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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -39.483817 0.0000000) to (19.740367 39.483817 3.0829274) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3332513 4.3332513 3.0829274 Created 165 atoms using lattice units in orthogonal box = (0.0000000 -39.483817 0.0000000) to (19.740367 39.483817 3.0829274) create_atoms CPU = 0.000 seconds 165 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3332513 4.3332513 3.0829274 Created 165 atoms using lattice units in orthogonal box = (0.0000000 -39.483817 0.0000000) to (19.740367 39.483817 3.0829274) create_atoms CPU = 0.000 seconds 165 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 24 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 6 atoms, new total = 324 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.815 | 4.815 | 4.815 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2038.4306 0 -2038.4306 33419.668 70 0 -2101.3016 0 -2101.3016 -19612.367 Loop time of 4.99418 on 1 procs for 70 steps with 324 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 = -2038.43061993359 -2101.29952294898 -2101.30161402454 Force two-norm initial, final = 188.41594 0.21747120 Force max component initial, final = 82.314180 0.057629240 Final line search alpha, max atom move = 1.0000000 0.057629240 Iterations, force evaluations = 70 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.9835 | 4.9835 | 4.9835 | 0.0 | 99.79 Neigh | 0.0064997 | 0.0064997 | 0.0064997 | 0.0 | 0.13 Comm | 0.0030492 | 0.0030492 | 0.0030492 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001153 | | | 0.02 Nlocal: 324.000 ave 324 max 324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3063.00 ave 3063 max 3063 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: 23588.0 ave 23588 max 23588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23588 Ave neighs/atom = 72.802469 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 24 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.813 | 4.813 | 4.813 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -2101.3016 0 -2101.3016 -19612.367 4805.8216 82 0 -2101.7244 0 -2101.7244 3512.1637 4751.3766 Loop time of 0.565189 on 1 procs for 12 steps with 324 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 = -2101.30161402453 -2101.72434854832 -2101.72441389289 Force two-norm initial, final = 98.188856 0.99084406 Force max component initial, final = 74.136576 0.77793481 Final line search alpha, max atom move = 0.0014577762 0.0011340549 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.56431 | 0.56431 | 0.56431 | 0.0 | 99.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001985 | 0.0001985 | 0.0001985 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006833 | | | 0.12 Nlocal: 324.000 ave 324 max 324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2841.00 ave 2841 max 2841 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: 23536.0 ave 23536 max 23536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23536 Ave neighs/atom = 72.641975 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.951 | 4.951 | 4.951 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2101.7244 0 -2101.7244 3512.1637 Loop time of 1.8e-06 on 1 procs for 0 steps with 324 atoms 111.1% 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 | | 1.8e-06 | | |100.00 Nlocal: 324.000 ave 324 max 324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2841.00 ave 2841 max 2841 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: 24140.0 ave 24140 max 24140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24140 Ave neighs/atom = 74.506173 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 6 24 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 4.951 | 4.951 | 4.951 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 -2101.7244 -2101.7244 19.735939 78.967634 3.0486849 3512.1637 3512.1637 262.26279 10197.716 76.512888 2.4920198 458.06512 Loop time of 1.8e-06 on 1 procs for 0 steps with 324 atoms 166.7% 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 | | 1.8e-06 | | |100.00 Nlocal: 324.000 ave 324 max 324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2841.00 ave 2841 max 2841 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12070.0 ave 12070 max 12070 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 24140.0 ave 24140 max 24140 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24140 Ave neighs/atom = 74.506173 Neighbor list builds = 0 Dangerous builds = 0 324 -2101.72441389289 eV 2.49201982270256 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05