.256 67 0 -4501.6706 0 -4501.6706 5575.799 Loop time of 1.59607 on 1 procs for 67 steps with 1344 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 = -4419.48266175961 -4501.66649310186 -4501.67056336963 Force two-norm initial, final = 51.710970 0.15770089 Force max component initial, final = 7.4121530 0.027523586 Final line search alpha, max atom move = 1.0000000 0.027523586 Iterations, force evaluations = 67 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5476 | 1.5476 | 1.5476 | 0.0 | 96.96 Neigh | 0.029616 | 0.029616 | 0.029616 | 0.0 | 1.86 Comm | 0.0096318 | 0.0096318 | 0.0096318 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00922 | | | 0.58 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6884.00 ave 6884 max 6884 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: 233302.0 ave 233302 max 233302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 233302 Ave neighs/atom = 173.58780 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 7 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.494 | 5.494 | 5.494 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -4501.6706 0 -4501.6706 5575.799 22024.862 77 0 -4502.2613 0 -4502.2613 15.15998 22165.038 Loop time of 0.161337 on 1 procs for 10 steps with 1344 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 = -4501.67056336962 -4502.26131131659 -4502.26134334374 Force two-norm initial, final = 158.73172 0.67039314 Force max component initial, final = 145.43638 0.48503991 Final line search alpha, max atom move = 0.00090236426 0.00043768268 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15645 | 0.15645 | 0.15645 | 0.0 | 96.97 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00075337 | 0.00075337 | 0.00075337 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004133 | | | 2.56 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6898.00 ave 6898 max 6898 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: 233334.0 ave 233334 max 233334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 233334 Ave neighs/atom = 173.61161 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 7 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.632 | 5.632 | 5.632 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4502.2613 0 -4502.2613 15.15998 Loop time of 2.12e-06 on 1 procs for 0 steps with 1344 atoms 141.5% 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 | | 2.12e-06 | | |100.00 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6894.00 ave 6894 max 6894 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: 232992.0 ave 232992 max 232992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 232992 Ave neighs/atom = 173.35714 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 7 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.632 | 5.632 | 5.632 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 -4502.2613 -4502.2613 30.17713 105.45096 6.9653027 15.15998 15.15998 -5.8451546 16.356831 34.968264 2.626649 969.6875 Loop time of 2.286e-06 on 1 procs for 0 steps with 1344 atoms 218.7% 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 | | 2.286e-06 | | |100.00 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6894.00 ave 6894 max 6894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 116496.0 ave 116496 max 116496 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 232992.0 ave 232992 max 232992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 232992 Ave neighs/atom = 173.35714 Neighbor list builds = 0 Dangerous builds = 0 1344 -4502.26134334374 eV 2.62664898108744 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02