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 = 2.8886457 2.8886457 2.8886457 Created orthogonal box = (0.0000000 -30.842296 0.0000000) to (21.808797 30.842296 4.0851619) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2087151 4.8698362 4.0851619 Created 228 atoms using lattice units in orthogonal box = (0.0000000 -30.842296 0.0000000) to (21.808797 30.842296 4.0851619) create_atoms CPU = 0.001 seconds 228 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2087151 4.8698362 4.0851619 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -30.842296 0.0000000) to (21.808797 30.842296 4.0851619) create_atoms CPU = 0.000 seconds 230 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 24 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 458 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_608695023236_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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.824 | 4.824 | 4.824 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1747.7597 0 -1747.7597 84741.349 43 0 -1899.0209 0 -1899.0209 15162.836 Loop time of 4.30491 on 1 procs for 43 steps with 458 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1747.75967192442 -1899.01911539486 -1899.02093179857 Force two-norm initial, final = 310.90545 0.19340098 Force max component initial, final = 103.73812 0.045723271 Final line search alpha, max atom move = 1.0000000 0.045723271 Iterations, force evaluations = 43 80 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.2958 | 4.2958 | 4.2958 | 0.0 | 99.79 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0046188 | 0.0046188 | 0.0046188 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004492 | | | 0.10 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2722.00 ave 2722 max 2722 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: 26496.0 ave 26496 max 26496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26496 Ave neighs/atom = 57.851528 Neighbor list builds = 0 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.824 | 4.824 | 4.824 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -1899.0209 0 -1899.0209 15162.836 5495.6323 55 0 -1899.6619 0 -1899.6619 -193.39732 5540.0283 Loop time of 0.911806 on 1 procs for 12 steps with 458 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 = -1899.02093179857 -1899.66153957145 -1899.66190453838 Force two-norm initial, final = 126.54638 1.6118124 Force max component initial, final = 124.05798 0.90602808 Final line search alpha, max atom move = 0.00069972436 0.00063396992 Iterations, force evaluations = 12 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.90784 | 0.90784 | 0.90784 | 0.0 | 99.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0006787 | 0.0006787 | 0.0006787 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003284 | | | 0.36 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2738.00 ave 2738 max 2738 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: 26296.0 ave 26296 max 26296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26296 Ave neighs/atom = 57.414847 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.962 | 4.962 | 4.962 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1899.6619 0 -1899.6619 -193.39732 Loop time of 3.247e-06 on 1 procs for 0 steps with 458 atoms 154.0% 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 | | 3.247e-06 | | |100.00 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2738.00 ave 2738 max 2738 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: 26256.0 ave 26256 max 26256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26256 Ave neighs/atom = 57.327511 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.962 | 4.962 | 4.962 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 -1899.6619 -1899.6619 21.777598 62.355087 4.0797178 -193.39732 -193.39732 -102.82643 -215.69136 -261.67419 2.2459451 397.50129 Loop time of 3.06e-06 on 1 procs for 0 steps with 458 atoms 130.7% 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 | | 3.06e-06 | | |100.00 Nlocal: 458.000 ave 458 max 458 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2738.00 ave 2738 max 2738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13128.0 ave 13128 max 13128 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26256.0 ave 26256 max 26256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26256 Ave neighs/atom = 57.327511 Neighbor list builds = 0 Dangerous builds = 0 458 -1899.66190453838 eV 2.24594508899955 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05