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 = 3.5181212 3.5181212 3.5181212 Created orthogonal box = (0.0000000 -63.719404 0.0000000) to (22.526967 63.719404 4.9753748) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0438205 5.4391610 4.9753748 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -63.719404 0.0000000) to (22.526967 63.719404 4.9753748) create_atoms CPU = 0.002 seconds 658 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0438205 5.4391610 4.9753748 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -63.719404 0.0000000) to (22.526967 63.719404 4.9753748) create_atoms CPU = 0.001 seconds 658 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 6 30 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 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1304 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_222110751402_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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 6 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 5.935 | 5.935 | 5.935 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5672.9134 0 -5672.9134 11650.329 29 0 -5706.786 0 -5706.786 -5282.8734 Loop time of 0.933409 on 1 procs for 29 steps with 1304 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 = -5672.913391948 -5706.78048616596 -5706.78604572635 Force two-norm initial, final = 87.631735 0.23532338 Force max component initial, final = 28.565637 0.037320002 Final line search alpha, max atom move = 1.0000000 0.037320002 Iterations, force evaluations = 29 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.90732 | 0.90732 | 0.90732 | 0.0 | 97.20 Neigh | 0.017706 | 0.017706 | 0.017706 | 0.0 | 1.90 Comm | 0.0046158 | 0.0046158 | 0.0046158 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003769 | | | 0.40 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10468.0 ave 10468 max 10468 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: 321752.0 ave 321752 max 321752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 321752 Ave neighs/atom = 246.74233 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 6 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.935 | 5.935 | 5.935 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -5706.786 0 -5706.786 -5282.8734 14283.355 32 0 -5706.8617 0 -5706.8617 -1593.7384 14252.737 Loop time of 0.0916088 on 1 procs for 3 steps with 1304 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5706.78604572636 -5706.8589384327 -5706.8617195232 Force two-norm initial, final = 65.595917 0.30866164 Force max component initial, final = 64.672560 0.13418452 Final line search alpha, max atom move = 0.00012788882 1.7160700e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.089758 | 0.089758 | 0.089758 | 0.0 | 97.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037178 | 0.00037178 | 0.00037178 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001479 | | | 1.61 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10468.0 ave 10468 max 10468 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: 321712.0 ave 321712 max 321712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 321712 Ave neighs/atom = 246.71166 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 6 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 6.073 | 6.073 | 6.073 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5706.8617 0 -5706.8617 -1593.7384 Loop time of 1.722e-06 on 1 procs for 0 steps with 1304 atoms 116.1% 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 | | 1.722e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10468.0 ave 10468 max 10468 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: 321896.0 ave 321896 max 321896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 321896 Ave neighs/atom = 246.85276 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 6 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 6.073 | 6.073 | 6.073 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 -5706.8617 -5706.8617 22.531969 127.43881 4.9636075 -1593.7384 -1593.7384 -14.152624 -4752.0142 -15.048255 2.2735148 374.8066 Loop time of 2.222e-06 on 1 procs for 0 steps with 1304 atoms 270.0% 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 | | 2.222e-06 | | |100.00 Nlocal: 1304.00 ave 1304 max 1304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10468.0 ave 10468 max 10468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 160948.0 ave 160948 max 160948 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 321896.0 ave 321896 max 321896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 321896 Ave neighs/atom = 246.85276 Neighbor list builds = 0 Dangerous builds = 0 1304 -5706.8617195232 eV 2.27351479377566 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01