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 -49.800000 0.0000000) to (24.900000 49.800000 3.5213918) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9840000 3.9840000 3.5213918 Created 400 atoms using lattice units in orthogonal box = (0.0000000 -49.800000 0.0000000) to (24.900000 49.800000 3.5213918) create_atoms CPU = 0.001 seconds 400 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9840000 3.9840000 3.5213918 Created 402 atoms using lattice units in orthogonal box = (0.0000000 -49.800000 0.0000000) to (24.900000 49.800000 3.5213918) create_atoms CPU = 0.000 seconds 402 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 = 9 34 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 6 atoms, new total = 796 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 = 9 34 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) = 4.547 | 4.547 | 4.547 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2955.5842 0 -2955.5842 151654.25 62 0 -3528.4923 0 -3528.4923 -260.81071 Loop time of 3.21054 on 1 procs for 62 steps with 796 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2955.58419748795 -3528.48882973356 -3528.49233093204 Force two-norm initial, final = 1397.1541 0.19386462 Force max component initial, final = 477.68391 0.031018368 Final line search alpha, max atom move = 1.0000000 0.031018368 Iterations, force evaluations = 62 115 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1928 | 3.1928 | 3.1928 | 0.0 | 99.45 Neigh | 0.0051143 | 0.0051143 | 0.0051143 | 0.0 | 0.16 Comm | 0.0065292 | 0.0065292 | 0.0065292 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006045 | | | 0.19 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5109.00 ave 5109 max 5109 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: 61996.0 ave 61996 max 61996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61996 Ave neighs/atom = 77.884422 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 = 9 34 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 : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.547 | 4.547 | 4.547 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -3528.4923 0 -3528.4923 -260.81071 8733.1924 64 0 -3528.4981 0 -3528.4981 -22.343974 8732.0693 Loop time of 0.111147 on 1 procs for 2 steps with 796 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 = -3528.49233093205 -3528.49697022953 -3528.49808155212 Force two-norm initial, final = 8.6375747 0.31127926 Force max component initial, final = 8.1729123 0.21633578 Final line search alpha, max atom move = 0.00016055145 3.4733024e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11031 | 0.11031 | 0.11031 | 0.0 | 99.25 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015478 | 0.00015478 | 0.00015478 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006783 | | | 0.61 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5111.00 ave 5111 max 5111 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: 62112.0 ave 62112 max 62112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62112 Ave neighs/atom = 78.030151 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 = 9 34 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) = 4.685 | 4.685 | 4.685 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3528.4981 0 -3528.4981 -22.343974 Loop time of 1.873e-06 on 1 procs for 0 steps with 796 atoms 213.6% 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 | | 1.873e-06 | | |100.00 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5111.00 ave 5111 max 5111 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: 62104.0 ave 62104 max 62104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62104 Ave neighs/atom = 78.020101 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 = 9 34 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) = 4.685 | 4.685 | 4.685 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 -3528.4981 -3528.4981 24.911525 99.654713 3.5173778 -22.343974 -22.343974 -19.510311 -7.8731594 -39.648451 2.3047574 222.74291 Loop time of 2.094e-06 on 1 procs for 0 steps with 796 atoms 191.0% 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 | | 2.094e-06 | | |100.00 Nlocal: 796.000 ave 796 max 796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5111.00 ave 5111 max 5111 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31052.0 ave 31052 max 31052 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 62104.0 ave 62104 max 62104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62104 Ave neighs/atom = 78.020101 Neighbor list builds = 0 Dangerous builds = 0 796 -3528.49808155212 eV 2.30475737791627 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03