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 = 2.4599767 2.4599767 2.4599767 Created orthogonal box = (0.0000000 -33.819088 0.0000000) to (9.2043899 33.819088 6.0256877) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9447385 3.7576765 4.0171251 Created 252 atoms using lattice units in orthogonal box = (0.0000000 -33.819088 0.0000000) to (9.2043899 33.819088 6.0256877) create_atoms CPU = 0.001 seconds 252 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9447385 3.7576765 4.0171251 Created 254 atoms using lattice units in orthogonal box = (0.0000000 -33.819088 0.0000000) to (9.2043899 33.819088 6.0256877) create_atoms CPU = 0.001 seconds 254 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 3 18 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 7.5466 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 504 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_677328661525_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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 3 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 4.963 | 4.963 | 4.963 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5906.4263 0 -5906.4263 380136.17 61 0 -6357.2572 0 -6357.2572 66526.251 Loop time of 7.17499 on 1 procs for 61 steps with 504 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 = -5906.42634008819 -6357.25119342101 -6357.25719246197 Force two-norm initial, final = 1406.7483 0.71248210 Force max component initial, final = 486.82429 0.11746510 Final line search alpha, max atom move = 0.37806743 0.044409728 Iterations, force evaluations = 61 117 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.1487 | 7.1487 | 7.1487 | 0.0 | 99.63 Neigh | 0.0082027 | 0.0082027 | 0.0082027 | 0.0 | 0.11 Comm | 0.01098 | 0.01098 | 0.01098 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00706 | | | 0.10 Nlocal: 504.000 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5179.00 ave 5179 max 5179 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: 128192.0 ave 128192 max 128192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128192 Ave neighs/atom = 254.34921 Neighbor list builds = 1 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 3 18 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.963 | 4.963 | 4.963 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -6357.2572 0 -6357.2572 66526.251 3751.4012 67 0 -6358.0846 0 -6358.0846 1009.5774 3785.0011 Loop time of 0.609434 on 1 procs for 6 steps with 504 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 = -6357.25719246196 -6358.08042027289 -6358.08464724312 Force two-norm initial, final = 280.12785 5.1490775 Force max component initial, final = 201.29390 4.8007120 Final line search alpha, max atom move = 6.8873835e-05 0.00033064345 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.60578 | 0.60578 | 0.60578 | 0.0 | 99.40 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069099 | 0.00069099 | 0.00069099 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002967 | | | 0.49 Nlocal: 504.000 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5176.00 ave 5176 max 5176 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: 128284.0 ave 128284 max 128284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128284 Ave neighs/atom = 254.53175 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 3 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 5.101 | 5.101 | 5.101 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6358.0846 0 -6358.0846 1009.5774 Loop time of 4.064e-06 on 1 procs for 0 steps with 504 atoms 172.2% 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 | | 4.064e-06 | | |100.00 Nlocal: 504.000 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5176.00 ave 5176 max 5176 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: 127956.0 ave 127956 max 127956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127956 Ave neighs/atom = 253.88095 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 = 7.5466 ghost atom cutoff = 7.5466 binsize = 3.7733, bins = 3 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.5466 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) = 5.101 | 5.101 | 5.101 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 -6358.0846 -6358.0846 9.2346051 67.987836 6.0285999 1009.5774 1009.5774 444.19428 2042.6282 541.90971 2.0109732 374.35233 Loop time of 4.133e-06 on 1 procs for 0 steps with 504 atoms 193.6% 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 | | 4.133e-06 | | |100.00 Nlocal: 504.000 ave 504 max 504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5176.00 ave 5176 max 5176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63978.0 ave 63978 max 63978 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 127956.0 ave 127956 max 127956 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127956 Ave neighs/atom = 253.88095 Neighbor list builds = 0 Dangerous builds = 0 504 -6358.08464724312 eV 2.01097315365219 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08