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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -43.551448 0.0000000) to (53.339413 43.551448 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1147382 5.3693566 5.8858683 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -43.551448 0.0000000) to (53.339413 43.551448 8.8288024) create_atoms CPU = 0.003 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1147382 5.3693566 5.8858683 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -43.551448 0.0000000) to (53.339413 43.551448 8.8288024) create_atoms CPU = 0.002 seconds 1756 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 18 29 3 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3506 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 18 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.677 | 5.677 | 5.677 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14266.306 0 -14266.306 56292.664 94 0 -14854.998 0 -14854.998 3765.8031 Loop time of 20.1439 on 1 procs for 94 steps with 3506 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 = -14266.3058633624 -14854.984693671 -14854.9978668411 Force two-norm initial, final = 762.58298 0.34332977 Force max component initial, final = 176.19082 0.050977902 Final line search alpha, max atom move = 1.0000000 0.050977902 Iterations, force evaluations = 94 157 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 19.994 | 19.994 | 19.994 | 0.0 | 99.25 Neigh | 0.09517 | 0.09517 | 0.09517 | 0.0 | 0.47 Comm | 0.020924 | 0.020924 | 0.020924 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03398 | | | 0.17 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8339.00 ave 8339 max 8339 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: 272918.0 ave 272918 max 272918 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272918 Ave neighs/atom = 77.843126 Neighbor list builds = 4 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 18 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 94 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.677 | 5.677 | 5.677 Mbytes Step Temp E_pair E_mol TotEng Press Volume 94 0 -14854.998 0 -14854.998 3765.8031 41018.769 98 0 -14855.345 0 -14855.345 -445.26 41125.06 Loop time of 0.724386 on 1 procs for 4 steps with 3506 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 = -14854.997866841 -14855.3317741873 -14855.3452503186 Force two-norm initial, final = 207.81008 21.121833 Force max component initial, final = 193.36362 17.033316 Final line search alpha, max atom move = 4.1532323e-05 0.00070743318 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.72089 | 0.72089 | 0.72089 | 0.0 | 99.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044524 | 0.00044524 | 0.00044524 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003051 | | | 0.42 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8339.00 ave 8339 max 8339 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: 272966.0 ave 272966 max 272966 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272966 Ave neighs/atom = 77.856817 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.815 | 5.815 | 5.815 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14855.345 0 -14855.345 -445.26 Loop time of 2.557e-06 on 1 procs for 0 steps with 3506 atoms 195.5% 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 | | 2.557e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8332.00 ave 8332 max 8332 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: 272828.0 ave 272828 max 272828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272828 Ave neighs/atom = 77.817456 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 18 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.815 | 5.815 | 5.815 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 -14855.345 -14855.345 53.365751 86.96454 8.8613873 -445.26 -445.26 -261.859 -662.5408 -411.38022 2.3198944 1614.0888 Loop time of 2.748e-06 on 1 procs for 0 steps with 3506 atoms 254.7% 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 | | 2.748e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8332.00 ave 8332 max 8332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 136414.0 ave 136414 max 136414 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 272828.0 ave 272828 max 272828 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 272828 Ave neighs/atom = 77.817456 Neighbor list builds = 0 Dangerous builds = 0 3506 -14855.3452503186 eV 2.31989443961177 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:21