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 = 3.5200244 3.5200244 3.5200244 Created orthogonal box = (0.0000000 -62.179547 0.0000000) to (35.897346 62.179547 6.0968610) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5226686 5.5798998 6.0968610 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -62.179547 0.0000000) to (35.897346 62.179547 6.0968610) create_atoms CPU = 0.008 seconds 1249 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5226686 5.5798998 6.0968610 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -62.179547 0.0000000) to (35.897346 62.179547 6.0968610) create_atoms CPU = 0.007 seconds 1249 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 9 30 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 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 17 atoms, new total = 2481 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_532072268679_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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 10.84 | 10.84 | 10.84 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10953.55 0 -10953.55 6793.231 48 0 -11000.505 0 -11000.505 -3116.6868 Loop time of 5.35212 on 1 procs for 48 steps with 2481 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 = -10953.5504202164 -11000.4949486658 -11000.5051263385 Force two-norm initial, final = 66.086629 0.32424395 Force max component initial, final = 9.8058545 0.080790403 Final line search alpha, max atom move = 1.0000000 0.080790403 Iterations, force evaluations = 48 89 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2193 | 5.2193 | 5.2193 | 0.0 | 97.52 Neigh | 0.07787 | 0.07787 | 0.07787 | 0.0 | 1.45 Comm | 0.030667 | 0.030667 | 0.030667 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02426 | | | 0.45 Nlocal: 2481.00 ave 2481 max 2481 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14063.0 ave 14063 max 14063 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: 552888.0 ave 552888 max 552888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 552888 Ave neighs/atom = 222.84885 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.84 | 10.84 | 10.84 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -11000.505 0 -11000.505 -3116.6868 27217.371 50 0 -11000.545 0 -11000.545 -1305.1252 27189.734 Loop time of 0.225204 on 1 procs for 2 steps with 2481 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 = -11000.5051263387 -11000.5424659087 -11000.5451936678 Force two-norm initial, final = 69.336478 2.9650206 Force max component initial, final = 68.206043 2.6333626 Final line search alpha, max atom move = 7.3323486e-05 0.00019308733 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.2204 | 0.2204 | 0.2204 | 0.0 | 97.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011843 | 0.0011843 | 0.0011843 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003623 | | | 1.61 Nlocal: 2481.00 ave 2481 max 2481 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14044.0 ave 14044 max 14044 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: 553008.0 ave 553008 max 553008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 553008 Ave neighs/atom = 222.89722 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 10.35 | 10.35 | 10.35 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11000.545 0 -11000.545 -1305.1252 Loop time of 6.595e-06 on 1 procs for 0 steps with 2481 atoms 212.3% 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 | | 6.595e-06 | | |100.00 Nlocal: 2481.00 ave 2481 max 2481 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14045.0 ave 14045 max 14045 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: 553046.0 ave 553046 max 553046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 553046 Ave neighs/atom = 222.91254 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 10.35 | 10.35 | 10.35 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 -11000.545 -11000.545 35.902443 124.35909 6.0898053 -1305.1252 -1305.1252 -77.9345 -3682.4477 -154.99339 2.1974369 948.7215 Loop time of 6.635e-06 on 1 procs for 0 steps with 2481 atoms 301.4% 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 | | 6.635e-06 | | |100.00 Nlocal: 2481.00 ave 2481 max 2481 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14045.0 ave 14045 max 14045 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 276523.0 ave 276523 max 276523 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 553046.0 ave 553046 max 553046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 553046 Ave neighs/atom = 222.91254 Neighbor list builds = 0 Dangerous builds = 0 2481 -10932.909655802 eV 2.19743689441171 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06