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 -43.388587 0.0000000) to (43.388587 43.388587 4.0816549) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7595470 5.7595470 4.0816549 Created 452 atoms using lattice units in orthogonal box = (0.0000000 -43.388587 0.0000000) to (43.388587 43.388587 4.0816549) create_atoms CPU = 0.002 seconds 452 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7595470 5.7595470 4.0816549 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -43.388587 0.0000000) to (43.388587 43.388587 4.0816549) create_atoms CPU = 0.002 seconds 454 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 = 8 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 0 atoms, new total = 906 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 = 8 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) = 5.834 | 5.834 | 5.834 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3169.746 0 -3169.746 14974.179 89 0 -3238.1138 0 -3238.1138 5083.373 Loop time of 9.3172 on 1 procs for 89 steps with 906 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 = -3169.74602458233 -3238.11118919604 -3238.11378772103 Force two-norm initial, final = 64.146948 0.10330137 Force max component initial, final = 11.446134 0.022468841 Final line search alpha, max atom move = 1.0000000 0.022468841 Iterations, force evaluations = 89 148 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.0826 | 9.0826 | 9.0826 | 0.0 | 97.48 Neigh | 0.17193 | 0.17193 | 0.17193 | 0.0 | 1.85 Comm | 0.040681 | 0.040681 | 0.040681 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02194 | | | 0.24 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11284.0 ave 11284 max 11284 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: 388832.0 ave 388832 max 388832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 388832 Ave neighs/atom = 429.17439 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 = 12.1025 ghost atom cutoff = 12.1025 binsize = 6.05125, bins = 8 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 : 89 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.827 | 5.827 | 5.827 Mbytes Step Temp E_pair E_mol TotEng Press Volume 89 0 -3238.1138 0 -3238.1138 5083.373 15367.998 97 0 -3238.3636 0 -3238.3636 64.546647 15452.004 Loop time of 0.612685 on 1 procs for 8 steps with 906 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 = -3238.113787721 -3238.36349304268 -3238.36364123007 Force two-norm initial, final = 92.451623 1.5084679 Force max component initial, final = 79.045478 1.2420171 Final line search alpha, max atom move = 0.00047199528 0.00058622619 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.60364 | 0.60364 | 0.60364 | 0.0 | 98.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0022879 | 0.0022879 | 0.0022879 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006755 | | | 1.10 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10807.0 ave 10807 max 10807 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: 388736.0 ave 388736 max 388736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 388736 Ave neighs/atom = 429.06843 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 = 8 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) = 5.965 | 5.965 | 5.965 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3238.3636 0 -3238.3636 64.546647 Loop time of 6.475e-06 on 1 procs for 0 steps with 906 atoms 185.3% 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 | | 6.475e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10780.0 ave 10780 max 10780 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: 387172.0 ave 387172 max 387172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 387172 Ave neighs/atom = 427.34216 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 = 8 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) = 5.965 | 5.965 | 5.965 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 -3238.3636 -3238.3636 43.354143 87.382036 4.0787967 64.546647 64.546647 128.67915 85.712292 -20.751504 2.5739038 176.49621 Loop time of 6.745e-06 on 1 procs for 0 steps with 906 atoms 311.3% 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 | | 6.745e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10780.0 ave 10780 max 10780 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 193586.0 ave 193586 max 193586 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 387172.0 ave 387172 max 387172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 387172 Ave neighs/atom = 427.34216 Neighbor list builds = 0 Dangerous builds = 0 906 -3238.36364123007 eV 2.57390375636371 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10