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 = 3.5239542 3.5239542 3.5239542 Created orthogonal box = (0.0000000 -67.420737 0.0000000) to (38.923346 67.420737 6.1036677) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7427888 5.1576010 6.1036677 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -67.420737 0.0000000) to (38.923346 67.420737 6.1036677) create_atoms CPU = 0.008 seconds 1465 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7427888 5.1576010 6.1036677 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -67.420737 0.0000000) to (38.923346 67.420737 6.1036677) create_atoms CPU = 0.007 seconds 1465 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 11 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 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 2904 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_036303866285_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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 11 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 6.996 | 6.996 | 6.996 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12799.559 0 -12799.559 1562.8288 34 0 -12835.65 0 -12835.65 -7342.5489 Loop time of 3.09353 on 1 procs for 34 steps with 2904 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 = -12799.5587621733 -12835.6397730333 -12835.650012191 Force two-norm initial, final = 34.299737 0.29679593 Force max component initial, final = 5.5471609 0.047546121 Final line search alpha, max atom move = 0.63115013 0.030008740 Iterations, force evaluations = 34 55 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9927 | 2.9927 | 2.9927 | 0.0 | 96.74 Neigh | 0.065307 | 0.065307 | 0.065307 | 0.0 | 2.11 Comm | 0.018083 | 0.018083 | 0.018083 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01744 | | | 0.56 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12117.0 ave 12117 max 12117 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: 508112.0 ave 508112 max 508112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 508112 Ave neighs/atom = 174.96970 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 11 35 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 34 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.997 | 6.997 | 6.997 Mbytes Step Temp E_pair E_mol TotEng Press Volume 34 0 -12835.65 0 -12835.65 -7342.5489 32034.986 36 0 -12835.752 0 -12835.752 -3418.028 31965.229 Loop time of 0.217352 on 1 procs for 2 steps with 2904 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 = -12835.6500121911 -12835.746644548 -12835.7523088868 Force two-norm initial, final = 130.78233 7.2502422 Force max component initial, final = 106.66459 7.0489550 Final line search alpha, max atom move = 3.5496644e-05 0.00025021425 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2126 | 0.2126 | 0.2126 | 0.0 | 97.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010757 | 0.0010757 | 0.0010757 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003675 | | | 1.69 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12135.0 ave 12135 max 12135 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: 508558.0 ave 508558 max 508558 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 508558 Ave neighs/atom = 175.12328 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 11 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 7.135 | 7.135 | 7.135 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12835.752 0 -12835.752 -3418.028 Loop time of 6.505e-06 on 1 procs for 0 steps with 2904 atoms 184.5% 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 | | 6.505e-06 | | |100.00 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12145.0 ave 12145 max 12145 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: 508652.0 ave 508652 max 508652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 508652 Ave neighs/atom = 175.15565 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 = 7.709524 ghost atom cutoff = 7.709524 binsize = 3.854762, bins = 11 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.709524 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) = 7.135 | 7.135 | 7.135 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 -12835.752 -12835.752 38.869593 134.84147 6.0987992 -3418.028 -3418.028 -83.560288 -10523.553 353.02929 2.2130901 726.00651 Loop time of 6.766e-06 on 1 procs for 0 steps with 2904 atoms 295.6% 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 | | 6.766e-06 | | |100.00 Nlocal: 2904.00 ave 2904 max 2904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12145.0 ave 12145 max 12145 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 254326.0 ave 254326 max 254326 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 508652.0 ave 508652 max 508652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 508652 Ave neighs/atom = 175.15565 Neighbor list builds = 0 Dangerous builds = 0 2904 -12835.7523088868 eV 2.21309006644345 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04