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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -74.596673 0.0000000) to (37.296314 74.596673 4.0453532) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7041421 5.7041421 4.0453532 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -74.596673 0.0000000) to (37.296314 74.596673 4.0453532) create_atoms CPU = 0.001 seconds 682 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7041421 5.7041421 4.0453532 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -74.596673 0.0000000) to (37.296314 74.596673 4.0453532) create_atoms CPU = 0.001 seconds 682 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 48 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1358 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 48 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.664 | 4.664 | 4.664 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4526.8299 0 -4526.8299 5323.0762 122 0 -4557.0929 0 -4557.0929 99.67748 Loop time of 7.70776 on 1 procs for 122 steps with 1358 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 = -4526.829930611 -4557.08879213866 -4557.09294791681 Force two-norm initial, final = 19.199825 0.16075885 Force max component initial, final = 5.2009143 0.030393847 Final line search alpha, max atom move = 1.0000000 0.030393847 Iterations, force evaluations = 122 198 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.652 | 7.652 | 7.652 | 0.0 | 99.28 Neigh | 0.025687 | 0.025687 | 0.025687 | 0.0 | 0.33 Comm | 0.015301 | 0.015301 | 0.015301 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01481 | | | 0.19 Nlocal: 1358.00 ave 1358 max 1358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6486.00 ave 6486 max 6486 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: 74004.0 ave 74004 max 74004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74004 Ave neighs/atom = 54.494845 Neighbor list builds = 4 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 48 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 122 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.664 | 4.664 | 4.664 Mbytes Step Temp E_pair E_mol TotEng Press Volume 122 0 -4557.0929 0 -4557.0929 99.67748 22509.809 123 0 -4557.0954 0 -4557.0954 440.65582 22499.321 Loop time of 0.113863 on 1 procs for 1 steps with 1358 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 = -4557.09294791682 -4557.09294791682 -4557.09543790363 Force two-norm initial, final = 7.1113893 4.5611766 Force max component initial, final = 6.8063660 4.3685179 Final line search alpha, max atom move = 0.00014692128 0.00064182823 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11309 | 0.11309 | 0.11309 | 0.0 | 99.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015907 | 0.00015907 | 0.00015907 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006181 | | | 0.54 Nlocal: 1358.00 ave 1358 max 1358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6486.00 ave 6486 max 6486 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: 73892.0 ave 73892 max 73892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73892 Ave neighs/atom = 54.412371 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 48 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.802 | 4.802 | 4.802 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4557.0954 0 -4557.0954 440.65582 Loop time of 2.091e-06 on 1 procs for 0 steps with 1358 atoms 143.5% 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 | | 2.091e-06 | | |100.00 Nlocal: 1358.00 ave 1358 max 1358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6486.00 ave 6486 max 6486 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: 73892.0 ave 73892 max 73892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73892 Ave neighs/atom = 54.412371 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 48 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.802 | 4.802 | 4.802 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 -4557.0954 -4557.0954 37.303823 149.19335 4.0426543 440.65582 440.65582 311.14477 918.19422 92.628468 2.539906 170.9627 Loop time of 2.146e-06 on 1 procs for 0 steps with 1358 atoms 233.0% 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 | | 2.146e-06 | | |100.00 Nlocal: 1358.00 ave 1358 max 1358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6486.00 ave 6486 max 6486 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36946.0 ave 36946 max 36946 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 73892.0 ave 73892 max 73892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73892 Ave neighs/atom = 54.412371 Neighbor list builds = 0 Dangerous builds = 0 1358 -4557.09543790363 eV 2.53990596585249 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08