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 = 4.0500102 4.0500102 4.0500102 Created orthogonal box = (0.0000000 -69.679010 0.0000000) to (34.839505 69.679010 4.0500102) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6496495 5.6496495 4.0500102 Created 592 atoms using lattice units in orthogonal box = (0.0000000 -69.679010 0.0000000) to (34.839505 69.679010 4.0500102) create_atoms CPU = 0.003 seconds 592 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6496495 5.6496495 4.0500102 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -69.679010 0.0000000) to (34.839505 69.679010 4.0500102) create_atoms CPU = 0.002 seconds 594 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 10 37 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 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1186 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_120808805541_005#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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 10 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 5.035 | 5.035 | 5.035 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3898.8863 0 -3898.8863 21754.968 57 0 -4012.3412 0 -4012.3412 3710.835 Loop time of 1.95891 on 1 procs for 57 steps with 1186 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3898.8862585476 -4012.33747514719 -4012.34119230563 Force two-norm initial, final = 116.44843 0.14842513 Force max component initial, final = 22.760444 0.029753304 Final line search alpha, max atom move = 1.0000000 0.029753304 Iterations, force evaluations = 57 105 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9198 | 1.9198 | 1.9198 | 0.0 | 98.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0215 | 0.0215 | 0.0215 | 0.0 | 1.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01762 | | | 0.90 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7329.00 ave 7329 max 7329 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: 157380.0 ave 157380 max 157380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 157380 Ave neighs/atom = 132.69815 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 10 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.035 | 5.035 | 5.035 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -4012.3412 0 -4012.3412 3710.835 19663.466 63 0 -4012.5408 0 -4012.5408 -3.5508906 19757.262 Loop time of 0.144708 on 1 procs for 6 steps with 1186 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4012.34119230565 -4012.54042881319 -4012.54079154609 Force two-norm initial, final = 89.746424 0.49047668 Force max component initial, final = 75.651880 0.32592759 Final line search alpha, max atom move = 0.00026418407 8.6104875e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13858 | 0.13858 | 0.13858 | 0.0 | 95.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013368 | 0.0013368 | 0.0013368 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004793 | | | 3.31 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7301.00 ave 7301 max 7301 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: 149344.0 ave 149344 max 149344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149344 Ave neighs/atom = 125.92243 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 10 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 5.173 | 5.173 | 5.173 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4012.5408 0 -4012.5408 -3.5508906 Loop time of 6.435e-06 on 1 procs for 0 steps with 1186 atoms 170.9% 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 | | 6.435e-06 | | |100.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7301.00 ave 7301 max 7301 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: 141216.0 ave 141216 max 141216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141216 Ave neighs/atom = 119.06914 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 10 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 5.173 | 5.173 | 5.173 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 -4012.5408 -4012.5408 34.786199 139.99541 4.0570092 -3.5508906 -3.5508906 -15.876604 -21.252203 26.476135 2.5681001 390.32439 Loop time of 8.019e-06 on 1 procs for 0 steps with 1186 atoms 212.0% 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 | | 8.019e-06 | | |100.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7301.00 ave 7301 max 7301 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70608.0 ave 70608 max 70608 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 141216.0 ave 141216 max 141216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141216 Ave neighs/atom = 119.06914 Neighbor list builds = 0 Dangerous builds = 0 1186 -4012.54079154609 eV 2.56810009211569 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02