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 = 4.0500004 4.0500004 4.0500004 Created orthogonal box = (0.0000000 -59.934533 0.0000000) to (48.936341 59.934533 9.9204345) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0332475 5.7471470 6.6136230 Created 1747 atoms using lattice units in orthogonal box = (0.0000000 -59.934533 0.0000000) to (48.936341 59.934533 9.9204345) create_atoms CPU = 0.007 seconds 1747 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0332475 5.7471470 6.6136230 Created 1755 atoms using lattice units in orthogonal box = (0.0000000 -59.934533 0.0000000) to (48.936341 59.934533 9.9204345) create_atoms CPU = 0.006 seconds 1755 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 13 31 3 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3502 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_820335782779_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 13 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.505 | 6.505 | 6.505 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11506.31 0 -11506.31 9515.7344 122 0 -11734.562 0 -11734.562 7251.644 Loop time of 10.2845 on 1 procs for 122 steps with 3502 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 = -11506.3100007657 -11734.5513037533 -11734.5621848005 Force two-norm initial, final = 64.840036 0.32395564 Force max component initial, final = 5.2059753 0.094991297 Final line search alpha, max atom move = 0.70668361 0.067128793 Iterations, force evaluations = 122 216 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.8852 | 9.8852 | 9.8852 | 0.0 | 96.12 Neigh | 0.26953 | 0.26953 | 0.26953 | 0.0 | 2.62 Comm | 0.053054 | 0.053054 | 0.053054 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07666 | | | 0.75 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9570.00 ave 9570 max 9570 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: 459974.0 ave 459974 max 459974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 459974 Ave neighs/atom = 131.34609 Neighbor list builds = 4 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 13 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 122 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.506 | 6.506 | 6.506 Mbytes Step Temp E_pair E_mol TotEng Press Volume 122 0 -11734.562 0 -11734.562 7251.644 58192.807 135 0 -11737.425 0 -11737.425 5.8271874 58726.842 Loop time of 0.851972 on 1 procs for 13 steps with 3502 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 = -11734.5621848004 -11737.4201006462 -11737.425341024 Force two-norm initial, final = 537.82705 1.6153617 Force max component initial, final = 488.63076 0.87591406 Final line search alpha, max atom move = 7.9801393e-05 6.9899162e-05 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.75181 | 0.75181 | 0.75181 | 0.0 | 88.24 Neigh | 0.073333 | 0.073333 | 0.073333 | 0.0 | 8.61 Comm | 0.004841 | 0.004841 | 0.004841 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02199 | | | 2.58 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9652.00 ave 9652 max 9652 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: 459680.0 ave 459680 max 459680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 459680 Ave neighs/atom = 131.26214 Neighbor list builds = 1 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 13 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.645 | 6.645 | 6.645 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11737.425 0 -11737.425 5.8271874 Loop time of 6.595e-06 on 1 procs for 0 steps with 3502 atoms 288.1% 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 | | 6.595e-06 | | |100.00 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9753.00 ave 9753 max 9753 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: 459566.0 ave 459566 max 459566 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 459566 Ave neighs/atom = 131.22958 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 13 32 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.645 | 6.645 | 6.645 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 -11737.425 -11737.425 48.942932 121.37455 9.8859638 5.8271874 5.8271874 -10.719431 4.3874769 23.813517 2.6268172 2935.8054 Loop time of 7.367e-06 on 1 procs for 0 steps with 3502 atoms 257.9% 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 | | 7.367e-06 | | |100.00 Nlocal: 3502.00 ave 3502 max 3502 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9753.00 ave 9753 max 9753 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 229783.0 ave 229783 max 229783 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 459566.0 ave 459566 max 459566 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 459566 Ave neighs/atom = 131.22958 Neighbor list builds = 0 Dangerous builds = 0 3502 -11737.425341024 eV 2.62681721102423 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12