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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -58.673406 0.0000000) to (20.744182 58.673406 5.1068645) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6575041 4.4449550 5.1068645 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -58.673406 0.0000000) to (20.744182 58.673406 5.1068645) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6575041 4.4449550 5.1068645 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -58.673406 0.0000000) to (20.744182 58.673406 5.1068645) create_atoms CPU = 0.001 seconds 530 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 = 7 37 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 6 atoms, new total = 1052 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 = 7 37 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) = 4.637 | 4.637 | 4.637 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4290.185 0 -4290.185 28706.592 249 0 -4464.2625 0 -4464.2625 -1253.2963 Loop time of 35.0602 on 1 procs for 249 steps with 1052 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 = -4290.18502990065 -4464.25818890983 -4464.26250768896 Force two-norm initial, final = 326.88900 0.21060113 Force max component initial, final = 110.48067 0.051488188 Final line search alpha, max atom move = 1.0000000 0.051488188 Iterations, force evaluations = 249 481 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 34.938 | 34.938 | 34.938 | 0.0 | 99.65 Neigh | 0.046203 | 0.046203 | 0.046203 | 0.0 | 0.13 Comm | 0.042165 | 0.042165 | 0.042165 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03394 | | | 0.10 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5649.00 ave 5649 max 5649 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: 101036.0 ave 101036 max 101036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101036 Ave neighs/atom = 96.041825 Neighbor list builds = 6 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 = 7 37 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 : 249 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.018 | 5.018 | 5.018 Mbytes Step Temp E_pair E_mol TotEng Press Volume 249 0 -4464.2625 0 -4464.2625 -1253.2963 12431.454 274 0 -4468.6221 0 -4468.6221 -4.0056713 12415.175 Loop time of 2.20731 on 1 procs for 25 steps with 1052 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 = -4464.26250768898 -4468.61854983247 -4468.62205845791 Force two-norm initial, final = 280.27878 2.2952469 Force max component initial, final = 210.72470 0.54021902 Final line search alpha, max atom move = 0.00016539307 8.9348482e-05 Iterations, force evaluations = 25 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1825 | 2.1825 | 2.1825 | 0.0 | 98.88 Neigh | 0.014857 | 0.014857 | 0.014857 | 0.0 | 0.67 Comm | 0.0018107 | 0.0018107 | 0.0018107 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008146 | | | 0.37 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5646.00 ave 5646 max 5646 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: 101676.0 ave 101676 max 101676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101676 Ave neighs/atom = 96.650190 Neighbor list builds = 2 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 = 7 37 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) = 5.157 | 5.157 | 5.157 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4468.6221 0 -4468.6221 -4.0056713 Loop time of 2.194e-06 on 1 procs for 0 steps with 1052 atoms 182.3% 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 | | 2.194e-06 | | |100.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5674.00 ave 5674 max 5674 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: 101956.0 ave 101956 max 101956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101956 Ave neighs/atom = 96.916350 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 = 7 37 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) = 5.157 | 5.157 | 5.157 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 -4468.6221 -4468.6221 20.530892 120.24816 5.0288255 -4.0056713 -4.0056713 39.430984 -71.438864 19.990866 2.3744603 2811.8796 Loop time of 2.446e-06 on 1 procs for 0 steps with 1052 atoms 245.3% 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 | | 2.446e-06 | | |100.00 Nlocal: 1052.00 ave 1052 max 1052 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5674.00 ave 5674 max 5674 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50978.0 ave 50978 max 50978 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 101956.0 ave 101956 max 101956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101956 Ave neighs/atom = 96.916350 Neighbor list builds = 0 Dangerous builds = 0 1052 -4468.62205845791 eV 2.37446025757284 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:37