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 = 3.4986965 3.4986965 3.4986965 Created orthogonal box = (0.0000000 -64.516275 0.0000000) to (32.256388 64.516275 3.4986965) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9333300 4.9333300 3.4986965 Created 681 atoms using lattice units in orthogonal box = (0.0000000 -64.516275 0.0000000) to (32.256388 64.516275 3.4986965) create_atoms CPU = 0.003 seconds 681 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9333300 4.9333300 3.4986965 Created 681 atoms using lattice units in orthogonal box = (0.0000000 -64.516275 0.0000000) to (32.256388 64.516275 3.4986965) create_atoms CPU = 0.002 seconds 681 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 34 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1358 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_677715648236_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 34 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.513 | 5.513 | 5.513 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5465.4083 0 -5465.4083 64408.643 77 0 -5581.9663 0 -5581.9663 -1652.4789 Loop time of 4.19182 on 1 procs for 77 steps with 1358 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 = -5465.40827567371 -5581.96150823691 -5581.96630207458 Force two-norm initial, final = 140.02270 0.35100031 Force max component initial, final = 39.134200 0.12878037 Final line search alpha, max atom move = 0.39267937 0.050569392 Iterations, force evaluations = 77 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0963 | 4.0963 | 4.0963 | 0.0 | 97.72 Neigh | 0.031797 | 0.031797 | 0.031797 | 0.0 | 0.76 Comm | 0.038495 | 0.038495 | 0.038495 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02519 | | | 0.60 Nlocal: 1358.00 ave 1358 max 1358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10917.0 ave 10917 max 10917 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: 237710.0 ave 237710 max 237710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 237710 Ave neighs/atom = 175.04418 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 34 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.513 | 5.513 | 5.513 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -5581.9663 0 -5581.9663 -1652.4789 14562.009 83 0 -5582.1715 0 -5582.1715 -3246.4385 14582.739 Loop time of 0.234677 on 1 procs for 6 steps with 1358 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 = -5581.96630207457 -5582.16931094355 -5582.17146049775 Force two-norm initial, final = 57.528532 0.48853705 Force max component initial, final = 41.510294 0.13285535 Final line search alpha, max atom move = 0.00019546420 2.5968465e-05 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.22674 | 0.22674 | 0.22674 | 0.0 | 96.62 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019091 | 0.0019091 | 0.0019091 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006027 | | | 2.57 Nlocal: 1358.00 ave 1358 max 1358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10926.0 ave 10926 max 10926 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: 238188.0 ave 238188 max 238188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238188 Ave neighs/atom = 175.39617 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 34 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.651 | 5.651 | 5.651 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5582.1715 0 -5582.1715 -3246.4385 Loop time of 6.956e-06 on 1 procs for 0 steps with 1358 atoms 172.5% 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 | | 6.956e-06 | | |100.00 Nlocal: 1358.00 ave 1358 max 1358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10932.0 ave 10932 max 10932 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: 238370.0 ave 238370 max 238370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238370 Ave neighs/atom = 175.53019 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 9 34 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.651 | 5.651 | 5.651 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 -5582.1715 -5582.1715 32.12364 129.03255 3.5181559 -3246.4385 -3246.4385 6.4353162 -9752.5496 6.7988304 2.261253 148.16299 Loop time of 9.613e-06 on 1 procs for 0 steps with 1358 atoms 187.2% 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 | | 9.613e-06 | | |100.00 Nlocal: 1358.00 ave 1358 max 1358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10932.0 ave 10932 max 10932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 119185.0 ave 119185 max 119185 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 238370.0 ave 238370 max 238370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238370 Ave neighs/atom = 175.53019 Neighbor list builds = 0 Dangerous builds = 0 1358 -5582.17146049775 eV 2.2612529610251 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05