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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -58.567254 0.0000000) to (11.954255 58.567254 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4337523 5.3239682 5.8858683 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.567254 0.0000000) to (11.954255 58.567254 8.8288024) create_atoms CPU = 0.001 seconds 530 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4337523 5.3239682 5.8858683 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.567254 0.0000000) to (11.954255 58.567254 8.8288024) create_atoms CPU = 0.001 seconds 530 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 4 39 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 1046 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 4 39 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.591 | 4.591 | 4.591 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4410.9786 0 -4410.9786 -2187.0806 43 0 -4429.2662 0 -4429.2662 -11626.912 Loop time of 2.5836 on 1 procs for 43 steps with 1046 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 = -4410.97862262676 -4429.26235583495 -4429.26624038435 Force two-norm initial, final = 21.162386 0.18477908 Force max component initial, final = 7.7062919 0.043948897 Final line search alpha, max atom move = 1.0000000 0.043948897 Iterations, force evaluations = 43 76 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5697 | 2.5697 | 2.5697 | 0.0 | 99.46 Neigh | 0.0069523 | 0.0069523 | 0.0069523 | 0.0 | 0.27 Comm | 0.0031367 | 0.0031367 | 0.0031367 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00376 | | | 0.15 Nlocal: 1046.00 ave 1046 max 1046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4532.00 ave 4532 max 4532 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: 81288.0 ave 81288 max 81288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81288 Ave neighs/atom = 77.713193 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 4 39 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.591 | 4.591 | 4.591 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -4429.2662 0 -4429.2662 -11626.912 12362.582 48 0 -4429.5098 0 -4429.5098 -2298.25 12289.966 Loop time of 0.274284 on 1 procs for 5 steps with 1046 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4429.26624038434 -4429.50732950581 -4429.50977270362 Force two-norm initial, final = 112.45963 0.21962154 Force max component initial, final = 86.965842 0.046308726 Final line search alpha, max atom move = 0.00013858653 6.4177656e-06 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2724 | 0.2724 | 0.2724 | 0.0 | 99.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030526 | 0.00030526 | 0.00030526 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00158 | | | 0.58 Nlocal: 1046.00 ave 1046 max 1046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4528.00 ave 4528 max 4528 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: 81292.0 ave 81292 max 81292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81292 Ave neighs/atom = 77.717017 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 4 39 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.729 | 4.729 | 4.729 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4429.5098 0 -4429.5098 -2298.25 Loop time of 1.594e-06 on 1 procs for 0 steps with 1046 atoms 125.5% 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 | | 1.594e-06 | | |100.00 Nlocal: 1046.00 ave 1046 max 1046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4528.00 ave 4528 max 4528 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: 81348.0 ave 81348 max 81348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81348 Ave neighs/atom = 77.770554 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 4 39 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.729 | 4.729 | 4.729 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 -4429.5098 -4429.5098 11.904036 117.13451 8.8139702 -2298.25 -2298.25 1.3624154 -6895.4259 -0.68661434 2.30348 516.97257 Loop time of 1.775e-06 on 1 procs for 0 steps with 1046 atoms 169.0% 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 | | 1.775e-06 | | |100.00 Nlocal: 1046.00 ave 1046 max 1046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4528.00 ave 4528 max 4528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40674.0 ave 40674 max 40674 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 81348.0 ave 81348 max 81348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81348 Ave neighs/atom = 77.770554 Neighbor list builds = 0 Dangerous builds = 0 1046 -4429.50977270362 eV 2.30347996070534 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03