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 = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -69.159024 0.0000000) to (39.928981 69.159024 6.2613638) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8911611 5.2908543 6.2613638 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -69.159024 0.0000000) to (39.928981 69.159024 6.2613638) create_atoms CPU = 0.003 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8911611 5.2908543 6.2613638 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -69.159024 0.0000000) to (39.928981 69.159024 6.2613638) create_atoms CPU = 0.002 seconds 1466 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 11 37 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 7.506786 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 2924 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_346334655118_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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 6.601 | 6.601 | 6.601 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9918.7214 0 -9918.7214 39181.771 92 0 -10323.984 0 -10323.984 1966.2059 Loop time of 3.44113 on 1 procs for 92 steps with 2924 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 = -9918.72136907573 -10323.9739079204 -10323.9840716958 Force two-norm initial, final = 717.18204 0.34193816 Force max component initial, final = 159.20866 0.058988141 Final line search alpha, max atom move = 1.0000000 0.058988141 Iterations, force evaluations = 92 167 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3045 | 3.3045 | 3.3045 | 0.0 | 96.03 Neigh | 0.079463 | 0.079463 | 0.079463 | 0.0 | 2.31 Comm | 0.028701 | 0.028701 | 0.028701 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02842 | | | 0.83 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11892.0 ave 11892 max 11892 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: 411620.0 ave 411620 max 411620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 411620 Ave neighs/atom = 140.77291 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 92 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.601 | 6.601 | 6.601 Mbytes Step Temp E_pair E_mol TotEng Press Volume 92 0 -10323.984 0 -10323.984 1966.2059 34580.878 94 0 -10324.02 0 -10324.02 -0.57142959 34629.903 Loop time of 0.107425 on 1 procs for 2 steps with 2924 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 = -10323.9840716959 -10324.0170565979 -10324.0200661043 Force two-norm initial, final = 75.541500 0.54158744 Force max component initial, final = 55.517134 0.33019519 Final line search alpha, max atom move = 0.00011079221 3.6583055e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10409 | 0.10409 | 0.10409 | 0.0 | 96.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053283 | 0.00053283 | 0.00053283 | 0.0 | 0.50 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002799 | | | 2.61 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11913.0 ave 11913 max 11913 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: 411568.0 ave 411568 max 411568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 411568 Ave neighs/atom = 140.75513 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 6.739 | 6.739 | 6.739 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10324.02 0 -10324.02 -0.57142959 Loop time of 2.715e-06 on 1 procs for 0 steps with 2924 atoms 184.2% 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 | | 2.715e-06 | | |100.00 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11904.0 ave 11904 max 11904 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: 411448.0 ave 411448 max 411448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 411448 Ave neighs/atom = 140.71409 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 = 7.506786 ghost atom cutoff = 7.506786 binsize = 3.753393, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.506786 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) = 6.739 | 6.739 | 6.739 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 -10324.02 -10324.02 39.929837 138.45431 6.2639352 -0.57142959 -0.57142959 -8.8019468 -8.1953255 15.282984 2.3335178 948.60746 Loop time of 2.694e-06 on 1 procs for 0 steps with 2924 atoms 259.8% 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 | | 2.694e-06 | | |100.00 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11904.0 ave 11904 max 11904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 205724.0 ave 205724 max 205724 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 411448.0 ave 411448 max 411448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 411448 Ave neighs/atom = 140.71409 Neighbor list builds = 0 Dangerous builds = 0 2924 -10324.0194786472 eV 2.33351776957591 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04