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 = 3.5200135 3.5200135 3.5200135 Created orthogonal box = (0.0000000 -53.154558 0.0000000) to (37.583460 53.154558 4.9780508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9342305 5.1286090 4.9780508 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -53.154558 0.0000000) to (37.583460 53.154558 4.9780508) create_atoms CPU = 0.009 seconds 916 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9342305 5.1286090 4.9780508 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -53.154558 0.0000000) to (37.583460 53.154558 4.9780508) create_atoms CPU = 0.007 seconds 916 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 26 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1808 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_871937946490_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.387 | 6.387 | 6.387 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7993.3145 0 -7993.3145 1392.6173 47 0 -8021.758 0 -8021.758 -9681.3933 Loop time of 4.18877 on 1 procs for 47 steps with 1808 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 = -7993.31449372732 -8021.75172138816 -8021.75801453953 Force two-norm initial, final = 22.495540 0.25129412 Force max component initial, final = 3.8905300 0.019731722 Final line search alpha, max atom move = 1.0000000 0.019731722 Iterations, force evaluations = 47 88 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.1441 | 4.1441 | 4.1441 | 0.0 | 98.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.025251 | 0.025251 | 0.025251 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01943 | | | 0.46 Nlocal: 1808.00 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11094.0 ave 11094 max 11094 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: 402936.0 ave 402936 max 402936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 402936 Ave neighs/atom = 222.86283 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.387 | 6.387 | 6.387 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -8021.758 0 -8021.758 -9681.3933 19889.625 50 0 -8021.8864 0 -8021.8864 -4079.371 19826.289 Loop time of 0.302266 on 1 procs for 3 steps with 1808 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8021.7580145396 -8021.88626612084 -8021.88642447514 Force two-norm initial, final = 112.97588 0.27549980 Force max component initial, final = 84.645197 0.045931239 Final line search alpha, max atom move = 0.00042840764 1.9677294e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29498 | 0.29498 | 0.29498 | 0.0 | 97.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016502 | 0.0016502 | 0.0016502 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005633 | | | 1.86 Nlocal: 1808.00 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11114.0 ave 11114 max 11114 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: 405384.0 ave 405384 max 405384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 405384 Ave neighs/atom = 224.21681 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.525 | 6.525 | 6.525 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8021.8864 0 -8021.8864 -4079.371 Loop time of 5.973e-06 on 1 procs for 0 steps with 1808 atoms 217.6% 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 | | 5.973e-06 | | |100.00 Nlocal: 1808.00 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11114.0 ave 11114 max 11114 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: 405664.0 ave 405664 max 405664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 405664 Ave neighs/atom = 224.37168 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 6.525 | 6.525 | 6.525 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 -8021.8864 -8021.8864 37.531499 106.30912 4.9690688 -4079.371 -4079.371 -3.7066044 -12233.237 -1.1695222 2.3274496 568.48972 Loop time of 6.645e-06 on 1 procs for 0 steps with 1808 atoms 270.9% 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 | | 6.645e-06 | | |100.00 Nlocal: 1808.00 ave 1808 max 1808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11114.0 ave 11114 max 11114 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 202832.0 ave 202832 max 202832 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 405664.0 ave 405664 max 405664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 405664 Ave neighs/atom = 224.37168 Neighbor list builds = 0 Dangerous builds = 0 1808 -7972.59781010757 eV 2.3274496373935 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05