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 = 2.8700001 2.8700001 2.8700001 Created orthogonal box = (0.0000000 -29.825916 0.0000000) to (21.090107 29.825916 4.0587930) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6866905 3.8663224 4.0587930 Created 216 atoms using lattice units in orthogonal box = (0.0000000 -29.825916 0.0000000) to (21.090107 29.825916 4.0587930) create_atoms CPU = 0.001 seconds 216 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6866905 3.8663224 4.0587930 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -29.825916 0.0000000) to (21.090107 29.825916 4.0587930) create_atoms CPU = 0.000 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 20 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.449 | 4.449 | 4.449 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1715.8378 0 -1715.8378 27780.532 53 0 -1816.9684 0 -1816.9684 898.46695 Loop time of 0.147873 on 1 procs for 53 steps with 428 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1715.83779286884 -1816.96682034857 -1816.9683580729 Force two-norm initial, final = 152.05600 0.12742662 Force max component initial, final = 50.275748 0.023780009 Final line search alpha, max atom move = 1.0000000 0.023780009 Iterations, force evaluations = 53 90 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13961 | 0.13961 | 0.13961 | 0.0 | 94.41 Neigh | 0.0028067 | 0.0028067 | 0.0028067 | 0.0 | 1.90 Comm | 0.0029538 | 0.0029538 | 0.0029538 | 0.0 | 2.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002507 | | | 1.70 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3253.00 ave 3253 max 3253 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: 28312.0 ave 28312 max 28312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28312 Ave neighs/atom = 66.149533 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.449 | 4.449 | 4.449 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -1816.9684 0 -1816.9684 898.46695 5106.2195 58 0 -1817.0287 0 -1817.0287 31.082542 5109.2506 Loop time of 0.0110253 on 1 procs for 5 steps with 428 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1816.96835807291 -1817.02748791403 -1817.02872374468 Force two-norm initial, final = 22.411672 0.29518957 Force max component initial, final = 20.429991 0.13099147 Final line search alpha, max atom move = 0.00039553419 5.1811604e-05 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.010144 | 0.010144 | 0.010144 | 0.0 | 92.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016371 | 0.00016371 | 0.00016371 | 0.0 | 1.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007172 | | | 6.51 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3208.00 ave 3208 max 3208 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: 28024.0 ave 28024 max 28024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28024 Ave neighs/atom = 65.476636 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.587 | 4.587 | 4.587 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1817.0287 0 -1817.0287 31.082542 Loop time of 1.657e-06 on 1 procs for 0 steps with 428 atoms 120.7% 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 | | 1.657e-06 | | |100.00 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3208.00 ave 3208 max 3208 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: 28024.0 ave 28024 max 28024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28024 Ave neighs/atom = 65.476636 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 7 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.587 | 4.587 | 4.587 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 -1817.0287 -1817.0287 21.057431 59.929054 4.0486888 31.082542 31.082542 41.013115 25.811626 26.422884 2.3113776 365.99547 Loop time of 1.578e-06 on 1 procs for 0 steps with 428 atoms 126.7% 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 | | 1.578e-06 | | |100.00 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3208.00 ave 3208 max 3208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 14012.0 ave 14012 max 14012 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 28024.0 ave 28024 max 28024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 28024 Ave neighs/atom = 65.476636 Neighbor list builds = 0 Dangerous builds = 0 428 -1817.02868094468 eV 2.31137758341236 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00