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 = 4.0452598 4.0452598 4.0452598 Created orthogonal box = (0.0000000 -48.879060 0.0000000) to (59.864378 48.879060 9.9088223) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7404198 6.0261855 6.6058816 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -48.879060 0.0000000) to (59.864378 48.879060 9.9088223) create_atoms CPU = 0.007 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7404198 6.0261855 6.6058816 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -48.879060 0.0000000) to (59.864378 48.879060 9.9088223) create_atoms CPU = 0.007 seconds 1756 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 15 24 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3506 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_106969701023_005#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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.958 | 6.958 | 6.958 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11698.713 0 -11698.713 15301.447 45 0 -11925.794 0 -11925.794 5397.3916 Loop time of 4.91538 on 1 procs for 45 steps with 3506 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 = -11698.7125722984 -11925.7873682954 -11925.7943039585 Force two-norm initial, final = 165.26524 0.17706672 Force max component initial, final = 29.865276 0.019120709 Final line search alpha, max atom move = 1.0000000 0.019120709 Iterations, force evaluations = 45 81 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.8683 | 4.8683 | 4.8683 | 0.0 | 99.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.019762 | 0.019762 | 0.019762 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0273 | | | 0.56 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10562.0 ave 10562 max 10562 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: 495224.0 ave 495224 max 495224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 495224 Ave neighs/atom = 141.25043 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 15 24 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 45 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.962 | 6.962 | 6.962 Mbytes Step Temp E_pair E_mol TotEng Press Volume 45 0 -11925.794 0 -11925.794 5397.3916 57988.698 55 0 -11927.2 0 -11927.2 36.485996 58364.537 Loop time of 0.735352 on 1 procs for 10 steps with 3506 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11925.7943039585 -11927.200051352 -11927.2002187545 Force two-norm initial, final = 388.21332 2.4921970 Force max component initial, final = 350.12888 2.0375086 Final line search alpha, max atom move = 0.00043036368 0.00087686972 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.71872 | 0.71872 | 0.71872 | 0.0 | 97.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0028701 | 0.0028701 | 0.0028701 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01376 | | | 1.87 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11000.0 ave 11000 max 11000 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: 502758.0 ave 502758 max 502758 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 502758 Ave neighs/atom = 143.39932 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.100 | 7.100 | 7.100 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11927.2 0 -11927.2 36.485996 Loop time of 6.765e-06 on 1 procs for 0 steps with 3506 atoms 206.9% 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 | | 6.765e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10979.0 ave 10979 max 10979 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: 498746.0 ave 498746 max 498746 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 498746 Ave neighs/atom = 142.25499 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 15 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 7.100 | 7.100 | 7.100 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 -11927.2 -11927.2 59.807423 98.643247 9.8929679 36.485996 36.485996 22.538332 56.438477 30.481178 2.4506913 1900.7086 Loop time of 6.856e-06 on 1 procs for 0 steps with 3506 atoms 277.1% 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 | | 6.856e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10979.0 ave 10979 max 10979 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 249373.0 ave 249373 max 249373 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 498746.0 ave 498746 max 498746 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 498746 Ave neighs/atom = 142.25499 Neighbor list builds = 0 Dangerous builds = 0 3506 -11927.2002187545 eV 2.45069129318281 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06