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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -53.754823 0.0000000) to (38.010400 53.754823 5.0346005) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0016421 5.1868689 5.0346005 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -53.754823 0.0000000) to (38.010400 53.754823 5.0346005) create_atoms CPU = 0.004 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0016421 5.1868689 5.0346005 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -53.754823 0.0000000) to (38.010400 53.754823 5.0346005) create_atoms CPU = 0.004 seconds 916 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 = 10 28 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1824 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 = 10 28 2 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) = 5.975 | 5.975 | 5.975 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7516.1007 0 -7516.1007 58643.681 173 0 -8006.9481 0 -8006.9481 9750.5524 Loop time of 6.55109 on 1 procs for 173 steps with 1824 atoms 97.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7516.10074841974 -8006.94104550837 -8006.94812657816 Force two-norm initial, final = 694.62664 0.40006990 Force max component initial, final = 113.21110 0.082277547 Final line search alpha, max atom move = 1.0000000 0.082277547 Iterations, force evaluations = 173 339 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.4138 | 6.4138 | 6.4138 | 0.0 | 97.90 Neigh | 0.04078 | 0.04078 | 0.04078 | 0.0 | 0.62 Comm | 0.045786 | 0.045786 | 0.045786 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05077 | | | 0.77 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9991.00 ave 9991 max 9991 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: 319592.0 ave 319592 max 319592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 319592 Ave neighs/atom = 175.21491 Neighbor list builds = 2 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 = 10 28 2 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 : 173 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.986 | 5.986 | 5.986 Mbytes Step Temp E_pair E_mol TotEng Press Volume 173 0 -8006.9481 0 -8006.9481 9750.5524 20573.817 183 0 -8007.8943 0 -8007.8943 -130.04907 20665.733 Loop time of 0.238854 on 1 procs for 10 steps with 1824 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 = -8006.94812657816 -8007.89363070001 -8007.89429169158 Force two-norm initial, final = 265.68072 3.1517732 Force max component initial, final = 249.15180 1.8809384 Final line search alpha, max atom move = 0.00027072108 0.00050920968 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21085 | 0.21085 | 0.21085 | 0.0 | 88.28 Neigh | 0.020733 | 0.020733 | 0.020733 | 0.0 | 8.68 Comm | 0.0013316 | 0.0013316 | 0.0013316 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005938 | | | 2.49 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10646.0 ave 10646 max 10646 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: 318872.0 ave 318872 max 318872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 318872 Ave neighs/atom = 174.82018 Neighbor list builds = 1 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 = 10 28 2 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) = 6.124 | 6.124 | 6.124 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8007.8943 0 -8007.8943 -130.04907 Loop time of 2.483e-06 on 1 procs for 0 steps with 1824 atoms 724.9% 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 | | 2.483e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10646.0 ave 10646 max 10646 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: 318936.0 ave 318936 max 318936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 318936 Ave neighs/atom = 174.85526 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 = 10 28 2 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) = 6.124 | 6.124 | 6.124 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 -8007.8943 -8007.8943 37.960943 108.50713 5.0171322 -130.04907 -130.04907 -121.02139 -123.80607 -145.31976 2.3835437 716.1097 Loop time of 2.543e-06 on 1 procs for 0 steps with 1824 atoms 275.3% 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 | | 2.543e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10646.0 ave 10646 max 10646 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 159468.0 ave 159468 max 159468 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 318936.0 ave 318936 max 318936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 318936 Ave neighs/atom = 174.85526 Neighbor list builds = 0 Dangerous builds = 0 1824 -8007.89429169158 eV 2.38354373157219 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07