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 = 3.5213918 3.5213918 3.5213918 Created orthogonal box = (0.0000000 -57.215844 0.0000000) to (20.228856 57.215844 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5169606 4.3345336 4.9800000 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -57.215844 0.0000000) to (20.228856 57.215844 4.9800000) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5169606 4.3345336 4.9800000 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -57.215844 0.0000000) to (20.228856 57.215844 4.9800000) create_atoms CPU = 0.001 seconds 530 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 ghost atom cutoff = 6 binsize = 3, bins = 7 39 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1058 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_700541006254_001#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 ghost atom cutoff = 6 binsize = 3, bins = 7 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.627 | 4.627 | 4.627 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3967.5104 0 -3967.5104 179291.1 59 0 -4693.2739 0 -4693.2739 10184.555 Loop time of 3.82096 on 1 procs for 59 steps with 1058 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 = -3967.51041184735 -4693.27015677386 -4693.27388805073 Force two-norm initial, final = 1606.0537 0.21791005 Force max component initial, final = 489.10371 0.023509751 Final line search alpha, max atom move = 1.0000000 0.023509751 Iterations, force evaluations = 59 102 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.8003 | 3.8003 | 3.8003 | 0.0 | 99.46 Neigh | 0.0063037 | 0.0063037 | 0.0063037 | 0.0 | 0.16 Comm | 0.0075924 | 0.0075924 | 0.0075924 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006761 | | | 0.18 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5416.00 ave 5416 max 5416 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: 82764.0 ave 82764 max 82764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82764 Ave neighs/atom = 78.226843 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 7 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.624 | 4.624 | 4.624 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -4693.2739 0 -4693.2739 10184.555 11527.814 65 0 -4693.5586 0 -4693.5586 -76.522223 11590.955 Loop time of 0.301341 on 1 procs for 6 steps with 1058 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 = -4693.27388805073 -4693.55728150026 -4693.55862028452 Force two-norm initial, final = 132.99694 1.4629086 Force max component initial, final = 105.39585 1.1282707 Final line search alpha, max atom move = 9.8676036e-05 0.00011133328 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29907 | 0.29907 | 0.29907 | 0.0 | 99.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035187 | 0.00035187 | 0.00035187 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001923 | | | 0.64 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5003.00 ave 5003 max 5003 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: 82628.0 ave 82628 max 82628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82628 Ave neighs/atom = 78.098299 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 ghost atom cutoff = 6 binsize = 3, bins = 7 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.762 | 4.762 | 4.762 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4693.5586 0 -4693.5586 -76.522223 Loop time of 2.154e-06 on 1 procs for 0 steps with 1058 atoms 185.7% 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 | | 2.154e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5003.00 ave 5003 max 5003 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: 82564.0 ave 82564 max 82564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82564 Ave neighs/atom = 78.037807 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 ghost atom cutoff = 6 binsize = 3, bins = 7 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.762 | 4.762 | 4.762 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 -4693.5586 -4693.5586 20.22674 115.03934 4.9813487 -76.522223 -76.522223 -115.06982 41.502232 -155.99909 2.3169822 417.2913 Loop time of 2.433e-06 on 1 procs for 0 steps with 1058 atoms 205.5% 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 | | 2.433e-06 | | |100.00 Nlocal: 1058.00 ave 1058 max 1058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5003.00 ave 5003 max 5003 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 41282.0 ave 41282 max 41282 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 82564.0 ave 82564 max 82564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 82564 Ave neighs/atom = 78.037807 Neighbor list builds = 0 Dangerous builds = 0 1058 -4693.55862028452 eV 2.31698216557705 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04