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 = 4.0499990 4.0499990 4.0499990 Created orthogonal box = (0.0000000 -57.845556 0.0000000) to (40.902985 57.845556 5.7275635) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4161545 5.1040197 5.7275635 Created 813 atoms using lattice units in orthogonal box = (0.0000000 -57.845556 0.0000000) to (40.902985 57.845556 5.7275635) create_atoms CPU = 0.001 seconds 813 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4161545 5.1040197 5.7275635 Created 821 atoms using lattice units in orthogonal box = (0.0000000 -57.845556 0.0000000) to (40.902985 57.845556 5.7275635) create_atoms CPU = 0.001 seconds 821 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 29 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1632 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_093637366498_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.525 | 5.525 | 5.525 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5076.9677 0 -5076.9677 35053.421 65 0 -5467.3102 0 -5467.3102 3129.6244 Loop time of 13.2475 on 1 procs for 65 steps with 1632 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5076.96770296981 -5467.30532239429 -5467.31019989791 Force two-norm initial, final = 421.65566 0.17833596 Force max component initial, final = 60.578840 0.022389194 Final line search alpha, max atom move = 1.0000000 0.022389194 Iterations, force evaluations = 65 117 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.211 | 13.211 | 13.211 | 0.0 | 99.73 Neigh | 0.012777 | 0.012777 | 0.012777 | 0.0 | 0.10 Comm | 0.012139 | 0.012139 | 0.012139 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01113 | | | 0.08 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8079.00 ave 8079 max 8079 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: 217186.0 ave 217186 max 217186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217186 Ave neighs/atom = 133.07966 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.533 | 5.533 | 5.533 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -5467.3102 0 -5467.3102 3129.6244 27103.471 70 0 -5467.5061 0 -5467.5061 -215.186 27216.76 Loop time of 0.784709 on 1 procs for 5 steps with 1632 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5467.3101998979 -5467.50341447939 -5467.50609812683 Force two-norm initial, final = 101.20265 7.5404030 Force max component initial, final = 86.291028 5.8532103 Final line search alpha, max atom move = 0.00010201678 0.00059712566 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.78174 | 0.78174 | 0.78174 | 0.0 | 99.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052226 | 0.00052226 | 0.00052226 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00245 | | | 0.31 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8656.00 ave 8656 max 8656 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: 217648.0 ave 217648 max 217648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217648 Ave neighs/atom = 133.36275 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.672 | 5.672 | 5.672 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5467.5061 0 -5467.5061 -215.186 Loop time of 7.974e-06 on 1 procs for 0 steps with 1632 atoms 37.6% 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 | | 7.974e-06 | | |100.00 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8656.00 ave 8656 max 8656 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: 217440.0 ave 217440 max 217440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217440 Ave neighs/atom = 133.23529 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.672 | 5.672 | 5.672 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 -5467.5061 -5467.5061 40.92857 116.21505 5.7219953 -215.186 -215.186 -278.87303 -22.457399 -344.22756 2.657306 811.45247 Loop time of 2.198e-06 on 1 procs for 0 steps with 1632 atoms 227.5% 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 | | 2.198e-06 | | |100.00 Nlocal: 1632.00 ave 1632 max 1632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8656.00 ave 8656 max 8656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 108720.0 ave 108720 max 108720 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 217440.0 ave 217440 max 217440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 217440 Ave neighs/atom = 133.23529 Neighbor list builds = 0 Dangerous builds = 0 1632 -5467.50609812683 eV 2.65730596697996 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14