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 = 4.0612135 4.0612135 4.0612135 Created orthogonal box = (0.0000000 -59.132161 0.0000000) to (29.566080 59.132161 4.0612135) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0206552 5.0206552 4.0612135 Created 424 atoms using lattice units in orthogonal box = (0.0000000 -59.132161 0.0000000) to (29.566080 59.132161 4.0612135) create_atoms CPU = 0.001 seconds 424 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0206552 5.0206552 4.0612135 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -59.132161 0.0000000) to (29.566080 59.132161 4.0612135) create_atoms CPU = 0.000 seconds 426 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 7 25 1 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 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 848 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_411898953661_004#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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 5.022 | 5.022 | 5.022 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2209.7073 0 -2209.7073 11954.383 65 0 -2275.3029 0 -2275.3029 4022.683 Loop time of 1.06182 on 1 procs for 65 steps with 848 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 = -2209.70733637094 -2275.30106185451 -2275.3028604895 Force two-norm initial, final = 102.80541 0.12642129 Force max component initial, final = 33.461288 0.015944016 Final line search alpha, max atom move = 1.0000000 0.015944016 Iterations, force evaluations = 65 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0371 | 1.0371 | 1.0371 | 0.0 | 97.67 Neigh | 0.010246 | 0.010246 | 0.010246 | 0.0 | 0.96 Comm | 0.008736 | 0.008736 | 0.008736 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005712 | | | 0.54 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8968.00 ave 8968 max 8968 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: 189696.0 ave 189696 max 189696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189696 Ave neighs/atom = 223.69811 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 5.022 | 5.022 | 5.022 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -2275.3029 0 -2275.3029 4022.683 14200.49 71 0 -2275.4486 0 -2275.4486 -21.409791 14276.541 Loop time of 0.0705336 on 1 procs for 6 steps with 848 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2275.30286048951 -2275.44803365201 -2275.44859835332 Force two-norm initial, final = 65.988943 0.80301303 Force max component initial, final = 52.988754 0.76114794 Final line search alpha, max atom move = 0.00021351252 0.00016251462 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.067895 | 0.067895 | 0.067895 | 0.0 | 96.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052966 | 0.00052966 | 0.00052966 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002109 | | | 2.99 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8980.00 ave 8980 max 8980 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: 189832.0 ave 189832 max 189832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189832 Ave neighs/atom = 223.85849 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 7 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 5.160 | 5.160 | 5.160 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2275.4486 0 -2275.4486 -21.409791 Loop time of 1.661e-06 on 1 procs for 0 steps with 848 atoms 120.4% 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 | | 1.661e-06 | | |100.00 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8980.00 ave 8980 max 8980 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: 189520.0 ave 189520 max 189520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189520 Ave neighs/atom = 223.49057 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 7 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 5.160 | 5.160 | 5.160 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 -2275.4486 -2275.4486 29.535846 118.87423 4.066173 -21.409791 -21.409791 9.387086 11.907241 -85.5237 2.5737321 480.47407 Loop time of 2.02e-06 on 1 procs for 0 steps with 848 atoms 247.5% 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 | | 2.02e-06 | | |100.00 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8980.00 ave 8980 max 8980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 94760.0 ave 94760 max 94760 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 189520.0 ave 189520 max 189520 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189520 Ave neighs/atom = 223.49057 Neighbor list builds = 0 Dangerous builds = 0 848 -2275.44859835332 eV 2.57373208092861 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01