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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -69.695965 0.0000000) to (42.677732 69.695965 8.6222040) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9355201 4.9780318 5.7481360 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -69.695965 0.0000000) to (42.677732 69.695965 8.6222040) create_atoms CPU = 0.003 seconds 2357 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9355201 4.9780318 5.7481360 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -69.695965 0.0000000) to (42.677732 69.695965 8.6222040) create_atoms CPU = 0.003 seconds 2357 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 33 3 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 47 atoms, new total = 4667 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_103383163946_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 13.21 | 13.21 | 13.21 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20660.849 0 -20660.849 664.5892 24 0 -20704.679 0 -20704.679 -6475.7506 Loop time of 1.6724 on 1 procs for 24 steps with 4667 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 = -20660.849162074 -20704.6597072338 -20704.6787536747 Force two-norm initial, final = 59.346519 0.41606250 Force max component initial, final = 11.857079 0.018062446 Final line search alpha, max atom move = 1.0000000 0.018062446 Iterations, force evaluations = 24 38 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6561 | 1.6561 | 1.6561 | 0.0 | 99.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0064525 | 0.0064525 | 0.0064525 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009813 | | | 0.59 Nlocal: 4667.00 ave 4667 max 4667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16667.0 ave 16667 max 16667 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: 1.03995e+06 ave 1.03995e+06 max 1.03995e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1039948 Ave neighs/atom = 222.83008 Neighbor list builds = 0 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 24 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 13.21 | 13.21 | 13.21 Mbytes Step Temp E_pair E_mol TotEng Press Volume 24 0 -20704.679 0 -20704.679 -6475.7506 51292.9 26 0 -20704.908 0 -20704.908 -1756.3997 51156.464 Loop time of 0.175646 on 1 procs for 2 steps with 4667 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 = -20704.6787536744 -20704.8912937339 -20704.9082407407 Force two-norm initial, final = 244.00532 9.2939592 Force max component initial, final = 177.34634 7.6098382 Final line search alpha, max atom move = 1.8453626e-05 0.00014042911 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17248 | 0.17248 | 0.17248 | 0.0 | 98.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049119 | 0.00049119 | 0.00049119 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002673 | | | 1.52 Nlocal: 4667.00 ave 4667 max 4667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16714.0 ave 16714 max 16714 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: 1.04378e+06 ave 1.04378e+06 max 1.04378e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1043782 Ave neighs/atom = 223.65160 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 12.72 | 12.72 | 12.72 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20704.908 0 -20704.908 -1756.3997 Loop time of 2.088e-06 on 1 procs for 0 steps with 4667 atoms 191.6% 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 | | 2.088e-06 | | |100.00 Nlocal: 4667.00 ave 4667 max 4667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16716.0 ave 16716 max 16716 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: 1.04398e+06 ave 1.04398e+06 max 1.04398e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1043982 Ave neighs/atom = 223.69445 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 12.72 | 12.72 | 12.72 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 -20704.908 -20704.908 42.616854 139.39193 8.6115534 -1756.3997 -1756.3997 -166.27883 -5340.9596 238.03919 2.1867705 1706.5352 Loop time of 2.342e-06 on 1 procs for 0 steps with 4667 atoms 256.2% 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 | | 2.342e-06 | | |100.00 Nlocal: 4667.00 ave 4667 max 4667 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 16716.0 ave 16716 max 16716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 521991.0 ave 521991 max 521991 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.04398e+06 ave 1.04398e+06 max 1.04398e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1043982 Ave neighs/atom = 223.69445 Neighbor list builds = 0 Dangerous builds = 0 4667 -20577.8196871019 eV 2.1867705449958 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02