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 = 3.5483741 3.5483741 3.5483741 Created orthogonal box = (0.0000000 -53.579274 0.0000000) to (37.886268 53.579274 5.0181587) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9820423 5.1699299 5.0181587 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -53.579274 0.0000000) to (37.886268 53.579274 5.0181587) create_atoms CPU = 0.006 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9820423 5.1699299 5.0181587 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -53.579274 0.0000000) to (37.886268 53.579274 5.0181587) create_atoms CPU = 0.005 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 ghost atom cutoff = 8 binsize = 4, bins = 10 27 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1816 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_922363340570_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 ghost atom cutoff = 8 binsize = 4, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.992 | 5.992 | 5.992 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6785.5316 0 -6785.5316 69885.601 63 0 -7329.9575 0 -7329.9575 3708.5762 Loop time of 4.28584 on 1 procs for 63 steps with 1816 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 = -6785.53164648508 -7329.95107316428 -7329.95745546549 Force two-norm initial, final = 867.29355 0.33966389 Force max component initial, final = 170.61307 0.054994547 Final line search alpha, max atom move = 1.0000000 0.054994547 Iterations, force evaluations = 63 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0976 | 4.0976 | 4.0976 | 0.0 | 95.61 Neigh | 0.13579 | 0.13579 | 0.13579 | 0.0 | 3.17 Comm | 0.029044 | 0.029044 | 0.029044 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02343 | | | 0.55 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10114.0 ave 10114 max 10114 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: 357376.0 ave 357376 max 357376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 357376 Ave neighs/atom = 196.79295 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 ghost atom cutoff = 8 binsize = 4, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.987 | 5.987 | 5.987 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -7329.9575 0 -7329.9575 3708.5762 20372.909 70 0 -7330.504 0 -7330.504 -23.724242 20406.687 Loop time of 0.390389 on 1 procs for 7 steps with 1816 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 = -7329.95745546549 -7330.50399067152 -7330.50401720399 Force two-norm initial, final = 172.80551 0.97082138 Force max component initial, final = 162.53214 0.59931533 Final line search alpha, max atom move = 0.00073604680 0.00044112413 Iterations, force evaluations = 7 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38041 | 0.38041 | 0.38041 | 0.0 | 97.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021411 | 0.0021411 | 0.0021411 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007843 | | | 2.01 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10056.0 ave 10056 max 10056 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: 357456.0 ave 357456 max 357456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 357456 Ave neighs/atom = 196.83700 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 ghost atom cutoff = 8 binsize = 4, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.126 | 6.126 | 6.126 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7330.504 0 -7330.504 -23.724242 Loop time of 6.054e-06 on 1 procs for 0 steps with 1816 atoms 198.2% 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 | | 6.054e-06 | | |100.00 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10316.0 ave 10316 max 10316 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: 356928.0 ave 356928 max 356928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 356928 Ave neighs/atom = 196.54626 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 ghost atom cutoff = 8 binsize = 4, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 6.126 | 6.126 | 6.126 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 -7330.504 -7330.504 37.863664 107.78176 5.0003981 -23.724242 -23.724242 -47.025569 -20.600302 -3.5468555 2.3387545 670.11644 Loop time of 6.746e-06 on 1 procs for 0 steps with 1816 atoms 266.8% 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 | | 6.746e-06 | | |100.00 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10316.0 ave 10316 max 10316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 178464.0 ave 178464 max 178464 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 356928.0 ave 356928 max 356928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 356928 Ave neighs/atom = 196.54626 Neighbor list builds = 0 Dangerous builds = 0 1816 -7330.50401720399 eV 2.33875453249052 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06