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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -70.071619 0.0000000) to (28.604967 70.071619 9.9090513) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8651921 6.0725230 6.6060342 Created 1206 atoms using lattice units in orthogonal box = (0.0000000 -70.071619 0.0000000) to (28.604967 70.071619 9.9090513) create_atoms CPU = 0.002 seconds 1206 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8651921 6.0725230 6.6060342 Created 1206 atoms using lattice units in orthogonal box = (0.0000000 -70.071619 0.0000000) to (28.604967 70.071619 9.9090513) create_atoms CPU = 0.002 seconds 1206 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 10 45 4 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 2384 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 10 45 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.121 | 5.121 | 5.121 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7976.1755 0 -7976.1755 361.77361 26 0 -7993.2974 0 -7993.2974 -3142.2861 Loop time of 2.79539 on 1 procs for 26 steps with 2384 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 = -7976.17550680822 -7993.29155484433 -7993.29738655375 Force two-norm initial, final = 15.804679 0.17365760 Force max component initial, final = 2.3894044 0.013392345 Final line search alpha, max atom move = 1.0000000 0.013392345 Iterations, force evaluations = 26 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7749 | 2.7749 | 2.7749 | 0.0 | 99.27 Neigh | 0.012034 | 0.012034 | 0.012034 | 0.0 | 0.43 Comm | 0.0031131 | 0.0031131 | 0.0031131 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005301 | | | 0.19 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5965.00 ave 5965 max 5965 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: 129392.0 ave 129392 max 129392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129392 Ave neighs/atom = 54.275168 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 10 45 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.126 | 5.126 | 5.126 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -7993.2974 0 -7993.2974 -3142.2861 39723.332 30 0 -7993.434 0 -7993.434 -720.32948 39591.027 Loop time of 0.472969 on 1 procs for 4 steps with 2384 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 = -7993.29738655375 -7993.43196331905 -7993.4339909045 Force two-norm initial, final = 98.718899 0.18068516 Force max component initial, final = 85.569521 0.026418470 Final line search alpha, max atom move = 8.7996093e-05 2.3247222e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.47013 | 0.47013 | 0.47013 | 0.0 | 99.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034727 | 0.00034727 | 0.00034727 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002497 | | | 0.53 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5970.00 ave 5970 max 5970 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: 129496.0 ave 129496 max 129496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129496 Ave neighs/atom = 54.318792 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 10 45 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.264 | 5.264 | 5.264 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7993.434 0 -7993.434 -720.32948 Loop time of 1.863e-06 on 1 procs for 0 steps with 2384 atoms 161.0% 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 | | 1.863e-06 | | |100.00 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5970.00 ave 5970 max 5970 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: 129500.0 ave 129500 max 129500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129500 Ave neighs/atom = 54.320470 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 10 45 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.264 | 5.264 | 5.264 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 -7993.434 -7993.434 28.594576 140.14324 9.8796364 -720.32948 -720.32948 -1.0687188 -2159.3608 -0.55888691 2.5851159 672.37646 Loop time of 2.047e-06 on 1 procs for 0 steps with 2384 atoms 195.4% 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 | | 2.047e-06 | | |100.00 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5970.00 ave 5970 max 5970 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 64750.0 ave 64750 max 64750 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 129500.0 ave 129500 max 129500 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129500 Ave neighs/atom = 54.320470 Neighbor list builds = 0 Dangerous builds = 0 2384 -7993.4339909045 eV 2.58511592637774 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03