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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -44.147617 0.0000000) to (6.2429061 44.147617 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2429061 5.8858683 5.0973115 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -44.147617 0.0000000) to (6.2429061 44.147617 5.0973115) create_atoms CPU = 0.001 seconds 122 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2429061 5.8858683 5.0973115 Created 122 atoms using lattice units in orthogonal box = (0.0000000 -44.147617 0.0000000) to (6.2429061 44.147617 5.0973115) create_atoms CPU = 0.001 seconds 122 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 3 29 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 240 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 3 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.443 | 4.443 | 4.443 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1008.4245 0 -1008.4245 13354.954 209 0 -1018.8996 0 -1018.8996 1684.0565 Loop time of 4.25823 on 1 procs for 209 steps with 240 atoms 96.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1008.4244724822 -1018.89863197732 -1018.89958072226 Force two-norm initial, final = 16.872158 0.081731598 Force max component initial, final = 5.5327155 0.014145623 Final line search alpha, max atom move = 1.0000000 0.014145623 Iterations, force evaluations = 209 408 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2353 | 4.2353 | 4.2353 | 0.0 | 99.46 Neigh | 0.0083869 | 0.0083869 | 0.0083869 | 0.0 | 0.20 Comm | 0.0087863 | 0.0087863 | 0.0087863 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005798 | | | 0.14 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2588.00 ave 2588 max 2588 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: 18714.0 ave 18714 max 18714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 18714 Ave neighs/atom = 77.975000 Neighbor list builds = 6 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 3 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 209 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.442 | 4.442 | 4.442 Mbytes Step Temp E_pair E_mol TotEng Press Volume 209 0 -1018.8996 0 -1018.8996 1684.0565 2809.7342 225 0 -1019.3836 0 -1019.3836 -9536.7802 2828.1948 Loop time of 0.173656 on 1 procs for 16 steps with 240 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 = -1018.89958072226 -1019.38316855135 -1019.38355845313 Force two-norm initial, final = 58.149807 0.31969583 Force max component initial, final = 57.088327 0.057961205 Final line search alpha, max atom move = 0.00098303831 5.6978085e-05 Iterations, force evaluations = 16 17 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17184 | 0.17184 | 0.17184 | 0.0 | 98.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034964 | 0.00034964 | 0.00034964 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00147 | | | 0.85 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2557.00 ave 2557 max 2557 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: 18640.0 ave 18640 max 18640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 18640 Ave neighs/atom = 77.666667 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 3 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.580 | 4.580 | 4.580 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1019.3836 0 -1019.3836 -9536.7802 Loop time of 1.509e-06 on 1 procs for 0 steps with 240 atoms 132.5% 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 | | 1.509e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2560.00 ave 2560 max 2560 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: 18634.0 ave 18634 max 18634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 18634 Ave neighs/atom = 77.641667 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 3 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.580 | 4.580 | 4.580 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 -1019.3836 -1019.3836 6.3388421 88.295233 5.0531492 -9536.7802 -9536.7802 -31.359563 -28599.654 20.672896 2.4305942 995.75055 Loop time of 1.441e-06 on 1 procs for 0 steps with 240 atoms 138.8% 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 | | 1.441e-06 | | |100.00 Nlocal: 240.000 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2560.00 ave 2560 max 2560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 9317.00 ave 9317 max 9317 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 18634.0 ave 18634 max 18634 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 18634 Ave neighs/atom = 77.641667 Neighbor list builds = 0 Dangerous builds = 0 240 -1019.38355845313 eV 2.4305941971139 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04