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 -49.550374 0.0000000) to (11.679135 49.550374 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3086978 6.0061059 4.9800000 Created 264 atoms using lattice units in orthogonal box = (0.0000000 -49.550374 0.0000000) to (11.679135 49.550374 4.9800000) create_atoms CPU = 0.001 seconds 264 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3086978 6.0061059 4.9800000 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -49.550374 0.0000000) to (11.679135 49.550374 4.9800000) create_atoms CPU = 0.001 seconds 266 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 31 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 528 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_008996216289_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.517 | 4.517 | 4.517 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2245.1592 0 -2245.1592 53171.893 56 0 -2340.5707 0 -2340.5707 9575.9986 Loop time of 2.87687 on 1 procs for 56 steps with 528 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 = -2245.15919102446 -2340.56882206176 -2340.57069664223 Force two-norm initial, final = 233.29614 0.14049639 Force max component initial, final = 71.453485 0.029141367 Final line search alpha, max atom move = 1.0000000 0.029141367 Iterations, force evaluations = 56 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8635 | 2.8635 | 2.8635 | 0.0 | 99.54 Neigh | 0.0039099 | 0.0039099 | 0.0039099 | 0.0 | 0.14 Comm | 0.0053111 | 0.0053111 | 0.0053111 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004131 | | | 0.14 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3917.00 ave 3917 max 3917 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: 46548.0 ave 46548 max 46548 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46548 Ave neighs/atom = 88.159091 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.517 | 4.517 | 4.517 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -2340.5707 0 -2340.5707 9575.9986 5763.9069 62 0 -2340.7244 0 -2340.7244 -73.987837 5793.507 Loop time of 0.226122 on 1 procs for 6 steps with 528 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 = -2340.57069664224 -2340.72432396942 -2340.72437070552 Force two-norm initial, final = 69.306383 0.62181477 Force max component initial, final = 62.872346 0.50813409 Final line search alpha, max atom move = 0.0011787849 0.00059898077 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22468 | 0.22468 | 0.22468 | 0.0 | 99.36 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028613 | 0.00028613 | 0.00028613 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001159 | | | 0.51 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3847.00 ave 3847 max 3847 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: 46260.0 ave 46260 max 46260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46260 Ave neighs/atom = 87.613636 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.655 | 4.655 | 4.655 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2340.7244 0 -2340.7244 -73.987837 Loop time of 1.616e-06 on 1 procs for 0 steps with 528 atoms 185.6% 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 | | 1.616e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3819.00 ave 3819 max 3819 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: 46148.0 ave 46148 max 46148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46148 Ave neighs/atom = 87.401515 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 4 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.655 | 4.655 | 4.655 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 -2340.7244 -2340.7244 11.684151 99.576824 4.9795042 -73.987837 -73.987837 -140.58327 -76.261027 -5.1192144 2.3218526 251.3485 Loop time of 1.606e-06 on 1 procs for 0 steps with 528 atoms 186.8% 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 | | 1.606e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3819.00 ave 3819 max 3819 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23074.0 ave 23074 max 23074 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 46148.0 ave 46148 max 46148 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46148 Ave neighs/atom = 87.401515 Neighbor list builds = 0 Dangerous builds = 0 528 -2340.72437070552 eV 2.32185255373191 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03