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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -53.150835 0.0000000) to (37.583316 53.150835 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9342077 6.0610601 4.9780318 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -53.150835 0.0000000) to (37.583316 53.150835 4.9780318) create_atoms CPU = 0.007 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9342077 6.0610601 4.9780318 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -53.150835 0.0000000) to (37.583316 53.150835 4.9780318) create_atoms CPU = 0.006 seconds 916 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 9 26 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 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1824 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_826591359508_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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 6.391 | 6.391 | 6.391 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8024.1612 0 -8024.1612 5903.875 66 0 -8097.069 0 -8097.069 5187.869 Loop time of 5.36236 on 1 procs for 66 steps with 1824 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 = -8024.16120806342 -8097.06107446809 -8097.06897072347 Force two-norm initial, final = 33.942342 0.29522346 Force max component initial, final = 5.0537065 0.035283360 Final line search alpha, max atom move = 1.0000000 0.035283360 Iterations, force evaluations = 66 117 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.1961 | 5.1961 | 5.1961 | 0.0 | 96.90 Neigh | 0.10695 | 0.10695 | 0.10695 | 0.0 | 1.99 Comm | 0.032851 | 0.032851 | 0.032851 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02646 | | | 0.49 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11222.0 ave 11222 max 11222 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: 410216.0 ave 410216 max 410216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 410216 Ave neighs/atom = 224.89912 Neighbor list builds = 2 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.391 | 6.391 | 6.391 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -8097.069 0 -8097.069 5187.869 19888.079 70 0 -8097.3131 0 -8097.3131 260.23963 19942.92 Loop time of 0.274828 on 1 procs for 4 steps with 1824 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8097.06897072349 -8097.30828887708 -8097.31305320428 Force two-norm initial, final = 147.86517 5.9515639 Force max component initial, final = 139.16923 4.7420625 Final line search alpha, max atom move = 7.0660190e-05 0.00033507504 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26862 | 0.26862 | 0.26862 | 0.0 | 97.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014247 | 0.0014247 | 0.0014247 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004782 | | | 1.74 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11227.0 ave 11227 max 11227 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: 409896.0 ave 409896 max 409896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 409896 Ave neighs/atom = 224.72368 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 6.529 | 6.529 | 6.529 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8097.3131 0 -8097.3131 260.23963 Loop time of 6.304e-06 on 1 procs for 0 steps with 1824 atoms 190.4% 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 | | 6.304e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11227.0 ave 11227 max 11227 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: 409488.0 ave 409488 max 409488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 409488 Ave neighs/atom = 224.50000 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 6.529 | 6.529 | 6.529 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 -8097.3131 -8097.3131 37.546665 106.65031 4.9802971 260.23963 260.23963 158.26847 382.21781 240.2326 2.3072668 604.95286 Loop time of 6.605e-06 on 1 procs for 0 steps with 1824 atoms 287.7% 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 | | 6.605e-06 | | |100.00 Nlocal: 1824.00 ave 1824 max 1824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11227.0 ave 11227 max 11227 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 204744.0 ave 204744 max 204744 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 409488.0 ave 409488 max 409488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 409488 Ave neighs/atom = 224.50000 Neighbor list builds = 0 Dangerous builds = 0 1824 -8097.31305320428 eV 2.3072667835248 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07