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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -43.560732 0.0000000) to (14.519070 43.560732 3.5213917) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2703147 4.2703147 3.5213917 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -43.560732 0.0000000) to (14.519070 43.560732 3.5213917) create_atoms CPU = 0.001 seconds 206 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2703147 4.2703147 3.5213917 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -43.560732 0.0000000) to (14.519070 43.560732 3.5213917) create_atoms CPU = 0.000 seconds 206 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 5 28 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 404 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.457 | 4.457 | 4.457 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1781.213 0 -1781.213 4156.7419 40 0 -1789.185 0 -1789.185 -5841.5591 Loop time of 1.10348 on 1 procs for 40 steps with 404 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1781.21299185456 -1789.18371213605 -1789.1850433018 Force two-norm initial, final = 22.063884 0.11360171 Force max component initial, final = 6.9933427 0.017227881 Final line search alpha, max atom move = 0.85146900 0.014669007 Iterations, force evaluations = 40 75 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0988 | 1.0988 | 1.0988 | 0.0 | 99.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0025653 | 0.0025653 | 0.0025653 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002161 | | | 0.20 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3440.00 ave 3440 max 3440 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: 34624.0 ave 34624 max 34624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34624 Ave neighs/atom = 85.702970 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.457 | 4.457 | 4.457 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -1789.185 0 -1789.185 -5841.5591 4454.2881 43 0 -1789.2134 0 -1789.2134 -308.98741 4440.8524 Loop time of 0.0914697 on 1 procs for 3 steps with 404 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 = -1789.1850433018 -1789.21227552046 -1789.21336602835 Force two-norm initial, final = 24.402974 0.14322245 Force max component initial, final = 19.752985 0.026045417 Final line search alpha, max atom move = 0.00045509937 1.1853253e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0907 | 0.0907 | 0.0907 | 0.0 | 99.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015227 | 0.00015227 | 0.00015227 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006179 | | | 0.68 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3471.00 ave 3471 max 3471 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: 34532.0 ave 34532 max 34532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34532 Ave neighs/atom = 85.475248 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.595 | 4.595 | 4.595 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1789.2134 0 -1789.2134 -308.98741 Loop time of 1.832e-06 on 1 procs for 0 steps with 404 atoms 163.8% 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 | | 1.832e-06 | | |100.00 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3471.00 ave 3471 max 3471 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: 34532.0 ave 34532 max 34532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34532 Ave neighs/atom = 85.475248 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.595 | 4.595 | 4.595 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 -1789.2134 -1789.2134 14.510816 87.121464 3.512767 -308.98741 -308.98741 -2.5404296 -926.52134 2.099547 2.2951517 181.34676 Loop time of 2.201e-06 on 1 procs for 0 steps with 404 atoms 181.7% 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 | | 2.201e-06 | | |100.00 Nlocal: 404.000 ave 404 max 404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3471.00 ave 3471 max 3471 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 17266.0 ave 17266 max 17266 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 34532.0 ave 34532 max 34532 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 34532 Ave neighs/atom = 85.475248 Neighbor list builds = 0 Dangerous builds = 0 404 -1789.21336602835 eV 2.29515170749592 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01