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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -39.358325 0.0000000) to (19.279838 39.358325 8.6222058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1412902 4.7225766 5.7481372 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -39.358325 0.0000000) to (19.279838 39.358325 8.6222058) create_atoms CPU = 0.001 seconds 612 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1412902 4.7225766 5.7481372 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -39.358325 0.0000000) to (19.279838 39.358325 8.6222058) create_atoms CPU = 0.001 seconds 612 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 21 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 48 atoms, new total = 1176 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.453 | 5.453 | 5.453 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5163.4623 0 -5163.4623 -3351.2876 54 0 -5198.7364 0 -5198.7364 -23084.07 Loop time of 0.979677 on 1 procs for 54 steps with 1176 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 = -5163.46227311405 -5198.73149898458 -5198.73639799047 Force two-norm initial, final = 26.603418 0.24137438 Force max component initial, final = 3.5369968 0.024928578 Final line search alpha, max atom move = 1.0000000 0.024928578 Iterations, force evaluations = 54 102 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.97057 | 0.97057 | 0.97057 | 0.0 | 99.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.004412 | 0.004412 | 0.004412 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004692 | | | 0.48 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5782.00 ave 5782 max 5782 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: 203664.0 ave 203664 max 203664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 203664 Ave neighs/atom = 173.18367 Neighbor list builds = 0 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.455 | 5.455 | 5.455 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -5198.7364 0 -5198.7364 -23084.07 13085.441 60 0 -5199.4294 0 -5199.4294 -6613.4272 12969.814 Loop time of 0.0872276 on 1 procs for 6 steps with 1176 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 = -5198.73639799051 -5199.42856874365 -5199.42938234979 Force two-norm initial, final = 220.62110 0.65468201 Force max component initial, final = 157.42569 0.092887491 Final line search alpha, max atom move = 0.00024798041 2.3034278e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.084967 | 0.084967 | 0.084967 | 0.0 | 97.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00039325 | 0.00039325 | 0.00039325 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001867 | | | 2.14 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6017.00 ave 6017 max 6017 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: 205464.0 ave 205464 max 205464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205464 Ave neighs/atom = 174.71429 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.593 | 5.593 | 5.593 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5199.4294 0 -5199.4294 -6613.4272 Loop time of 1.565e-06 on 1 procs for 0 steps with 1176 atoms 127.8% 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 | | 1.565e-06 | | |100.00 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6051.00 ave 6051 max 6051 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: 206088.0 ave 206088 max 206088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206088 Ave neighs/atom = 175.24490 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.593 | 5.593 | 5.593 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 -5199.4294 -5199.4294 19.184371 78.71665 8.588545 -6613.4272 -6613.4272 5.1011611 -19836.163 -9.2193946 2.3063016 796.65279 Loop time of 1.501e-06 on 1 procs for 0 steps with 1176 atoms 199.9% 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 | | 1.501e-06 | | |100.00 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6051.00 ave 6051 max 6051 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 103044.0 ave 103044 max 103044 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 206088.0 ave 206088 max 206088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 206088 Ave neighs/atom = 175.24490 Neighbor list builds = 0 Dangerous builds = 0 1176 -5199.42938234979 eV 2.30630161762991 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01