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 = 3.5483741 3.5483741 3.5483741 Created orthogonal box = (0.0000000 -42.875167 0.0000000) to (52.511141 42.875167 8.6917059) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0353149 5.2859795 5.7944706 Created 1751 atoms using lattice units in orthogonal box = (0.0000000 -42.875167 0.0000000) to (52.511141 42.875167 8.6917059) create_atoms CPU = 0.002 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0353149 5.2859795 5.7944706 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -42.875167 0.0000000) to (52.511141 42.875167 8.6917059) create_atoms CPU = 0.002 seconds 1757 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 14 22 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 40 atoms, new total = 3468 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_922363340570_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 7.427 | 7.427 | 7.427 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12982.972 0 -12982.972 62150.721 86 0 -13990.193 0 -13990.193 2031.7796 Loop time of 4.89276 on 1 procs for 86 steps with 3468 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12982.9717235124 -13990.180913989 -13990.1926300919 Force two-norm initial, final = 1172.7335 0.34960829 Force max component initial, final = 225.85399 0.057985103 Final line search alpha, max atom move = 1.0000000 0.057985103 Iterations, force evaluations = 86 154 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.7306 | 4.7306 | 4.7306 | 0.0 | 96.68 Neigh | 0.11618 | 0.11618 | 0.11618 | 0.0 | 2.37 Comm | 0.019161 | 0.019161 | 0.019161 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02687 | | | 0.55 Nlocal: 3468.00 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11735.0 ave 11735 max 11735 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: 676092.0 ave 676092 max 676092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 676092 Ave neighs/atom = 194.95156 Neighbor list builds = 3 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 86 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.427 | 7.427 | 7.427 Mbytes Step Temp E_pair E_mol TotEng Press Volume 86 0 -13990.193 0 -13990.193 2031.7796 39137.43 89 0 -13990.311 0 -13990.311 -8.6887934 39167.379 Loop time of 0.199625 on 1 procs for 3 steps with 3468 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 = -13990.1926300919 -13990.3065065042 -13990.3108951723 Force two-norm initial, final = 139.04946 1.6472910 Force max component initial, final = 138.46706 1.3279445 Final line search alpha, max atom move = 2.4950358e-05 3.3132690e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19542 | 0.19542 | 0.19542 | 0.0 | 97.89 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00059866 | 0.00059866 | 0.00059866 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003605 | | | 1.81 Nlocal: 3468.00 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11712.0 ave 11712 max 11712 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: 676892.0 ave 676892 max 676892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 676892 Ave neighs/atom = 195.18224 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 7.565 | 7.565 | 7.565 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13990.311 0 -13990.311 -8.6887934 Loop time of 2.122e-06 on 1 procs for 0 steps with 3468 atoms 235.6% 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 | | 2.122e-06 | | |100.00 Nlocal: 3468.00 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11709.0 ave 11709 max 11709 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: 676712.0 ave 676712 max 676712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 676712 Ave neighs/atom = 195.13033 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 7.565 | 7.565 | 7.565 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 -13990.311 -13990.311 52.479718 85.717949 8.7068538 -8.6887934 -8.6887934 34.252747 -54.300235 -6.0188918 2.3051484 1682.4097 Loop time of 2.106e-06 on 1 procs for 0 steps with 3468 atoms 332.4% 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 | | 2.106e-06 | | |100.00 Nlocal: 3468.00 ave 3468 max 3468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11709.0 ave 11709 max 11709 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 338356.0 ave 338356 max 338356 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 676712.0 ave 676712 max 676712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 676712 Ave neighs/atom = 195.13033 Neighbor list builds = 0 Dangerous builds = 0 3468 -13990.3108951723 eV 2.305148419955 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05