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 = 4.0816549 4.0816549 4.0816549 Created orthogonal box = (0.0000000 -43.580149 0.0000000) to (30.815819 43.580149 5.7723318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 7.0281692 6.8810762 5.7723318 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -43.580149 0.0000000) to (30.815819 43.580149 5.7723318) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 7.0281692 6.8810762 5.7723318 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -43.580149 0.0000000) to (30.815819 43.580149 5.7723318) create_atoms CPU = 0.001 seconds 458 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 6 15 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 12.102500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 912 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_049243498555_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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 6 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 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) = 5.849 | 5.849 | 5.849 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3186.1352 0 -3186.1352 12522.708 69 0 -3257.6523 0 -3257.6523 4751.9096 Loop time of 2.99166 on 1 procs for 69 steps with 912 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3186.13520450094 -3257.64930692119 -3257.65229161959 Force two-norm initial, final = 97.917077 0.11083290 Force max component initial, final = 30.583822 0.020415917 Final line search alpha, max atom move = 1.0000000 0.020415917 Iterations, force evaluations = 69 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.955 | 2.955 | 2.955 | 0.0 | 98.78 Neigh | 0.01826 | 0.01826 | 0.01826 | 0.0 | 0.61 Comm | 0.01166 | 0.01166 | 0.01166 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006707 | | | 0.22 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9981.00 ave 9981 max 9981 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: 390172.0 ave 390172 max 390172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 390172 Ave neighs/atom = 427.82018 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 6 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.846 | 5.846 | 5.846 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -3257.6523 0 -3257.6523 4751.9096 15503.998 76 0 -3257.8859 0 -3257.8859 -9.2327675 15584.626 Loop time of 0.210459 on 1 procs for 7 steps with 912 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 = -3257.65229161959 -3257.88368897661 -3257.8858643313 Force two-norm initial, final = 88.377981 0.34288436 Force max component initial, final = 76.967590 0.24765748 Final line search alpha, max atom move = 0.00023014833 5.6997956e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20741 | 0.20741 | 0.20741 | 0.0 | 98.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00058113 | 0.00058113 | 0.00058113 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002463 | | | 1.17 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9528.00 ave 9528 max 9528 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: 390224.0 ave 390224 max 390224 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 390224 Ave neighs/atom = 427.87719 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 6 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 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) = 5.983 | 5.983 | 5.983 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3257.8859 0 -3257.8859 -9.2327675 Loop time of 1.579e-06 on 1 procs for 0 steps with 912 atoms 126.7% 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 | | 1.579e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9488.00 ave 9488 max 9488 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: 389604.0 ave 389604 max 389604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 389604 Ave neighs/atom = 427.19737 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 6 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.102500000000001 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) = 5.983 | 5.983 | 5.983 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 -3257.8859 -3257.8859 30.781712 87.744254 5.7701212 -9.2327675 -9.2327675 7.6735015 -9.9211433 -25.450661 2.6788956 892.70932 Loop time of 2.276e-06 on 1 procs for 0 steps with 912 atoms 175.7% 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 | | 2.276e-06 | | |100.00 Nlocal: 912.000 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9488.00 ave 9488 max 9488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 194802.0 ave 194802 max 194802 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 389604.0 ave 389604 max 389604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 389604 Ave neighs/atom = 427.19737 Neighbor list builds = 0 Dangerous builds = 0 912 -3257.8858643313 eV 2.67889555238396 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03