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 = 3.5200135 3.5200135 3.5200135 Created orthogonal box = (0.0000000 -44.805978 0.0000000) to (10.560041 44.805978 4.9780508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8666892 4.9780508 4.9780508 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -44.805978 0.0000000) to (10.560041 44.805978 4.9780508) create_atoms CPU = 0.005 seconds 218 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8666892 4.9780508 4.9780508 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -44.805978 0.0000000) to (10.560041 44.805978 4.9780508) create_atoms CPU = 0.003 seconds 218 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 = 3 22 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 428 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_871937946490_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 = 3 22 2 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) = 4.541 | 4.541 | 4.541 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1887.9467 0 -1887.9467 2552.9296 42 0 -1897.1965 0 -1897.1965 -8983.8632 Loop time of 1.53512 on 1 procs for 42 steps with 428 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 = -1887.94669991121 -1897.19509985234 -1897.19646004528 Force two-norm initial, final = 12.757747 0.11901638 Force max component initial, final = 3.7870840 0.017065171 Final line search alpha, max atom move = 1.0000000 0.017065171 Iterations, force evaluations = 42 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5078 | 1.5078 | 1.5078 | 0.0 | 98.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.017147 | 0.017147 | 0.017147 | 0.0 | 1.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01012 | | | 0.66 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5557.00 ave 5557 max 5557 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: 95496.0 ave 95496 max 95496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95496 Ave neighs/atom = 223.12150 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 = 3 22 2 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 : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.540 | 4.540 | 4.540 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -1897.1965 0 -1897.1965 -8983.8632 4710.7588 45 0 -1897.2174 0 -1897.2174 -4345.9828 4698.2954 Loop time of 0.127163 on 1 procs for 3 steps with 428 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 = -1897.19646004527 -1897.21738246398 -1897.21741397256 Force two-norm initial, final = 22.032797 0.12807210 Force max component initial, final = 17.052346 0.026237254 Final line search alpha, max atom move = 0.0019120687 5.0167434e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1219 | 0.1219 | 0.1219 | 0.0 | 95.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001334 | 0.001334 | 0.001334 | 0.0 | 1.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003926 | | | 3.09 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5503.00 ave 5503 max 5503 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: 95936.0 ave 95936 max 95936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95936 Ave neighs/atom = 224.14953 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 = 3 22 2 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) = 4.678 | 4.678 | 4.678 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1897.2174 0 -1897.2174 -4345.9828 Loop time of 9.633e-06 on 1 procs for 0 steps with 428 atoms 145.3% 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 | | 9.633e-06 | | |100.00 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5503.00 ave 5503 max 5503 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: 95952.0 ave 95952 max 95952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95952 Ave neighs/atom = 224.18692 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 = 3 22 2 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) = 4.678 | 4.678 | 4.678 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 -1897.2174 -1897.2174 10.548672 89.611955 4.9702312 -4345.9828 -4345.9828 -8.9375938 -13031.155 2.1446519 2.3237774 169.71571 Loop time of 1.2569e-05 on 1 procs for 0 steps with 428 atoms 183.0% 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 | | 1.257e-05 | | |100.00 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5503.00 ave 5503 max 5503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47976.0 ave 47976 max 47976 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 95952.0 ave 95952 max 95952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95952 Ave neighs/atom = 224.18692 Neighbor list builds = 0 Dangerous builds = 0 428 -1885.54953402271 eV 2.32377735672813 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02