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 = 3.5200010 3.5200010 3.5200010 Created orthogonal box = (0.0000000 -69.692464 0.0000000) to (42.677744 69.692464 8.6222063) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9355214 4.9780331 5.7481376 Created 2351 atoms using lattice units in orthogonal box = (0.0000000 -69.692464 0.0000000) to (42.677744 69.692464 8.6222063) create_atoms CPU = 0.003 seconds 2351 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9355214 4.9780331 5.7481376 Created 2357 atoms using lattice units in orthogonal box = (0.0000000 -69.692464 0.0000000) to (42.677744 69.692464 8.6222063) create_atoms CPU = 0.003 seconds 2357 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 37 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 29 atoms, new total = 4679 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_469343973171_005#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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 37 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 12.31 | 12.31 | 12.31 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -19893.187 0 -19893.187 42543.403 112 0 -20762.075 0 -20762.075 -268.24686 Loop time of 8.11898 on 1 procs for 112 steps with 4679 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -19893.1866428972 -20762.0587442611 -20762.0754378612 Force two-norm initial, final = 1064.8258 0.56258948 Force max component initial, final = 193.32540 0.075858891 Final line search alpha, max atom move = 1.0000000 0.075858891 Iterations, force evaluations = 112 199 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.8418 | 7.8418 | 7.8418 | 0.0 | 96.59 Neigh | 0.19425 | 0.19425 | 0.19425 | 0.0 | 2.39 Comm | 0.033603 | 0.033603 | 0.033603 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04935 | | | 0.61 Nlocal: 4679.00 ave 4679 max 4679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14680.0 ave 14680 max 14680 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: 815668.0 ave 815668 max 815668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 815668 Ave neighs/atom = 174.32528 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 37 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 112 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.31 | 12.31 | 12.31 Mbytes Step Temp E_pair E_mol TotEng Press Volume 112 0 -20762.075 0 -20762.075 -268.24686 51290.352 114 0 -20762.151 0 -20762.151 -148.97652 51287.029 Loop time of 0.154717 on 1 procs for 2 steps with 4679 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 = -20762.0754378616 -20762.1476748126 -20762.1513135863 Force two-norm initial, final = 94.300353 13.194054 Force max component initial, final = 65.624065 12.700823 Final line search alpha, max atom move = 3.5875360e-05 0.00045564661 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15169 | 0.15169 | 0.15169 | 0.0 | 98.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00048657 | 0.00048657 | 0.00048657 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002544 | | | 1.64 Nlocal: 4679.00 ave 4679 max 4679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14667.0 ave 14667 max 14667 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: 815800.0 ave 815800 max 815800 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 815800 Ave neighs/atom = 174.35349 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 37 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 11.82 | 11.82 | 11.82 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20762.151 0 -20762.151 -148.97652 Loop time of 1.961e-06 on 1 procs for 0 steps with 4679 atoms 153.0% 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 | | 1.961e-06 | | |100.00 Nlocal: 4679.00 ave 4679 max 4679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14710.0 ave 14710 max 14710 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: 815750.0 ave 815750 max 815750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 815750 Ave neighs/atom = 174.34281 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 12 37 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 11.82 | 11.82 | 11.82 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 -20762.151 -20762.151 42.662516 139.55062 8.614485 -148.97652 -148.97652 -396.62464 48.383232 -98.688148 2.2387561 1677.8132 Loop time of 2.44e-06 on 1 procs for 0 steps with 4679 atoms 327.9% 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 | | 2.44e-06 | | |100.00 Nlocal: 4679.00 ave 4679 max 4679 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14710.0 ave 14710 max 14710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 407875.0 ave 407875 max 407875 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 815750.0 ave 815750 max 815750 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 815750 Ave neighs/atom = 174.34281 Neighbor list builds = 0 Dangerous builds = 0 4679 -20591.5913923381 eV 2.23875609960446 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09