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 = 3.5240105 3.5240105 3.5240105 Created orthogonal box = (0.0000000 -63.822545 0.0000000) to (22.564677 63.822545 4.9837035) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0539378 5.4482660 4.9837035 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -63.822545 0.0000000) to (22.564677 63.822545 4.9837035) create_atoms CPU = 0.005 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0539378 5.4482660 4.9837035 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -63.822545 0.0000000) to (22.564677 63.822545 4.9837035) create_atoms CPU = 0.005 seconds 658 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 6 34 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1312 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_535504325462_003#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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 6 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.511 | 5.511 | 5.511 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5855.5878 0 -5855.5878 10103.026 46 0 -5930.068 0 -5930.068 5892.9572 Loop time of 1.96111 on 1 procs for 46 steps with 1312 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 = -5855.58780067945 -5930.06295037062 -5930.06800152882 Force two-norm initial, final = 49.759902 0.24978124 Force max component initial, final = 11.760119 0.016834502 Final line search alpha, max atom move = 1.0000000 0.016834502 Iterations, force evaluations = 46 71 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8694 | 1.8694 | 1.8694 | 0.0 | 95.32 Neigh | 0.062406 | 0.062406 | 0.062406 | 0.0 | 3.18 Comm | 0.01601 | 0.01601 | 0.01601 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01331 | | | 0.68 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8576.00 ave 8576 max 8576 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: 229624.0 ave 229624 max 229624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229624 Ave neighs/atom = 175.01829 Neighbor list builds = 2 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 6 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.511 | 5.511 | 5.511 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -5930.068 0 -5930.068 5892.9572 14354.413 50 0 -5930.1994 0 -5930.1994 -14.229053 14401.169 Loop time of 0.208958 on 1 procs for 4 steps with 1312 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 = -5930.06800152881 -5930.19856078514 -5930.19940631856 Force two-norm initial, final = 99.643903 1.1063374 Force max component initial, final = 78.312070 0.98366703 Final line search alpha, max atom move = 0.00011307151 0.00011122471 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20171 | 0.20171 | 0.20171 | 0.0 | 96.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015341 | 0.0015341 | 0.0015341 | 0.0 | 0.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00571 | | | 2.73 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8576.00 ave 8576 max 8576 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: 229236.0 ave 229236 max 229236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229236 Ave neighs/atom = 174.72256 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 6 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.649 | 5.649 | 5.649 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5930.1994 0 -5930.1994 -14.229053 Loop time of 6.525e-06 on 1 procs for 0 steps with 1312 atoms 183.9% 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 | | 6.525e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8576.00 ave 8576 max 8576 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: 229048.0 ave 229048 max 229048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229048 Ave neighs/atom = 174.57927 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 6 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.649 | 5.649 | 5.649 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 -5930.1994 -5930.1994 22.590936 127.99007 4.9806639 -14.229053 -14.229053 -109.56348 25.167832 41.708493 2.3049242 386.79405 Loop time of 6.695e-06 on 1 procs for 0 steps with 1312 atoms 268.9% 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 | | 6.695e-06 | | |100.00 Nlocal: 1312.00 ave 1312 max 1312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8576.00 ave 8576 max 8576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 114524.0 ave 114524 max 114524 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 229048.0 ave 229048 max 229048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 229048 Ave neighs/atom = 174.57927 Neighbor list builds = 0 Dangerous builds = 0 1312 -5930.19940631856 eV 2.30492418725937 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02