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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -42.378259 0.0000000) to (34.601703 42.378259 7.0144993) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2659634 4.0636686 4.6763329 Created 875 atoms using lattice units in orthogonal box = (0.0000000 -42.378259 0.0000000) to (34.601703 42.378259 7.0144993) create_atoms CPU = 0.001 seconds 875 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2659634 4.0636686 4.6763329 Created 877 atoms using lattice units in orthogonal box = (0.0000000 -42.378259 0.0000000) to (34.601703 42.378259 7.0144993) create_atoms CPU = 0.001 seconds 877 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 31 3 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1752 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.022 | 5.022 | 5.022 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7293.8346 0 -7293.8346 32894.093 45 0 -7476.2728 0 -7476.2728 7845.6237 Loop time of 2.95907 on 1 procs for 45 steps with 1752 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7293.83458024339 -7476.26530253736 -7476.272776293 Force two-norm initial, final = 205.04769 0.38244524 Force max component initial, final = 55.733326 0.069036286 Final line search alpha, max atom move = 1.0000000 0.069036286 Iterations, force evaluations = 45 82 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9489 | 2.9489 | 2.9489 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0036867 | 0.0036867 | 0.0036867 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006435 | | | 0.22 Nlocal: 1752.00 ave 1752 max 1752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4800.00 ave 4800 max 4800 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: 102092.0 ave 102092 max 102092 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102092 Ave neighs/atom = 58.271689 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 31 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 45 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.022 | 5.022 | 5.022 Mbytes Step Temp E_pair E_mol TotEng Press Volume 45 0 -7476.2728 0 -7476.2728 7845.6237 20571.561 54 0 -7477.2616 0 -7477.2616 -58.017352 20661.267 Loop time of 0.391988 on 1 procs for 9 steps with 1752 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 = -7476.27277629299 -7477.26003990615 -7477.26160695901 Force two-norm initial, final = 255.94579 1.5782671 Force max component initial, final = 253.43887 0.75594931 Final line search alpha, max atom move = 0.00018064714 0.00013656008 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38893 | 0.38893 | 0.38893 | 0.0 | 99.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00040749 | 0.00040749 | 0.00040749 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002651 | | | 0.68 Nlocal: 1752.00 ave 1752 max 1752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4804.00 ave 4804 max 4804 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: 101954.0 ave 101954 max 101954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101954 Ave neighs/atom = 58.192922 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.160 | 5.160 | 5.160 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7477.2616 0 -7477.2616 -58.017352 Loop time of 1.667e-06 on 1 procs for 0 steps with 1752 atoms 120.0% 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 | | 1.667e-06 | | |100.00 Nlocal: 1752.00 ave 1752 max 1752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4797.00 ave 4797 max 4797 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: 101896.0 ave 101896 max 101896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101896 Ave neighs/atom = 58.159817 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 31 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 5.160 | 5.160 | 5.160 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 -7477.2616 -7477.2616 34.515682 85.457808 7.0046871 -58.017352 -58.017352 -57.470906 -59.105069 -57.476082 2.239373 1183.5038 Loop time of 2.092e-06 on 1 procs for 0 steps with 1752 atoms 143.4% 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 | | 2.092e-06 | | |100.00 Nlocal: 1752.00 ave 1752 max 1752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4797.00 ave 4797 max 4797 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 50948.0 ave 50948 max 50948 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 101896.0 ave 101896 max 101896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 101896 Ave neighs/atom = 58.159817 Neighbor list builds = 0 Dangerous builds = 0 1752 -7477.26160695901 eV 2.23937302217204 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03