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 -62.175596 0.0000000) to (35.897097 62.175596 6.0968188) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5226304 5.5798612 6.0968188 Created 1246 atoms using lattice units in orthogonal box = (0.0000000 -62.175596 0.0000000) to (35.897097 62.175596 6.0968188) create_atoms CPU = 0.003 seconds 1246 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5226304 5.5798612 6.0968188 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -62.175596 0.0000000) to (35.897097 62.175596 6.0968188) create_atoms CPU = 0.003 seconds 1250 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 9 30 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2488 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_592013496703_005#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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 10.84 | 10.84 | 10.84 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10556.923 0 -10556.923 30258.434 110 0 -11038.236 0 -11038.236 2086.05 Loop time of 5.37687 on 1 procs for 110 steps with 2488 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 = -10556.9233842371 -11038.2252225795 -11038.2358941865 Force two-norm initial, final = 478.60216 0.39709535 Force max component initial, final = 91.003651 0.12793475 Final line search alpha, max atom move = 1.0000000 0.12793475 Iterations, force evaluations = 110 187 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.1645 | 5.1645 | 5.1645 | 0.0 | 96.05 Neigh | 0.14346 | 0.14346 | 0.14346 | 0.0 | 2.67 Comm | 0.037722 | 0.037722 | 0.037722 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03118 | | | 0.58 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14124.0 ave 14124 max 14124 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: 555948.0 ave 555948 max 555948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 555948 Ave neighs/atom = 223.45177 Neighbor list builds = 4 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 110 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.84 | 10.84 | 10.84 Mbytes Step Temp E_pair E_mol TotEng Press Volume 110 0 -11038.236 0 -11038.236 2086.05 27215.266 112 0 -11038.287 0 -11038.287 9.3634046 27247.142 Loop time of 0.139606 on 1 procs for 2 steps with 2488 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11038.2358941875 -11038.2796104275 -11038.2872642022 Force two-norm initial, final = 78.764451 2.8666504 Force max component initial, final = 69.259846 2.1470420 Final line search alpha, max atom move = 4.0296550e-05 8.6518388e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13637 | 0.13637 | 0.13637 | 0.0 | 97.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00057858 | 0.00057858 | 0.00057858 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002657 | | | 1.90 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14128.0 ave 14128 max 14128 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: 555854.0 ave 555854 max 555854 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 555854 Ave neighs/atom = 223.41399 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 10.36 | 10.36 | 10.36 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11038.287 0 -11038.287 9.3634046 Loop time of 2.149e-06 on 1 procs for 0 steps with 2488 atoms 186.1% 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 | | 2.149e-06 | | |100.00 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14128.0 ave 14128 max 14128 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: 555762.0 ave 555762 max 555762 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 555762 Ave neighs/atom = 223.37701 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 10.36 | 10.36 | 10.36 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 -11038.287 -11038.287 35.9114 124.50868 6.0938113 9.3634046 9.3634046 -126.29988 77.14724 77.242859 2.2632475 937.54117 Loop time of 4.603e-06 on 1 procs for 0 steps with 2488 atoms 260.7% 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 | | 4.603e-06 | | |100.00 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14128.0 ave 14128 max 14128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 277881.0 ave 277881 max 277881 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 555762.0 ave 555762 max 555762 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 555762 Ave neighs/atom = 223.37701 Neighbor list builds = 0 Dangerous builds = 0 2488 -11038.2872642022 eV 2.2632474940875 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06