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 = 3.6133157 3.6133157 3.6133157 Created orthogonal box = (0.0000000 -38.583267 0.0000000) to (27.279935 38.583267 5.1100000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2645489 6.0915243 5.1100000 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.583267 0.0000000) to (27.279935 38.583267 5.1100000) create_atoms CPU = 0.003 seconds 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2645489 6.0915243 5.1100000 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.583267 0.0000000) to (27.279935 38.583267 5.1100000) create_atoms CPU = 0.003 seconds 458 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, 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, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 900 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_353393547686_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.577 | 4.577 | 4.577 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3147.2465 0 -3147.2465 5077.2064 60 0 -3169.9811 0 -3169.9811 -8474.4327 Loop time of 6.1571 on 1 procs for 60 steps with 900 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 = -3147.24649274341 -3169.97837711514 -3169.98112283936 Force two-norm initial, final = 36.884445 0.15669299 Force max component initial, final = 12.356619 0.042601521 Final line search alpha, max atom move = 1.0000000 0.042601521 Iterations, force evaluations = 60 105 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.1187 | 6.1187 | 6.1187 | 0.0 | 99.38 Neigh | 0.013818 | 0.013818 | 0.013818 | 0.0 | 0.22 Comm | 0.012101 | 0.012101 | 0.012101 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01252 | | | 0.20 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4525.00 ave 4525 max 4525 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: 77400.0 ave 77400 max 77400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77400 Ave neighs/atom = 86.000000 Neighbor list builds = 1 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 60 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.577 | 4.577 | 4.577 Mbytes Step Temp E_pair E_mol TotEng Press Volume 60 0 -3169.9811 0 -3169.9811 -8474.4327 10757.051 65 0 -3170.1004 0 -3170.1004 -2383.6117 10709.559 Loop time of 0.466479 on 1 procs for 5 steps with 900 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3169.98112283937 -3170.10008801125 -3170.10037453087 Force two-norm initial, final = 68.144012 0.20124265 Force max component initial, final = 56.172329 0.040392922 Final line search alpha, max atom move = 0.00027451264 1.1088368e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.46256 | 0.46256 | 0.46256 | 0.0 | 99.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000798 | 0.000798 | 0.000798 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003125 | | | 0.67 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4539.00 ave 4539 max 4539 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: 77396.0 ave 77396 max 77396 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77396 Ave neighs/atom = 85.995556 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.715 | 4.715 | 4.715 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3170.1004 0 -3170.1004 -2383.6117 Loop time of 6.174e-06 on 1 procs for 0 steps with 900 atoms 194.4% 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 | | 6.174e-06 | | |100.00 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4539.00 ave 4539 max 4539 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: 77424.0 ave 77424 max 77424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77424 Ave neighs/atom = 86.026667 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.715 | 4.715 | 4.715 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 -3170.1004 -3170.1004 27.176334 77.166535 5.1068339 -2383.6117 -2383.6117 0.97343808 -7148.2772 -3.531418 2.3546654 686.11171 Loop time of 6.424e-06 on 1 procs for 0 steps with 900 atoms 280.2% 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 | | 6.424e-06 | | |100.00 Nlocal: 900.000 ave 900 max 900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4539.00 ave 4539 max 4539 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 38712.0 ave 38712 max 38712 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 77424.0 ave 77424 max 77424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 77424 Ave neighs/atom = 86.026667 Neighbor list builds = 0 Dangerous builds = 0 900 -3170.10037453087 eV 2.3546654042107 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07