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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -63.827493 0.0000000) to (36.848734 63.827493 6.2584463) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6690360 5.7277841 6.2584463 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -63.827493 0.0000000) to (36.848734 63.827493 6.2584463) create_atoms CPU = 0.008 seconds 1249 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6690360 5.7277841 6.2584463 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -63.827493 0.0000000) to (36.848734 63.827493 6.2584463) create_atoms CPU = 0.007 seconds 1249 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 37 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 17 atoms, new total = 2481 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_813575892799_001#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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.103 | 6.103 | 6.103 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8701.7753 0 -8701.7753 6074.8162 44 0 -8752.7459 0 -8752.7459 -2556.0263 Loop time of 15.7847 on 1 procs for 44 steps with 2481 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 = -8701.7752930627 -8752.73806209112 -8752.74592818382 Force two-norm initial, final = 71.135030 0.30162079 Force max component initial, final = 10.931425 0.10592000 Final line search alpha, max atom move = 1.0000000 0.10592000 Iterations, force evaluations = 44 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.704 | 15.704 | 15.704 | 0.0 | 99.49 Neigh | 0.041437 | 0.041437 | 0.041437 | 0.0 | 0.26 Comm | 0.017157 | 0.017157 | 0.017157 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0217 | | | 0.14 Nlocal: 2481.00 ave 2481 max 2481 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8865.00 ave 8865 max 8865 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: 328870.0 ave 328870 max 328870 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 328870 Ave neighs/atom = 132.55542 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.103 | 6.103 | 6.103 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -8752.7459 0 -8752.7459 -2556.0263 29439.26 46 0 -8752.7851 0 -8752.7851 -728.54337 29400.935 Loop time of 0.721214 on 1 procs for 2 steps with 2481 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 = -8752.74592818381 -8752.7820770683 -8752.78508293546 Force two-norm initial, final = 63.434658 0.51424028 Force max component initial, final = 59.787504 0.30397458 Final line search alpha, max atom move = 0.00010119368 3.0760307e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.71758 | 0.71758 | 0.71758 | 0.0 | 99.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00074004 | 0.00074004 | 0.00074004 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002893 | | | 0.40 Nlocal: 2481.00 ave 2481 max 2481 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8865.00 ave 8865 max 8865 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: 329162.0 ave 329162 max 329162 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 329162 Ave neighs/atom = 132.67312 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.241 | 6.241 | 6.241 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8752.7851 0 -8752.7851 -728.54337 Loop time of 6.334e-06 on 1 procs for 0 steps with 2481 atoms 173.7% 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 | | 6.334e-06 | | |100.00 Nlocal: 2481.00 ave 2481 max 2481 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8865.00 ave 8865 max 8865 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: 329186.0 ave 329186 max 329186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 329186 Ave neighs/atom = 132.68279 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.241 | 6.241 | 6.241 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 -8752.7851 -8752.7851 36.848713 127.65499 6.2503025 -728.54337 -728.54337 -16.564802 -2153.7483 -15.31698 2.2679897 1038.7289 Loop time of 6.485e-06 on 1 procs for 0 steps with 2481 atoms 308.4% 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 | | 6.485e-06 | | |100.00 Nlocal: 2481.00 ave 2481 max 2481 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8865.00 ave 8865 max 8865 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 164593.0 ave 164593 max 164593 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 329186.0 ave 329186 max 329186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 329186 Ave neighs/atom = 132.68279 Neighbor list builds = 0 Dangerous builds = 0 2481 -8752.78508293546 eV 2.26798971330277 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17