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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -39.354805 0.0000000) to (19.279838 39.354805 8.6222058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1412902 4.7225766 5.7481372 Created 600 atoms using lattice units in orthogonal box = (0.0000000 -39.354805 0.0000000) to (19.279838 39.354805 8.6222058) create_atoms CPU = 0.001 seconds 600 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1412902 4.7225766 5.7481372 Created 612 atoms using lattice units in orthogonal box = (0.0000000 -39.354805 0.0000000) to (19.279838 39.354805 8.6222058) create_atoms CPU = 0.001 seconds 612 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 21 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1188 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.465 | 5.465 | 5.465 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5214.0863 0 -5214.0863 3801.0788 32 0 -5253.9632 0 -5253.9632 -3646.9841 Loop time of 0.64246 on 1 procs for 32 steps with 1188 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 = -5214.08627134489 -5253.9590023175 -5253.96315929805 Force two-norm initial, final = 55.902335 0.29965248 Force max component initial, final = 11.470340 0.045521529 Final line search alpha, max atom move = 1.0000000 0.045521529 Iterations, force evaluations = 32 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.63564 | 0.63564 | 0.63564 | 0.0 | 98.94 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0032383 | 0.0032383 | 0.0032383 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003581 | | | 0.56 Nlocal: 1188.00 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6039.00 ave 6039 max 6039 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: 207552.0 ave 207552 max 207552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 207552 Ave neighs/atom = 174.70707 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.466 | 5.466 | 5.466 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -5253.9632 0 -5253.9632 -3646.9841 13084.271 35 0 -5254.0163 0 -5254.0163 -102.75709 13059.56 Loop time of 0.0625464 on 1 procs for 3 steps with 1188 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 = -5253.9631592981 -5254.01603398298 -5254.01630909236 Force two-norm initial, final = 58.625518 1.5461016 Force max component initial, final = 46.147328 1.1498374 Final line search alpha, max atom move = 0.00049126705 0.00056487722 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.060917 | 0.060917 | 0.060917 | 0.0 | 97.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028096 | 0.00028096 | 0.00028096 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001348 | | | 2.16 Nlocal: 1188.00 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6119.00 ave 6119 max 6119 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: 208368.0 ave 208368 max 208368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208368 Ave neighs/atom = 175.39394 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.604 | 5.604 | 5.604 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5254.0163 0 -5254.0163 -102.75709 Loop time of 1.9469e-05 on 1 procs for 0 steps with 1188 atoms 113.0% 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 | | 1.947e-05 | | |100.00 Nlocal: 1188.00 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6119.00 ave 6119 max 6119 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: 208536.0 ave 208536 max 208536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208536 Ave neighs/atom = 175.53535 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 5 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.604 | 5.604 | 5.604 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 -5254.0163 -5254.0163 19.257143 78.771942 8.6092465 -102.75709 -102.75709 -140.89861 -97.628534 -69.744126 2.2862249 757.05315 Loop time of 2.273e-06 on 1 procs for 0 steps with 1188 atoms 264.0% 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 | | 2.273e-06 | | |100.00 Nlocal: 1188.00 ave 1188 max 1188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6119.00 ave 6119 max 6119 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 104268.0 ave 104268 max 104268 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 208536.0 ave 208536 max 208536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208536 Ave neighs/atom = 175.53535 Neighbor list builds = 0 Dangerous builds = 0 1188 -5254.01630909236 eV 2.28622493085041 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01