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 = 3.6580991 3.6580991 3.6580991 Created orthogonal box = (0.0000000 -66.250993 0.0000000) to (23.423263 66.250993 5.1733334) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2842902 5.6555726 5.1733334 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -66.250993 0.0000000) to (23.423263 66.250993 5.1733334) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2842902 5.6555726 5.1733334 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -66.250993 0.0000000) to (23.423263 66.250993 5.1733334) create_atoms CPU = 0.001 seconds 658 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1308 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_634187028437_000#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.104 | 5.104 | 5.104 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4907.6263 0 -4907.6263 33767.039 302 0 -5142.7032 0 -5142.7032 -67249.331 Loop time of 5.51602 on 1 procs for 302 steps with 1308 atoms 98.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4907.62626282779 -5142.69835616631 -5142.70324535328 Force two-norm initial, final = 499.11814 0.21047370 Force max component initial, final = 170.11806 0.021958810 Final line search alpha, max atom move = 1.0000000 0.021958810 Iterations, force evaluations = 302 563 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.3401 | 5.3401 | 5.3401 | 0.0 | 96.81 Neigh | 0.091356 | 0.091356 | 0.091356 | 0.0 | 1.66 Comm | 0.046427 | 0.046427 | 0.046427 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03812 | | | 0.69 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7721.00 ave 7721 max 7721 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: 178304.0 ave 178304 max 178304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178304 Ave neighs/atom = 136.31804 Neighbor list builds = 8 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 302 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.106 | 5.106 | 5.106 Mbytes Step Temp E_pair E_mol TotEng Press Volume 302 0 -5142.7032 0 -5142.7032 -67249.331 16056.107 338 0 -5165.137 0 -5165.137 -2966.1028 15303.169 Loop time of 0.402613 on 1 procs for 36 steps with 1308 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 = -5142.70324535329 -5165.13333200855 -5165.13702379775 Force two-norm initial, final = 1220.3369 50.201446 Force max component initial, final = 854.33222 30.823113 Final line search alpha, max atom move = 2.3444562e-05 0.00072263438 Iterations, force evaluations = 36 39 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38627 | 0.38627 | 0.38627 | 0.0 | 95.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0025406 | 0.0025406 | 0.0025406 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0138 | | | 3.43 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7726.00 ave 7726 max 7726 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: 178260.0 ave 178260 max 178260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178260 Ave neighs/atom = 136.28440 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.250 | 5.250 | 5.250 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5165.137 0 -5165.137 -2966.1028 Loop time of 1.989e-06 on 1 procs for 0 steps with 1308 atoms 150.8% 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 | | 1.989e-06 | | |100.00 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7977.00 ave 7977 max 7977 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: 186444.0 ave 186444 max 186444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186444 Ave neighs/atom = 142.54128 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.250 | 5.250 | 5.250 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 -5165.137 -5165.137 22.90618 133.12356 5.0184984 -2966.1028 -2966.1028 -3155.8093 -2739.4146 -3003.0846 2.3081654 3516.1673 Loop time of 2.653e-06 on 1 procs for 0 steps with 1308 atoms 263.9% 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 | | 2.653e-06 | | |100.00 Nlocal: 1308.00 ave 1308 max 1308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7977.00 ave 7977 max 7977 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 93222.0 ave 93222 max 93222 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 186444.0 ave 186444 max 186444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 186444 Ave neighs/atom = 142.54128 Neighbor list builds = 0 Dangerous builds = 0 1308 -4980.15753971923 eV 2.3081654207694 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06