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 -54.559870 0.0000000) to (38.579654 54.559870 5.1100000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0915243 5.2645488 5.1100000 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -54.559870 0.0000000) to (38.579654 54.559870 5.1100000) create_atoms CPU = 0.006 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0915243 5.2645488 5.1100000 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -54.559870 0.0000000) to (38.579654 54.559870 5.1100000) create_atoms CPU = 0.006 seconds 916 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 ghost atom cutoff = 6 binsize = 3, bins = 13 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1828 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_087820130586_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 13 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.156 | 5.156 | 5.156 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6000.3526 0 -6000.3526 66169.748 54 0 -6455.7335 0 -6455.7335 6915.3342 Loop time of 7.43267 on 1 procs for 54 steps with 1828 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 = -6000.35261414373 -6455.72855303383 -6455.73349461703 Force two-norm initial, final = 466.30099 0.20840243 Force max component initial, final = 88.282973 0.029753343 Final line search alpha, max atom move = 1.0000000 0.029753343 Iterations, force evaluations = 54 93 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.3711 | 7.3711 | 7.3711 | 0.0 | 99.17 Neigh | 0.023267 | 0.023267 | 0.023267 | 0.0 | 0.31 Comm | 0.01836 | 0.01836 | 0.01836 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01993 | | | 0.27 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7366.00 ave 7366 max 7366 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: 141576.0 ave 141576 max 141576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141576 Ave neighs/atom = 77.448578 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 ghost atom cutoff = 6 binsize = 3, bins = 13 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.155 | 5.155 | 5.155 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -6455.7335 0 -6455.7335 6915.3342 21512.087 59 0 -6456.0102 0 -6456.0102 2.3505551 21616.366 Loop time of 0.604632 on 1 procs for 5 steps with 1828 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 = -6455.73349461702 -6456.00935667279 -6456.01020016979 Force two-norm initial, final = 165.11540 1.1779690 Force max component initial, final = 121.00029 0.82215150 Final line search alpha, max atom move = 9.6400343e-05 7.9255686e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.59804 | 0.59804 | 0.59804 | 0.0 | 98.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013377 | 0.0013377 | 0.0013377 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005255 | | | 0.87 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7482.00 ave 7482 max 7482 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: 141544.0 ave 141544 max 141544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141544 Ave neighs/atom = 77.431072 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 ghost atom cutoff = 6 binsize = 3, bins = 13 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.293 | 5.293 | 5.293 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6456.0102 0 -6456.0102 2.3505551 Loop time of 8.781e-06 on 1 procs for 0 steps with 1828 atoms 170.8% 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 | | 8.781e-06 | | |100.00 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7475.00 ave 7475 max 7475 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: 141456.0 ave 141456 max 141456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141456 Ave neighs/atom = 77.382932 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 ghost atom cutoff = 6 binsize = 3, bins = 13 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.293 | 5.293 | 5.293 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 -6456.0102 -6456.0102 38.623114 109.53891 5.1093657 2.3505551 2.3505551 -59.28848 5.4109264 60.929219 2.3799 851.46811 Loop time of 7.617e-06 on 1 procs for 0 steps with 1828 atoms 249.4% 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 | | 7.617e-06 | | |100.00 Nlocal: 1828.00 ave 1828 max 1828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7475.00 ave 7475 max 7475 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 70728.0 ave 70728 max 70728 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 141456.0 ave 141456 max 141456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 141456 Ave neighs/atom = 77.382932 Neighbor list builds = 0 Dangerous builds = 0 1828 -6456.01020016979 eV 2.37989998036457 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08