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 = 2.8548760 2.8548760 2.8548760 Created orthogonal box = (0.0000000 -31.921339 0.0000000) to (15.636800 31.921339 6.9929895) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1698133 3.8302181 4.6619930 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -31.921339 0.0000000) to (15.636800 31.921339 6.9929895) create_atoms CPU = 0.002 seconds 306 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1698133 3.8302181 4.6619930 Created 306 atoms using lattice units in orthogonal box = (0.0000000 -31.921339 0.0000000) to (15.636800 31.921339 6.9929895) create_atoms CPU = 0.001 seconds 306 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 18 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 588 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.545 | 4.545 | 4.545 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2330.8924 0 -2330.8924 -1214.8204 49 0 -2345.3654 0 -2345.3654 -19807.995 Loop time of 0.817027 on 1 procs for 49 steps with 588 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 = -2330.89239764827 -2345.36373328598 -2345.36536127084 Force two-norm initial, final = 15.179307 0.11081257 Force max component initial, final = 3.3620544 0.0091454170 Final line search alpha, max atom move = 1.0000000 0.0091454170 Iterations, force evaluations = 49 89 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.79051 | 0.79051 | 0.79051 | 0.0 | 96.75 Neigh | 0.011635 | 0.011635 | 0.011635 | 0.0 | 1.42 Comm | 0.007237 | 0.007237 | 0.007237 | 0.0 | 0.89 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007642 | | | 0.94 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3597.00 ave 3597 max 3597 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: 79476.0 ave 79476 max 79476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79476 Ave neighs/atom = 135.16327 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.545 | 4.545 | 4.545 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -2345.3654 0 -2345.3654 -19807.995 6981.0676 55 0 -2345.7328 0 -2345.7328 -4241.8322 6916.0918 Loop time of 0.0827577 on 1 procs for 6 steps with 588 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2345.36536127083 -2345.73248693959 -2345.73280251191 Force two-norm initial, final = 110.91733 0.32703099 Force max component initial, final = 79.093672 0.041690276 Final line search alpha, max atom move = 0.00063384501 2.6425174e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.07947 | 0.07947 | 0.07947 | 0.0 | 96.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00068231 | 0.00068231 | 0.00068231 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002605 | | | 3.15 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3585.00 ave 3585 max 3585 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: 79440.0 ave 79440 max 79440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79440 Ave neighs/atom = 135.10204 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.683 | 4.683 | 4.683 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2345.7328 0 -2345.7328 -4241.8322 Loop time of 6.545e-06 on 1 procs for 0 steps with 588 atoms 137.5% 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 | | 6.545e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3585.00 ave 3585 max 3585 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: 79572.0 ave 79572 max 79572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79572 Ave neighs/atom = 135.32653 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 18 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.683 | 4.683 | 4.683 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 -2345.7328 -2345.7328 15.557056 63.842678 6.9634143 -4241.8322 -4241.8322 7.2868757 -12723.286 -9.4975593 2.4007639 409.00694 Loop time of 6.555e-06 on 1 procs for 0 steps with 588 atoms 244.1% 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 | | 6.555e-06 | | |100.00 Nlocal: 588.000 ave 588 max 588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3585.00 ave 3585 max 3585 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39786.0 ave 39786 max 39786 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 79572.0 ave 79572 max 79572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79572 Ave neighs/atom = 135.32653 Neighbor list builds = 0 Dangerous builds = 0 588 -2262.57688765092 eV 2.40076390449812 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01