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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -45.096739 0.0000000) to (27.616000 45.096739 7.0144710) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4541935 4.3642005 4.6763140 Created 740 atoms using lattice units in orthogonal box = (0.0000000 -45.096739 0.0000000) to (27.616000 45.096739 7.0144710) create_atoms CPU = 0.001 seconds 740 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4541935 4.3642005 4.6763140 Created 746 atoms using lattice units in orthogonal box = (0.0000000 -45.096739 0.0000000) to (27.616000 45.096739 7.0144710) create_atoms CPU = 0.001 seconds 746 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 9 29 3 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 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1486 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_343168101490_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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 9 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.062 | 5.062 | 5.062 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6205.2717 0 -6205.2717 30604.294 47 0 -6348.6319 0 -6348.6319 3844.7018 Loop time of 10.4586 on 1 procs for 47 steps with 1486 atoms 83.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6205.2717183414 -6348.62595886364 -6348.63185916877 Force two-norm initial, final = 158.48932 0.27163204 Force max component initial, final = 25.136702 0.069376964 Final line search alpha, max atom move = 1.0000000 0.069376964 Iterations, force evaluations = 47 77 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.431 | 10.431 | 10.431 | 0.0 | 99.73 Neigh | 0.011316 | 0.011316 | 0.011316 | 0.0 | 0.11 Comm | 0.0079305 | 0.0079305 | 0.0079305 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008701 | | | 0.08 Nlocal: 1486.00 ave 1486 max 1486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5538.00 ave 5538 max 5538 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: 145338.0 ave 145338 max 145338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 145338 Ave neighs/atom = 97.804845 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 9 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.062 | 5.062 | 5.062 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -6348.6319 0 -6348.6319 3844.7018 17471.525 53 0 -6348.9898 0 -6348.9898 -104.17908 17511.081 Loop time of 0.928401 on 1 procs for 6 steps with 1486 atoms 96.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6348.63185916876 -6348.98764629159 -6348.98975993766 Force two-norm initial, final = 130.28279 2.0233050 Force max component initial, final = 128.66721 1.2212937 Final line search alpha, max atom move = 0.00012899908 0.00015754577 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.92569 | 0.92569 | 0.92569 | 0.0 | 99.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038717 | 0.00038717 | 0.00038717 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002324 | | | 0.25 Nlocal: 1486.00 ave 1486 max 1486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5528.00 ave 5528 max 5528 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: 149050.0 ave 149050 max 149050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 149050 Ave neighs/atom = 100.30283 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 9 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.200 | 5.200 | 5.200 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6348.9898 0 -6348.9898 -104.17908 Loop time of 2.402e-06 on 1 procs for 0 steps with 1486 atoms 166.5% 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 | | 2.402e-06 | | |100.00 Nlocal: 1486.00 ave 1486 max 1486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5540.00 ave 5540 max 5540 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: 147722.0 ave 147722 max 147722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147722 Ave neighs/atom = 99.409152 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 9 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.200 | 5.200 | 5.200 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 -6348.9898 -6348.9898 27.552632 90.681685 7.0085842 -104.17908 -104.17908 -111.32798 -89.560769 -111.6485 2.2647486 1043.4421 Loop time of 3.894e-06 on 1 procs for 0 steps with 1486 atoms 231.1% 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 | | 3.894e-06 | | |100.00 Nlocal: 1486.00 ave 1486 max 1486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5540.00 ave 5540 max 5540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73861.0 ave 73861 max 73861 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 147722.0 ave 147722 max 147722 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147722 Ave neighs/atom = 99.409152 Neighbor list builds = 0 Dangerous builds = 0 1486 -6348.98975993766 eV 2.26474861044992 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12