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 = 3.6239511 3.6239511 3.6239511 Created orthogonal box = (0.0000000 -48.077144 0.0000000) to (16.997837 48.077144 5.1250408) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1810318 5.4633118 5.1250408 Created 350 atoms using lattice units in orthogonal box = (0.0000000 -48.077144 0.0000000) to (16.997837 48.077144 5.1250408) create_atoms CPU = 0.001 seconds 350 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1810318 5.4633118 5.1250408 Created 358 atoms using lattice units in orthogonal box = (0.0000000 -48.077144 0.0000000) to (16.997837 48.077144 5.1250408) create_atoms CPU = 0.001 seconds 358 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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 28 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 708 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_427873955970_001#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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.559 | 4.559 | 4.559 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2668.5225 0 -2668.5225 148729.06 588 0 -2993.9477 0 -2993.9477 5929.3881 Loop time of 56.8328 on 1 procs for 588 steps with 708 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 = -2668.5225498129 -2993.94504648692 -2993.94768994309 Force two-norm initial, final = 468.90320 0.17372739 Force max component initial, final = 69.626125 0.042216841 Final line search alpha, max atom move = 1.0000000 0.042216841 Iterations, force evaluations = 588 1111 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 56.63 | 56.63 | 56.63 | 0.0 | 99.64 Neigh | 0.10457 | 0.10457 | 0.10457 | 0.0 | 0.18 Comm | 0.056158 | 0.056158 | 0.056158 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04247 | | | 0.07 Nlocal: 708.000 ave 708 max 708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4803.00 ave 4803 max 4803 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: 87470.0 ave 87470 max 87470 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 87470 Ave neighs/atom = 123.54520 Neighbor list builds = 18 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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 588 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.559 | 4.559 | 4.559 Mbytes Step Temp E_pair E_mol TotEng Press Volume 588 0 -2993.9477 0 -2993.9477 5929.3881 8376.4433 616 0 -3001.0792 0 -3001.0792 31.033098 8394.8066 Loop time of 1.72979 on 1 procs for 28 steps with 708 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 = -2993.94768994309 -3001.07877655919 -3001.07920880575 Force two-norm initial, final = 387.75379 2.4588303 Force max component initial, final = 283.68800 1.7335538 Final line search alpha, max atom move = 0.0011143196 0.0019317330 Iterations, force evaluations = 28 30 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7113 | 1.7113 | 1.7113 | 0.0 | 98.93 Neigh | 0.011397 | 0.011397 | 0.011397 | 0.0 | 0.66 Comm | 0.0014455 | 0.0014455 | 0.0014455 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005673 | | | 0.33 Nlocal: 708.000 ave 708 max 708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4884.00 ave 4884 max 4884 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: 86524.0 ave 86524 max 86524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86524 Ave neighs/atom = 122.20904 Neighbor list builds = 2 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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.697 | 4.697 | 4.697 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3001.0792 0 -3001.0792 31.033098 Loop time of 1.889e-06 on 1 procs for 0 steps with 708 atoms 158.8% 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 | | 1.889e-06 | | |100.00 Nlocal: 708.000 ave 708 max 708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4904.00 ave 4904 max 4904 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: 86388.0 ave 86388 max 86388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86388 Ave neighs/atom = 122.01695 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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.697 | 4.697 | 4.697 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 -3001.0792 -3001.0792 17.034282 98.677236 4.9942456 31.033098 31.033098 331.56383 -67.676785 -170.78775 2.3214134 1858.8263 Loop time of 2.036e-06 on 1 procs for 0 steps with 708 atoms 245.6% 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 | | 2.036e-06 | | |100.00 Nlocal: 708.000 ave 708 max 708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4904.00 ave 4904 max 4904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 43194.0 ave 43194 max 43194 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 86388.0 ave 86388 max 86388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86388 Ave neighs/atom = 122.01695 Neighbor list builds = 0 Dangerous builds = 0 708 -3001.07920880575 eV 2.32141337947601 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:59