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 = 3.5200001 3.5200001 3.5200001 Created orthogonal box = (0.0000000 -63.749912 0.0000000) to (22.538998 63.749912 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0470482 5.4420657 4.9780318 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -63.749912 0.0000000) to (22.538998 63.749912 4.9780318) create_atoms CPU = 0.005 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0470482 5.4420657 4.9780318 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -63.749912 0.0000000) to (22.538998 63.749912 4.9780318) create_atoms CPU = 0.005 seconds 658 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 6 31 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1312 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_751354403791_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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 6 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.540 | 5.540 | 5.540 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5761.7135 0 -5761.7135 4586.0342 109 0 -5827.4438 0 -5827.4438 4240.9839 Loop time of 6.71327 on 1 procs for 109 steps with 1312 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 = -5761.7134556249 -5827.43809793422 -5827.44376474942 Force two-norm initial, final = 24.279406 0.24642506 Force max component initial, final = 3.9671664 0.025260097 Final line search alpha, max atom move = 1.0000000 0.025260097 Iterations, force evaluations = 109 204 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.5194 | 6.5194 | 6.5194 | 0.0 | 97.11 Neigh | 0.11208 | 0.11208 | 0.11208 | 0.0 | 1.67 Comm | 0.04832 | 0.04832 | 0.04832 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03348 | | | 0.50 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9985.00 ave 9985 max 9985 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: 289244.0 ave 289244 max 289244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289244 Ave neighs/atom = 220.46037 Neighbor list builds = 3 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 6 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 109 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.544 | 5.544 | 5.544 Mbytes Step Temp E_pair E_mol TotEng Press Volume 109 0 -5827.4438 0 -5827.4438 4240.9839 14305.461 111 0 -5827.49 0 -5827.49 -0.87989763 14339.288 Loop time of 0.179237 on 1 procs for 2 steps with 1312 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5827.44376474943 -5827.489527667 -5827.49000521985 Force two-norm initial, final = 66.108120 0.53576798 Force max component initial, final = 43.736502 0.37691596 Final line search alpha, max atom move = 0.00028351942 0.00010686299 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17461 | 0.17461 | 0.17461 | 0.0 | 97.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012141 | 0.0012141 | 0.0012141 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003418 | | | 1.91 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10289.0 ave 10289 max 10289 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: 290312.0 ave 290312 max 290312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 290312 Ave neighs/atom = 221.27439 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 6 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.682 | 5.682 | 5.682 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5827.49 0 -5827.49 -0.87989763 Loop time of 6.114e-06 on 1 procs for 0 steps with 1312 atoms 179.9% 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 | | 6.114e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10262.0 ave 10262 max 10262 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: 289676.0 ave 289676 max 289676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289676 Ave neighs/atom = 220.78963 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 6 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 5.682 | 5.682 | 5.682 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 -5827.49 -5827.49 22.562663 127.60226 4.9805679 -0.87989763 -0.87989763 -26.632962 42.147913 -18.154644 2.3116422 415.78343 Loop time of 6.395e-06 on 1 procs for 0 steps with 1312 atoms 312.7% 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 | | 6.395e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10262.0 ave 10262 max 10262 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 144838.0 ave 144838 max 144838 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 289676.0 ave 289676 max 289676 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 289676 Ave neighs/atom = 220.78963 Neighbor list builds = 0 Dangerous builds = 0 1312 -5797.90908031275 eV 2.31164217185992 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07