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 = 2.8548760 2.8548760 2.8548760 Created orthogonal box = (0.0000000 -42.248307 0.0000000) to (34.495598 42.248307 6.9929895) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2528819 4.0512075 4.6619930 Created 875 atoms using lattice units in orthogonal box = (0.0000000 -42.248307 0.0000000) to (34.495598 42.248307 6.9929895) create_atoms CPU = 0.001 seconds 875 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2528819 4.0512075 4.6619930 Created 877 atoms using lattice units in orthogonal box = (0.0000000 -42.248307 0.0000000) to (34.495598 42.248307 6.9929895) create_atoms CPU = 0.001 seconds 877 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 24 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1744 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.560 | 5.560 | 5.560 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5123.4898 0 -5123.4898 216366.58 115 0 -6964.1055 0 -6964.1055 1549.6396 Loop time of 2.35481 on 1 procs for 115 steps with 1744 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 = -5123.48982071901 -6964.09941935323 -6964.1054781043 Force two-norm initial, final = 3434.3742 0.26078413 Force max component initial, final = 752.37691 0.039762891 Final line search alpha, max atom move = 1.0000000 0.039762891 Iterations, force evaluations = 115 204 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2844 | 2.2844 | 2.2844 | 0.0 | 97.01 Neigh | 0.043506 | 0.043506 | 0.043506 | 0.0 | 1.85 Comm | 0.011915 | 0.011915 | 0.011915 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01497 | | | 0.64 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6953.00 ave 6953 max 6953 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: 237844.0 ave 237844 max 237844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237844 Ave neighs/atom = 136.37844 Neighbor list builds = 3 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 115 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.560 | 5.560 | 5.560 Mbytes Step Temp E_pair E_mol TotEng Press Volume 115 0 -6964.1055 0 -6964.1055 1549.6396 20382.894 120 0 -6964.31 0 -6964.31 61.694331 20400.972 Loop time of 0.0899122 on 1 procs for 5 steps with 1744 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 = -6964.10547810429 -6964.3098567051 -6964.30998723389 Force two-norm initial, final = 98.780848 1.5038716 Force max component initial, final = 93.095316 1.1742859 Final line search alpha, max atom move = 0.00040701947 0.00047795721 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.087418 | 0.087418 | 0.087418 | 0.0 | 97.23 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00037899 | 0.00037899 | 0.00037899 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002115 | | | 2.35 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6980.00 ave 6980 max 6980 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: 237388.0 ave 237388 max 237388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237388 Ave neighs/atom = 136.11697 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.698 | 5.698 | 5.698 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6964.31 0 -6964.31 61.694331 Loop time of 1.482e-06 on 1 procs for 0 steps with 1744 atoms 202.4% 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 | | 1.482e-06 | | |100.00 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6980.00 ave 6980 max 6980 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: 237250.0 ave 237250 max 237250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237250 Ave neighs/atom = 136.03784 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.698 | 5.698 | 5.698 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 -6964.31 -6964.31 34.45868 84.813595 6.9805034 61.694331 61.694331 36.414283 56.611629 92.057082 2.2438313 1131.2707 Loop time of 1.609e-06 on 1 procs for 0 steps with 1744 atoms 186.5% 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 | | 1.609e-06 | | |100.00 Nlocal: 1744.00 ave 1744 max 1744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6980.00 ave 6980 max 6980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 118625.0 ave 118625 max 118625 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 237250.0 ave 237250 max 237250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237250 Ave neighs/atom = 136.03784 Neighbor list builds = 0 Dangerous builds = 0 1744 -6717.6706751292 eV 2.2438312972868 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02