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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -53.865396 0.0000000) to (38.088587 53.865396 5.0449566) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0139874 6.1425452 5.0449566 Created 912 atoms using lattice units in orthogonal box = (0.0000000 -53.865396 0.0000000) to (38.088587 53.865396 5.0449566) create_atoms CPU = 0.003 seconds 912 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0139874 6.1425452 5.0449566 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -53.865396 0.0000000) to (38.088587 53.865396 5.0449566) create_atoms CPU = 0.002 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 14 39 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1812 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_058735400462_001#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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 14 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.143 | 5.143 | 5.143 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7382.7214 0 -7382.7214 27128.446 134 0 -7651.6425 0 -7651.6425 38809.2 Loop time of 13.2966 on 1 procs for 134 steps with 1812 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7382.7214393317 -7651.63670016076 -7651.6425294299 Force two-norm initial, final = 370.97574 0.29857400 Force max component initial, final = 89.411673 0.027308887 Final line search alpha, max atom move = 1.0000000 0.027308887 Iterations, force evaluations = 134 255 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.242 | 13.242 | 13.242 | 0.0 | 99.59 Neigh | 0.0093103 | 0.0093103 | 0.0093103 | 0.0 | 0.07 Comm | 0.020815 | 0.020815 | 0.020815 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02425 | | | 0.18 Nlocal: 1812.00 ave 1812 max 1812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6633.00 ave 6633 max 6633 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: 105808.0 ave 105808 max 105808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 105808 Ave neighs/atom = 58.392936 Neighbor list builds = 1 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 14 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 134 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.144 | 5.144 | 5.144 Mbytes Step Temp E_pair E_mol TotEng Press Volume 134 0 -7651.6425 0 -7651.6425 38809.2 20701.039 144 0 -7655.2026 0 -7655.2026 0.53800452 20957.815 Loop time of 0.663647 on 1 procs for 10 steps with 1812 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 = -7651.6425294299 -7655.19772750652 -7655.20258519438 Force two-norm initial, final = 882.11056 2.6663669 Force max component initial, final = 608.63504 0.18290594 Final line search alpha, max atom move = 3.3468708e-05 6.1216255e-06 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.65811 | 0.65811 | 0.65811 | 0.0 | 99.17 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00074081 | 0.00074081 | 0.00074081 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004798 | | | 0.72 Nlocal: 1812.00 ave 1812 max 1812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6638.00 ave 6638 max 6638 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: 107888.0 ave 107888 max 107888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107888 Ave neighs/atom = 59.540839 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 14 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.281 | 5.281 | 5.281 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7655.2026 0 -7655.2026 0.53800452 Loop time of 2.34e-06 on 1 procs for 0 steps with 1812 atoms 170.9% 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 | | 2.34e-06 | | |100.00 Nlocal: 1812.00 ave 1812 max 1812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6619.00 ave 6619 max 6619 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: 104296.0 ave 104296 max 104296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104296 Ave neighs/atom = 57.558499 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 14 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.281 | 5.281 | 5.281 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 -7655.2026 -7655.2026 38.433542 107.72728 5.0618574 0.53800452 0.53800452 -14.109373 13.534208 2.1891788 2.3757675 969.48177 Loop time of 2.397e-06 on 1 procs for 0 steps with 1812 atoms 250.3% 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 | | 2.397e-06 | | |100.00 Nlocal: 1812.00 ave 1812 max 1812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6619.00 ave 6619 max 6619 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52148.0 ave 52148 max 52148 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 104296.0 ave 104296 max 104296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104296 Ave neighs/atom = 57.558499 Neighbor list builds = 0 Dangerous builds = 0 1812 -7655.20258519438 eV 2.37576752819465 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14