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 = 3.6330168 3.6330168 3.6330168 Created orthogonal box = (0.0000000 -71.933695 0.0000000) to (44.047987 71.933695 8.8990373) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0939849 5.1378616 5.9326915 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -71.933695 0.0000000) to (44.047987 71.933695 8.8990373) create_atoms CPU = 0.009 seconds 2358 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0939849 5.1378616 5.9326915 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -71.933695 0.0000000) to (44.047987 71.933695 8.8990373) create_atoms CPU = 0.008 seconds 2358 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 12 38 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 36 atoms, new total = 4680 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 12 38 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 12.32 | 12.32 | 12.32 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19848.502 0 -19848.502 6344.1552 25 0 -19944.78 0 -19944.78 -1624.7512 Loop time of 2.76541 on 1 procs for 25 steps with 4680 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -19848.5021649168 -19944.764240446 -19944.7804464688 Force two-norm initial, final = 101.83378 0.52928252 Force max component initial, final = 15.434820 0.050147046 Final line search alpha, max atom move = 1.0000000 0.050147046 Iterations, force evaluations = 25 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7308 | 2.7308 | 2.7308 | 0.0 | 98.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.014753 | 0.014753 | 0.014753 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01985 | | | 0.72 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14454.0 ave 14454 max 14454 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: 815688.0 ave 815688 max 815688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 815688 Ave neighs/atom = 174.29231 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 12 38 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.94 | 11.94 | 11.94 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -19944.78 0 -19944.78 -1624.7512 56393.814 26 0 -19944.79 0 -19944.79 -914.16191 56367.184 Loop time of 0.185822 on 1 procs for 1 steps with 4680 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 = -19944.7804464687 -19944.7804464687 -19944.7899348523 Force two-norm initial, final = 46.230038 9.7719372 Force max component initial, final = 45.580591 9.6099692 Final line search alpha, max atom move = 2.1939163e-05 0.00021083468 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18178 | 0.18178 | 0.18178 | 0.0 | 97.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000863 | 0.000863 | 0.000863 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003177 | | | 1.71 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14503.0 ave 14503 max 14503 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: 758292.0 ave 758292 max 758292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 758292 Ave neighs/atom = 162.02821 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 12 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 11.45 | 11.45 | 11.45 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19944.79 0 -19944.79 -914.16191 Loop time of 6.325e-06 on 1 procs for 0 steps with 4680 atoms 205.5% 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 | | 6.325e-06 | | |100.00 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14503.0 ave 14503 max 14503 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: 766212.0 ave 766212 max 766212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 766212 Ave neighs/atom = 163.72051 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 12 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 11.45 | 11.45 | 11.45 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 -19944.79 -19944.79 44.04498 143.86739 8.8954424 -914.16191 -914.16191 273.13438 -2967.6222 -47.997899 2.3027892 1680.0804 Loop time of 6.305e-06 on 1 procs for 0 steps with 4680 atoms 333.1% 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 | | 6.305e-06 | | |100.00 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14503.0 ave 14503 max 14503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 383106.0 ave 383106 max 383106 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 766212.0 ave 766212 max 766212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 766212 Ave neighs/atom = 163.72051 Neighbor list builds = 0 Dangerous builds = 0 4680 -19944.7899348523 eV 2.30278921266788 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04