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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -33.395562 0.0000000) to (11.807114 33.395562 4.0498067) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8617529 4.9111120 4.0498067 Created 136 atoms using lattice units in orthogonal box = (0.0000000 -33.395562 0.0000000) to (11.807114 33.395562 4.0498067) create_atoms CPU = 0.001 seconds 136 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8617529 4.9111120 4.0498067 Created 138 atoms using lattice units in orthogonal box = (0.0000000 -33.395562 0.0000000) to (11.807114 33.395562 4.0498067) create_atoms CPU = 0.000 seconds 138 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 21 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 = 272 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_179420363944_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 21 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) = 4.424 | 4.424 | 4.424 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -978.78741 0 -978.78741 115884.13 74 0 -1160.1602 0 -1160.1602 9462.6504 Loop time of 3.05823 on 1 procs for 74 steps with 272 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 = -978.787408640625 -1160.15924628189 -1160.16023894363 Force two-norm initial, final = 429.33963 0.10061888 Force max component initial, final = 143.40195 0.022870344 Final line search alpha, max atom move = 1.0000000 0.022870344 Iterations, force evaluations = 74 134 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0508 | 3.0508 | 3.0508 | 0.0 | 99.76 Neigh | 0.0019457 | 0.0019457 | 0.0019457 | 0.0 | 0.06 Comm | 0.0032189 | 0.0032189 | 0.0032189 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002311 | | | 0.08 Nlocal: 272.000 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2818.00 ave 2818 max 2818 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: 29372.0 ave 29372 max 29372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29372 Ave neighs/atom = 107.98529 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 21 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 : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.424 | 4.424 | 4.424 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -1160.1602 0 -1160.1602 9462.6504 3193.7198 81 0 -1160.2724 0 -1160.2724 -58.133307 3211.2343 Loop time of 0.228773 on 1 procs for 7 steps with 272 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 = -1160.16023894363 -1160.27232927254 -1160.27235871967 Force two-norm initial, final = 40.331746 0.30541226 Force max component initial, final = 37.486271 0.18348703 Final line search alpha, max atom move = 0.0016771065 0.00030772730 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22774 | 0.22774 | 0.22774 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00020908 | 0.00020908 | 0.00020908 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008197 | | | 0.36 Nlocal: 272.000 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2793.00 ave 2793 max 2793 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: 29800.0 ave 29800 max 29800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29800 Ave neighs/atom = 109.55882 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 21 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) = 4.562 | 4.562 | 4.562 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1160.2724 0 -1160.2724 -58.133307 Loop time of 1.488e-06 on 1 procs for 0 steps with 272 atoms 134.4% 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 | | 1.488e-06 | | |100.00 Nlocal: 272.000 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2793.00 ave 2793 max 2793 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: 29740.0 ave 29740 max 29740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29740 Ave neighs/atom = 109.33824 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 21 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) = 4.562 | 4.562 | 4.562 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 -1160.2724 -1160.2724 11.819706 67.182291 4.0439942 -58.133307 -58.133307 7.8221867 -92.083072 -90.139037 2.2833416 179.07736 Loop time of 1.458e-06 on 1 procs for 0 steps with 272 atoms 137.2% 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 | | 1.458e-06 | | |100.00 Nlocal: 272.000 ave 272 max 272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2793.00 ave 2793 max 2793 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14870.0 ave 14870 max 14870 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 29740.0 ave 29740 max 29740 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 29740 Ave neighs/atom = 109.33824 Neighbor list builds = 0 Dangerous builds = 0 272 -1160.27235871967 eV 2.28334161132758 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03