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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -37.559378 0.0000000) to (26.556466 37.559378 4.0498230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9407378 4.8037402 4.0498230 Created 346 atoms using lattice units in orthogonal box = (0.0000000 -37.559378 0.0000000) to (26.556466 37.559378 4.0498230) create_atoms CPU = 0.003 seconds 346 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9407378 4.8037402 4.0498230 Created 346 atoms using lattice units in orthogonal box = (0.0000000 -37.559378 0.0000000) to (26.556466 37.559378 4.0498230) create_atoms CPU = 0.003 seconds 346 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 = 10 27 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 8 atoms, new total = 684 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 27 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) = 4.501 | 4.501 | 4.501 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2881.985 0 -2881.985 15337.677 31 0 -2921.9508 0 -2921.9508 -3992.3405 Loop time of 2.14983 on 1 procs for 31 steps with 684 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 = -2881.98501274936 -2921.94902676569 -2921.95077224915 Force two-norm initial, final = 68.579330 0.13803923 Force max component initial, final = 19.512762 0.024312864 Final line search alpha, max atom move = 1.0000000 0.024312864 Iterations, force evaluations = 31 54 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1402 | 2.1402 | 2.1402 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0043282 | 0.0043282 | 0.0043282 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005263 | | | 0.24 Nlocal: 684.000 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3254.00 ave 3254 max 3254 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: 39692.0 ave 39692 max 39692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39692 Ave neighs/atom = 58.029240 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 27 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 : 31 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.501 | 4.501 | 4.501 Mbytes Step Temp E_pair E_mol TotEng Press Volume 31 0 -2921.9508 0 -2921.9508 -3992.3405 8078.946 34 0 -2921.9792 0 -2921.9792 -1816.7947 8068.5964 Loop time of 0.199113 on 1 procs for 3 steps with 684 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 = -2921.95077224915 -2921.97897637587 -2921.97924837824 Force two-norm initial, final = 27.651458 0.66352851 Force max component initial, final = 27.590308 0.63727429 Final line search alpha, max atom move = 0.00031936466 0.00020352289 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19732 | 0.19732 | 0.19732 | 0.0 | 99.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035719 | 0.00035719 | 0.00035719 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001431 | | | 0.72 Nlocal: 684.000 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3275.00 ave 3275 max 3275 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: 39916.0 ave 39916 max 39916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39916 Ave neighs/atom = 58.356725 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 = 10 27 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) = 4.639 | 4.639 | 4.639 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2921.9792 0 -2921.9792 -1816.7947 Loop time of 6.305e-06 on 1 procs for 0 steps with 684 atoms 174.5% 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 | | 6.305e-06 | | |100.00 Nlocal: 684.000 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3275.00 ave 3275 max 3275 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: 39924.0 ave 39924 max 39924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39924 Ave neighs/atom = 58.368421 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 = 10 27 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) = 4.639 | 4.639 | 4.639 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 -2921.9792 -2921.9792 26.574714 75.118755 4.0418576 -1816.7947 -1816.7947 21.231461 -5345.3212 -126.29429 2.3011254 392.71314 Loop time of 6.755e-06 on 1 procs for 0 steps with 684 atoms 281.3% 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 | | 6.755e-06 | | |100.00 Nlocal: 684.000 ave 684 max 684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3275.00 ave 3275 max 3275 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19962.0 ave 19962 max 19962 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39924.0 ave 39924 max 39924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39924 Ave neighs/atom = 58.368421 Neighbor list builds = 0 Dangerous builds = 0 684 -2921.97924837824 eV 2.30112535570869 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02