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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -55.726934 0.0000000) to (27.861683 55.726934 3.5673230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0242380 5.0242380 3.5673230 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -55.726934 0.0000000) to (27.861683 55.726934 3.5673230) create_atoms CPU = 0.003 seconds 490 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0242380 5.0242380 3.5673230 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -55.726934 0.0000000) to (27.861683 55.726934 3.5673230) create_atoms CPU = 0.002 seconds 490 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 40 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 964 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_058735400462_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.573 | 4.573 | 4.573 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4034.915 0 -4034.915 -2289.8713 119 0 -4070.0634 0 -4070.0634 18818.003 Loop time of 15.437 on 1 procs for 119 steps with 964 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4034.91495512272 -4070.06033197514 -4070.06344129289 Force two-norm initial, final = 33.745192 0.16946848 Force max component initial, final = 9.9412661 0.022673469 Final line search alpha, max atom move = 1.0000000 0.022673469 Iterations, force evaluations = 119 223 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 15.357 | 15.357 | 15.357 | 0.0 | 99.48 Neigh | 0.022718 | 0.022718 | 0.022718 | 0.0 | 0.15 Comm | 0.028555 | 0.028555 | 0.028555 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02894 | | | 0.19 Nlocal: 964.000 ave 964 max 964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4992.00 ave 4992 max 4992 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: 57200.0 ave 57200 max 57200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57200 Ave neighs/atom = 59.336100 Neighbor list builds = 2 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 119 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes Step Temp E_pair E_mol TotEng Press Volume 119 0 -4070.0634 0 -4070.0634 18818.003 11077.581 137 0 -4072.8499 0 -4072.8499 5471.8594 11201.405 Loop time of 1.23817 on 1 procs for 18 steps with 964 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 = -4070.06344129289 -4072.84701607831 -4072.8498513151 Force two-norm initial, final = 309.03610 3.1576721 Force max component initial, final = 290.08163 0.93023360 Final line search alpha, max atom move = 0.00013580732 0.00012633253 Iterations, force evaluations = 18 19 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2275 | 1.2275 | 1.2275 | 0.0 | 99.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.002123 | 0.002123 | 0.002123 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008578 | | | 0.69 Nlocal: 964.000 ave 964 max 964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4996.00 ave 4996 max 4996 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: 57756.0 ave 57756 max 57756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57756 Ave neighs/atom = 59.912863 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.713 | 4.713 | 4.713 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4072.8499 0 -4072.8499 5471.8594 Loop time of 6.656e-06 on 1 procs for 0 steps with 964 atoms 180.3% 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 | | 6.656e-06 | | |100.00 Nlocal: 964.000 ave 964 max 964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4984.00 ave 4984 max 4984 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: 56268.0 ave 56268 max 56268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56268 Ave neighs/atom = 58.369295 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.713 | 4.713 | 4.713 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 -4072.8499 -4072.8499 28.35226 111.45387 3.5447832 5471.8594 5471.8594 -135.39736 16487.924 63.051909 2.3137801 171.6872 Loop time of 6.595e-06 on 1 procs for 0 steps with 964 atoms 288.1% 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 | | 6.595e-06 | | |100.00 Nlocal: 964.000 ave 964 max 964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4984.00 ave 4984 max 4984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28134.0 ave 28134 max 28134 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 56268.0 ave 56268 max 56268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56268 Ave neighs/atom = 58.369295 Neighbor list builds = 0 Dangerous builds = 0 964 -4072.8498513151 eV 2.31378010623387 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17