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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -70.603685 0.0000000) to (40.763057 70.603685 6.0992294) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4756345 5.6201938 6.0992294 Created 1608 atoms using lattice units in orthogonal box = (0.0000000 -70.603685 0.0000000) to (40.763057 70.603685 6.0992294) create_atoms CPU = 0.003 seconds 1608 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4756345 5.6201938 6.0992294 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -70.603685 0.0000000) to (40.763057 70.603685 6.0992294) create_atoms CPU = 0.003 seconds 1610 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 = 13 44 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 2 atoms, new total = 3216 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_876687166519_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 = 13 44 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) = 5.872 | 5.872 | 5.872 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13409.018 0 -13409.018 56824.695 79 0 -14261.7 0 -14261.7 8439.6833 Loop time of 21.0008 on 1 procs for 79 steps with 3216 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13409.0177241429 -14261.6910736632 -14261.6998818347 Force two-norm initial, final = 897.35856 0.39179267 Force max component initial, final = 198.04646 0.091377705 Final line search alpha, max atom move = 1.0000000 0.091377705 Iterations, force evaluations = 79 139 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 20.859 | 20.859 | 20.859 | 0.0 | 99.33 Neigh | 0.090002 | 0.090002 | 0.090002 | 0.0 | 0.43 Comm | 0.026025 | 0.026025 | 0.026025 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02541 | | | 0.12 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12208.0 ave 12208 max 12208 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: 280456.0 ave 280456 max 280456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280456 Ave neighs/atom = 87.206468 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 13 44 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 : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.872 | 5.872 | 5.872 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -14261.7 0 -14261.7 8439.6833 35107.433 85 0 -14262.552 0 -14262.552 -38.959369 35265.749 Loop time of 1.30239 on 1 procs for 6 steps with 3216 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 = -14261.6998818346 -14262.5514528068 -14262.5520952039 Force two-norm initial, final = 386.36926 3.1609376 Force max component initial, final = 353.06155 2.8177808 Final line search alpha, max atom move = 0.00010741910 0.00030268347 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2966 | 1.2966 | 1.2966 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00085781 | 0.00085781 | 0.00085781 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004915 | | | 0.38 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12200.0 ave 12200 max 12200 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: 280152.0 ave 280152 max 280152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 280152 Ave neighs/atom = 87.111940 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 = 13 44 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) = 6.010 | 6.010 | 6.010 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14262.552 0 -14262.552 -38.959369 Loop time of 2.257e-06 on 1 procs for 0 steps with 3216 atoms 177.2% 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 | | 2.257e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12184.0 ave 12184 max 12184 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: 279732.0 ave 279732 max 279732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 279732 Ave neighs/atom = 86.981343 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 = 13 44 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) = 6.010 | 6.010 | 6.010 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 -14262.552 -14262.552 40.781872 141.88619 6.0946087 -38.959369 -38.959369 -128.07515 -36.281244 47.478289 2.2270604 931.14251 Loop time of 2.715e-06 on 1 procs for 0 steps with 3216 atoms 257.8% 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 | | 2.715e-06 | | |100.00 Nlocal: 3216.00 ave 3216 max 3216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12184.0 ave 12184 max 12184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 139866.0 ave 139866 max 139866 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 279732.0 ave 279732 max 279732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 279732 Ave neighs/atom = 86.981343 Neighbor list builds = 0 Dangerous builds = 0 3216 -14262.5520952039 eV 2.22706035080366 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:23