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 = 2.8603420 2.8603420 2.8603420 Created orthogonal box = (0.0000000 -50.523713 0.0000000) to (29.169879 50.523713 4.9542577) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4876737 4.5341794 4.9542577 Created 622 atoms using lattice units in orthogonal box = (0.0000000 -50.523713 0.0000000) to (29.169879 50.523713 4.9542577) create_atoms CPU = 0.002 seconds 622 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4876737 4.5341794 4.9542577 Created 626 atoms using lattice units in orthogonal box = (0.0000000 -50.523713 0.0000000) to (29.169879 50.523713 4.9542577) create_atoms CPU = 0.001 seconds 626 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 26 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1248 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.462 | 5.462 | 5.462 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4888.644 0 -4888.644 70041.613 211 0 -5455.0779 0 -5455.0779 -7023.0218 Loop time of 3.93499 on 1 procs for 211 steps with 1248 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 = -4888.64403045892 -5455.07302065681 -5455.07793544535 Force two-norm initial, final = 718.31011 0.30922772 Force max component initial, final = 151.06915 0.12067731 Final line search alpha, max atom move = 0.69393061 0.083741676 Iterations, force evaluations = 211 357 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.784 | 3.784 | 3.784 | 0.0 | 96.16 Neigh | 0.094568 | 0.094568 | 0.094568 | 0.0 | 2.40 Comm | 0.031257 | 0.031257 | 0.031257 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02515 | | | 0.64 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8105.00 ave 8105 max 8105 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: 201886.0 ave 201886 max 201886 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201886 Ave neighs/atom = 161.76763 Neighbor list builds = 7 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 211 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.462 | 5.462 | 5.462 Mbytes Step Temp E_pair E_mol TotEng Press Volume 211 0 -5455.0779 0 -5455.0779 -7023.0218 14602.879 237 0 -5459.0177 0 -5459.0177 239.9871 14514.193 Loop time of 0.344696 on 1 procs for 26 steps with 1248 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 = -5455.07793544536 -5459.01356945688 -5459.01771404527 Force two-norm initial, final = 371.66677 5.2711455 Force max component initial, final = 335.41634 4.3541298 Final line search alpha, max atom move = 6.8551932e-05 0.00029848401 Iterations, force evaluations = 26 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30785 | 0.30785 | 0.30785 | 0.0 | 89.31 Neigh | 0.025411 | 0.025411 | 0.025411 | 0.0 | 7.37 Comm | 0.0022247 | 0.0022247 | 0.0022247 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009215 | | | 2.67 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8116.00 ave 8116 max 8116 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: 201588.0 ave 201588 max 201588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 201588 Ave neighs/atom = 161.52885 Neighbor list builds = 2 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.600 | 5.600 | 5.600 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5459.0177 0 -5459.0177 239.9871 Loop time of 2.368e-06 on 1 procs for 0 steps with 1248 atoms 168.9% 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 | | 2.368e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8109.00 ave 8109 max 8109 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: 200970.0 ave 200970 max 200970 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200970 Ave neighs/atom = 161.03365 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.600 | 5.600 | 5.600 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 -5459.0177 -5459.0177 29.292753 99.070144 5.0013807 239.9871 239.9871 482.66343 144.6615 92.63638 2.2999932 6809.9563 Loop time of 2.393e-06 on 1 procs for 0 steps with 1248 atoms 208.9% 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 | | 2.393e-06 | | |100.00 Nlocal: 1248.00 ave 1248 max 1248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8109.00 ave 8109 max 8109 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 100485.0 ave 100485 max 100485 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 200970.0 ave 200970 max 200970 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 200970 Ave neighs/atom = 161.03365 Neighbor list builds = 0 Dangerous builds = 0 1248 -5459.01771404527 eV 2.29999320292446 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04