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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -58.266577 0.0000000) to (29.131482 58.266577 3.6133156) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9299431 4.9299431 3.6133156 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.266577 0.0000000) to (29.131482 58.266577 3.6133156) create_atoms CPU = 0.003 seconds 522 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9299431 4.9299431 3.6133156 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.266577 0.0000000) to (29.131482 58.266577 3.6133156) create_atoms CPU = 0.002 seconds 522 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 35 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1032 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_694335101831_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.013 | 5.013 | 5.013 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3617.8045 0 -3617.8045 5786.9243 72 0 -3641.4611 0 -3641.4611 -4037.9909 Loop time of 12.2903 on 1 procs for 72 steps with 1032 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 = -3617.80450572286 -3641.45815492627 -3641.46112813934 Force two-norm initial, final = 33.071884 0.15732053 Force max component initial, final = 9.0083928 0.036418735 Final line search alpha, max atom move = 1.0000000 0.036418735 Iterations, force evaluations = 72 133 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.228 | 12.228 | 12.228 | 0.0 | 99.49 Neigh | 0.018967 | 0.018967 | 0.018967 | 0.0 | 0.15 Comm | 0.023699 | 0.023699 | 0.023699 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0194 | | | 0.16 Nlocal: 1032.00 ave 1032 max 1032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7373.00 ave 7373 max 7373 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: 131496.0 ave 131496 max 131496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131496 Ave neighs/atom = 127.41860 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.013 | 5.013 | 5.013 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -3641.4611 0 -3641.4611 -4037.9909 12266.424 75 0 -3641.516 0 -3641.516 187.71852 12229.342 Loop time of 0.503212 on 1 procs for 3 steps with 1032 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 = -3641.46112813934 -3641.51535390619 -3641.51596255124 Force two-norm initial, final = 51.233231 0.20839357 Force max component initial, final = 36.547116 0.053410795 Final line search alpha, max atom move = 0.00051955049 2.7749605e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4994 | 0.4994 | 0.4994 | 0.0 | 99.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00089379 | 0.00089379 | 0.00089379 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002918 | | | 0.58 Nlocal: 1032.00 ave 1032 max 1032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7413.00 ave 7413 max 7413 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: 133768.0 ave 133768 max 133768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133768 Ave neighs/atom = 129.62016 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.151 | 5.151 | 5.151 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3641.516 0 -3641.516 187.71852 Loop time of 6.414e-06 on 1 procs for 0 steps with 1032 atoms 202.7% 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 | | 6.414e-06 | | |100.00 Nlocal: 1032.00 ave 1032 max 1032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7413.00 ave 7413 max 7413 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: 134168.0 ave 134168 max 134168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134168 Ave neighs/atom = 130.00775 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.151 | 5.151 | 5.151 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 -3641.516 -3641.516 29.098509 116.53315 3.6064744 187.71852 187.71852 -5.5340982 569.1418 -0.45213458 2.3095726 471.08326 Loop time of 7.337e-06 on 1 procs for 0 steps with 1032 atoms 259.0% 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 | | 7.337e-06 | | |100.00 Nlocal: 1032.00 ave 1032 max 1032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7413.00 ave 7413 max 7413 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 67084.0 ave 67084 max 67084 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 134168.0 ave 134168 max 134168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134168 Ave neighs/atom = 130.00775 Neighbor list builds = 0 Dangerous builds = 0 1032 -3641.51596255124 eV 2.30957261915323 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13