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 = 3.4301372 3.4301372 3.4301372 Created orthogonal box = (0.0000000 -59.017742 0.0000000) to (29.507156 59.017742 3.4301372) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7849442 4.7849442 3.4301372 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -59.017742 0.0000000) to (29.507156 59.017742 3.4301372) create_atoms CPU = 0.001 seconds 594 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7849442 4.7849442 3.4301372 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -59.017742 0.0000000) to (29.507156 59.017742 3.4301372) create_atoms CPU = 0.001 seconds 594 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 = 8 30 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1172 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_044341472608_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 = 8 30 1 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) = 5.481 | 5.481 | 5.481 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4653.763 0 -4653.763 2353.5724 54 0 -4669.2368 0 -4669.2368 5285.5739 Loop time of 1.27694 on 1 procs for 54 steps with 1172 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 = -4653.7630107596 -4669.23248547614 -4669.236820166 Force two-norm initial, final = 23.086224 0.23455888 Force max component initial, final = 7.1202566 0.045630831 Final line search alpha, max atom move = 1.0000000 0.045630831 Iterations, force evaluations = 54 100 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2601 | 1.2601 | 1.2601 | 0.0 | 98.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0097222 | 0.0097222 | 0.0097222 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007094 | | | 0.56 Nlocal: 1172.00 ave 1172 max 1172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10147.0 ave 10147 max 10147 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: 232816.0 ave 232816 max 232816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 232816 Ave neighs/atom = 198.64846 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 ghost atom cutoff = 8 binsize = 4, bins = 8 30 1 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 : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.481 | 5.481 | 5.481 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -4669.2368 0 -4669.2368 5285.5739 11946.796 56 0 -4669.2487 0 -4669.2487 1835.0906 11956.208 Loop time of 0.0687287 on 1 procs for 2 steps with 1172 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 = -4669.23682016606 -4669.24869002667 -4669.24874915278 Force two-norm initial, final = 42.655587 0.23964465 Force max component initial, final = 31.345066 0.044368028 Final line search alpha, max atom move = 0.00074797081 3.3185990e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.066625 | 0.066625 | 0.066625 | 0.0 | 96.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00043509 | 0.00043509 | 0.00043509 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001668 | | | 2.43 Nlocal: 1172.00 ave 1172 max 1172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10093.0 ave 10093 max 10093 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: 233300.0 ave 233300 max 233300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 233300 Ave neighs/atom = 199.06143 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 = 8 30 1 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) = 5.619 | 5.619 | 5.619 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4669.2487 0 -4669.2487 1835.0906 Loop time of 2.228e-06 on 1 procs for 0 steps with 1172 atoms 179.5% 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 | | 2.228e-06 | | |100.00 Nlocal: 1172.00 ave 1172 max 1172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10093.0 ave 10093 max 10093 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: 233260.0 ave 233260 max 233260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 233260 Ave neighs/atom = 199.02730 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 = 8 30 1 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) = 5.619 | 5.619 | 5.619 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 -4669.2487 -4669.2487 29.517026 118.03548 3.4316917 1835.0906 1835.0906 -2.7142958 5513.9126 -5.9266725 2.2525243 430.60029 Loop time of 2.662e-06 on 1 procs for 0 steps with 1172 atoms 263.0% 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 | | 2.662e-06 | | |100.00 Nlocal: 1172.00 ave 1172 max 1172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10093.0 ave 10093 max 10093 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 116630.0 ave 116630 max 116630 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 233260.0 ave 233260 max 233260 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 233260 Ave neighs/atom = 199.02730 Neighbor list builds = 0 Dangerous builds = 0 1172 -4669.2487491528 eV 2.25252429803867 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01