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 = 2.8675702 2.8675702 2.8675702 Created orthogonal box = (0.0000000 -42.147370 0.0000000) to (14.900332 42.147370 4.0553566) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.8630490 4.6827225 4.0553566 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -42.147370 0.0000000) to (14.900332 42.147370 4.0553566) create_atoms CPU = 0.001 seconds 218 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.8630490 4.6827225 4.0553566 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -42.147370 0.0000000) to (14.900332 42.147370 4.0553566) create_atoms CPU = 0.001 seconds 218 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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 25 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 428 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_427873955970_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.472 | 4.472 | 4.472 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1812.4768 0 -1812.4768 1641.7813 38 0 -1822.4724 0 -1822.4724 -8503.0013 Loop time of 2.98138 on 1 procs for 38 steps with 428 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 = -1812.47681240016 -1822.47097342861 -1822.47244450096 Force two-norm initial, final = 18.146086 0.10687809 Force max component initial, final = 5.2257522 0.017509434 Final line search alpha, max atom move = 1.0000000 0.017509434 Iterations, force evaluations = 38 68 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9746 | 2.9746 | 2.9746 | 0.0 | 99.77 Neigh | 0.0029216 | 0.0029216 | 0.0029216 | 0.0 | 0.10 Comm | 0.0020866 | 0.0020866 | 0.0020866 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001747 | | | 0.06 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3444.00 ave 3444 max 3444 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: 48716.0 ave 48716 max 48716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48716 Ave neighs/atom = 113.82243 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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.472 | 4.472 | 4.472 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -1822.4724 0 -1822.4724 -8503.0013 5093.6073 42 0 -1822.5196 0 -1822.5196 -3249.0024 5077.3201 Loop time of 0.259179 on 1 procs for 4 steps with 428 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 = -1822.47244450096 -1822.51832559263 -1822.51964077781 Force two-norm initial, final = 30.449131 2.3030474 Force max component initial, final = 27.170738 2.1476276 Final line search alpha, max atom move = 0.00025795989 0.00055400179 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2584 | 0.2584 | 0.2584 | 0.0 | 99.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015857 | 0.00015857 | 0.00015857 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006239 | | | 0.24 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3460.00 ave 3460 max 3460 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: 48620.0 ave 48620 max 48620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48620 Ave neighs/atom = 113.59813 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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.610 | 4.610 | 4.610 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1822.5196 0 -1822.5196 -3249.0024 Loop time of 1.645e-06 on 1 procs for 0 steps with 428 atoms 121.6% 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 | | 1.645e-06 | | |100.00 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3460.00 ave 3460 max 3460 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: 48772.0 ave 48772 max 48772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48772 Ave neighs/atom = 113.95327 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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.610 | 4.610 | 4.610 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 -1822.5196 -1822.5196 14.852284 84.29474 4.0554667 -3249.0024 -3249.0024 -675.51048 -8812.1176 -259.37911 2.2733217 231.41049 Loop time of 1.47e-06 on 1 procs for 0 steps with 428 atoms 136.1% 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 | | 1.47e-06 | | |100.00 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3460.00 ave 3460 max 3460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 24386.0 ave 24386 max 24386 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 48772.0 ave 48772 max 48772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48772 Ave neighs/atom = 113.95327 Neighbor list builds = 0 Dangerous builds = 0 428 -1822.51964077781 eV 2.2733217158154 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03