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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -41.517449 0.0000000) to (29.354715 41.517449 5.1100000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2267577 5.6609777 5.1100000 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -41.517449 0.0000000) to (29.354715 41.517449 5.1100000) create_atoms CPU = 0.004 seconds 532 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2267577 5.6609777 5.1100000 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -41.517449 0.0000000) to (29.354715 41.517449 5.1100000) create_atoms CPU = 0.003 seconds 532 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 11 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 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1048 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_849011491644_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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.597 | 4.597 | 4.597 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3658.3791 0 -3658.3791 9380.0233 37 0 -3699.4793 0 -3699.4793 -6302.1789 Loop time of 2.47998 on 1 procs for 37 steps with 1048 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3658.37907921817 -3699.47636458198 -3699.4792916965 Force two-norm initial, final = 47.400054 0.13751589 Force max component initial, final = 12.255843 0.023787052 Final line search alpha, max atom move = 1.0000000 0.023787052 Iterations, force evaluations = 37 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4535 | 2.4535 | 2.4535 | 0.0 | 98.93 Neigh | 0.010982 | 0.010982 | 0.010982 | 0.0 | 0.44 Comm | 0.0070478 | 0.0070478 | 0.0070478 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00843 | | | 0.34 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4319.00 ave 4319 max 4319 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: 61792.0 ave 61792 max 61792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61792 Ave neighs/atom = 58.961832 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.597 | 4.597 | 4.597 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -3699.4793 0 -3699.4793 -6302.1789 12455.45 41 0 -3699.5725 0 -3699.5725 -2128.332 12417.973 Loop time of 0.240255 on 1 procs for 4 steps with 1048 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 = -3699.4792916965 -3699.57119222145 -3699.57254767952 Force two-norm initial, final = 60.512595 2.2176443 Force max component initial, final = 57.856180 2.0966180 Final line search alpha, max atom move = 0.00016186141 0.00033936156 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23746 | 0.23746 | 0.23746 | 0.0 | 98.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005652 | 0.0005652 | 0.0005652 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00223 | | | 0.93 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4297.00 ave 4297 max 4297 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: 62848.0 ave 62848 max 62848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 62848 Ave neighs/atom = 59.969466 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.734 | 4.734 | 4.734 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3699.5725 0 -3699.5725 -2128.332 Loop time of 6.224e-06 on 1 procs for 0 steps with 1048 atoms 176.7% 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 | | 6.224e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4297.00 ave 4297 max 4297 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: 66320.0 ave 66320 max 66320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66320 Ave neighs/atom = 63.282443 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 = 5.7 ghost atom cutoff = 5.7 binsize = 2.85, bins = 11 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.7 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) = 4.734 | 4.734 | 4.734 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 -3699.5725 -3699.5725 29.358266 83.034899 5.0940084 -2128.332 -2128.332 -90.352168 -6024.9831 -269.66074 2.3954732 636.76338 Loop time of 6.976e-06 on 1 procs for 0 steps with 1048 atoms 243.7% 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 | | 6.976e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4297.00 ave 4297 max 4297 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33160.0 ave 33160 max 33160 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 66320.0 ave 66320 max 66320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 66320 Ave neighs/atom = 63.282443 Neighbor list builds = 0 Dangerous builds = 0 1048 -3699.57254767952 eV 2.39547324076381 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03