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 = 2.8659524 2.8659524 2.8659524 Created orthogonal box = (0.0000000 -46.917663 0.0000000) to (33.175798 46.917663 4.0530688) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9516116 4.5517136 4.0530688 Created 536 atoms using lattice units in orthogonal box = (0.0000000 -46.917663 0.0000000) to (33.175798 46.917663 4.0530688) create_atoms CPU = 0.002 seconds 536 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9516116 4.5517136 4.0530688 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -46.917663 0.0000000) to (33.175798 46.917663 4.0530688) create_atoms CPU = 0.001 seconds 538 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 9 25 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 7.549891651270771 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1072 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_681088298208_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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 5.016 | 5.016 | 5.016 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2730.9904 0 -2730.9904 298912.78 75 0 -4583.4033 0 -4583.4033 4496.7838 Loop time of 1.20603 on 1 procs for 75 steps with 1072 atoms 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2730.99037102261 -4583.3999424488 -4583.40332411911 Force two-norm initial, final = 3651.6323 0.23851156 Force max component initial, final = 1051.9312 0.046253160 Final line search alpha, max atom move = 1.0000000 0.046253160 Iterations, force evaluations = 75 135 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1746 | 1.1746 | 1.1746 | 0.0 | 97.39 Neigh | 0.011023 | 0.011023 | 0.011023 | 0.0 | 0.91 Comm | 0.011149 | 0.011149 | 0.011149 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00928 | | | 0.77 Nlocal: 1072.00 ave 1072 max 1072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7507.00 ave 7507 max 7507 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: 176328.0 ave 176328 max 176328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176328 Ave neighs/atom = 164.48507 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.029 | 5.029 | 5.029 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -4583.4033 0 -4583.4033 4496.7838 12617.454 80 0 -4583.5814 0 -4583.5814 -57.472335 12652.063 Loop time of 0.0637677 on 1 procs for 5 steps with 1072 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4583.4033241191 -4583.579920262 -4583.58135575089 Force two-norm initial, final = 87.364550 0.85804508 Force max component initial, final = 85.638539 0.54870920 Final line search alpha, max atom move = 0.00019386879 0.00010637759 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.061125 | 0.061125 | 0.061125 | 0.0 | 95.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045936 | 0.00045936 | 0.00045936 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002183 | | | 3.42 Nlocal: 1072.00 ave 1072 max 1072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7963.00 ave 7963 max 7963 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: 177368.0 ave 177368 max 177368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177368 Ave neighs/atom = 165.45522 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 5.167 | 5.167 | 5.167 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4583.5814 0 -4583.5814 -57.472335 Loop time of 1.979e-06 on 1 procs for 0 steps with 1072 atoms 151.6% 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 | | 1.979e-06 | | |100.00 Nlocal: 1072.00 ave 1072 max 1072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7963.00 ave 7963 max 7963 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: 177176.0 ave 177176 max 177176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177176 Ave neighs/atom = 165.27612 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 = 7.5498917 ghost atom cutoff = 7.5498917 binsize = 3.7749458, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891651270771 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) = 5.167 | 5.167 | 5.167 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 -4583.5814 -4583.5814 33.145105 94.245805 4.050232 -57.472335 -57.472335 -43.875852 -59.104753 -69.436401 2.2632358 474.6076 Loop time of 2.545e-06 on 1 procs for 0 steps with 1072 atoms 196.5% 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 | | 2.545e-06 | | |100.00 Nlocal: 1072.00 ave 1072 max 1072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7963.00 ave 7963 max 7963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 88588.0 ave 88588 max 88588 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 177176.0 ave 177176 max 177176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177176 Ave neighs/atom = 165.27612 Neighbor list builds = 0 Dangerous builds = 0 1072 -4583.58135575089 eV 2.26323576584987 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01