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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -30.034171 0.0000000) to (36.784196 30.034171 7.0144710) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6816250 4.3686066 4.6763140 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -30.034171 0.0000000) to (36.784196 30.034171 7.0144710) create_atoms CPU = 0.001 seconds 658 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6816250 4.3686066 4.6763140 Created 664 atoms using lattice units in orthogonal box = (0.0000000 -30.034171 0.0000000) to (36.784196 30.034171 7.0144710) create_atoms CPU = 0.001 seconds 664 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 = 12 19 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1320 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_179420363944_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 = 12 19 3 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) = 5.015 | 5.015 | 5.015 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4470.0618 0 -4470.0618 145133.32 50 0 -5628.1365 0 -5628.1365 11449.354 Loop time of 8.07102 on 1 procs for 50 steps with 1320 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4470.06183710886 -5628.13114251115 -5628.13654084661 Force two-norm initial, final = 1230.8946 0.24971251 Force max component initial, final = 170.22604 0.030151373 Final line search alpha, max atom move = 1.0000000 0.030151373 Iterations, force evaluations = 50 77 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.0484 | 8.0484 | 8.0484 | 0.0 | 99.72 Neigh | 0.0096615 | 0.0096615 | 0.0096615 | 0.0 | 0.12 Comm | 0.0051378 | 0.0051378 | 0.0051378 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007845 | | | 0.10 Nlocal: 1320.00 ave 1320 max 1320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4835.00 ave 4835 max 4835 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: 142956.0 ave 142956 max 142956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142956 Ave neighs/atom = 108.30000 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 19 3 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 : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.017 | 5.017 | 5.017 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -5628.1365 0 -5628.1365 11449.354 15498.934 59 0 -5629.0575 0 -5629.0575 -76.733759 15601.311 Loop time of 1.18147 on 1 procs for 9 steps with 1320 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 = -5628.13654084661 -5629.05459912919 -5629.05747241902 Force two-norm initial, final = 237.94764 1.4515175 Force max component initial, final = 219.99035 0.94401813 Final line search alpha, max atom move = 0.00011904522 0.00011238084 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1776 | 1.1776 | 1.1776 | 0.0 | 99.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00051778 | 0.00051778 | 0.00051778 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003371 | | | 0.29 Nlocal: 1320.00 ave 1320 max 1320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5126.00 ave 5126 max 5126 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: 143010.0 ave 143010 max 143010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 143010 Ave neighs/atom = 108.34091 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 = 12 19 3 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) = 5.155 | 5.155 | 5.155 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5629.0575 0 -5629.0575 -76.733759 Loop time of 2.207e-06 on 1 procs for 0 steps with 1320 atoms 135.9% 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 | | 2.207e-06 | | |100.00 Nlocal: 1320.00 ave 1320 max 1320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5139.00 ave 5139 max 5139 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: 142322.0 ave 142322 max 142322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142322 Ave neighs/atom = 107.81970 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 = 12 19 3 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) = 5.155 | 5.155 | 5.155 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 -5629.0575 -5629.0575 36.809566 60.578133 6.9965593 -76.733759 -76.733759 -97.012795 -68.558283 -64.630198 2.3179451 1840.6234 Loop time of 2.17e-06 on 1 procs for 0 steps with 1320 atoms 276.5% 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 | | 2.17e-06 | | |100.00 Nlocal: 1320.00 ave 1320 max 1320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5139.00 ave 5139 max 5139 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 71161.0 ave 71161 max 71161 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 142322.0 ave 142322 max 142322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142322 Ave neighs/atom = 107.81970 Neighbor list builds = 0 Dangerous builds = 0 1320 -5629.05747241902 eV 2.31794514319203 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09