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 = 2.8700001 2.8700001 2.8700001 Created orthogonal box = (0.0000000 -46.986796 0.0000000) to (33.222653 46.986796 4.0587930) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9586049 4.5581421 4.0587930 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -46.986796 0.0000000) to (33.222653 46.986796 4.0587930) create_atoms CPU = 0.003 seconds 538 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9586049 4.5581421 4.0587930 Created 538 atoms using lattice units in orthogonal box = (0.0000000 -46.986796 0.0000000) to (33.222653 46.986796 4.0587930) create_atoms CPU = 0.002 seconds 538 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 11 31 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1064 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.612 | 4.612 | 4.612 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4497.5477 0 -4497.5477 6790.9249 65 0 -4538.7692 0 -4538.7692 -5568.0753 Loop time of 0.896589 on 1 procs for 65 steps with 1064 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 = -4497.54766203292 -4538.76590753178 -4538.76915768176 Force two-norm initial, final = 58.963522 0.19347355 Force max component initial, final = 18.333145 0.034185534 Final line search alpha, max atom move = 1.0000000 0.034185534 Iterations, force evaluations = 65 120 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.86048 | 0.86048 | 0.86048 | 0.0 | 95.97 Neigh | 0.013705 | 0.013705 | 0.013705 | 0.0 | 1.53 Comm | 0.011769 | 0.011769 | 0.011769 | 0.0 | 1.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01063 | | | 1.19 Nlocal: 1064.00 ave 1064 max 1064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6358.00 ave 6358 max 6358 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: 69300.0 ave 69300 max 69300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69300 Ave neighs/atom = 65.131579 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 11 31 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 65 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.614 | 4.614 | 4.614 Mbytes Step Temp E_pair E_mol TotEng Press Volume 65 0 -4538.7692 0 -4538.7692 -5568.0753 12671.763 68 0 -4538.8748 0 -4538.8748 431.28718 12626.261 Loop time of 0.0374788 on 1 procs for 3 steps with 1064 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 = -4538.76915768177 -4538.87135351776 -4538.87480950603 Force two-norm initial, final = 78.884302 3.6820767 Force max component initial, final = 67.735934 3.6757386 Final line search alpha, max atom move = 7.7761679e-05 0.00028583161 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.035044 | 0.035044 | 0.035044 | 0.0 | 93.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045784 | 0.00045784 | 0.00045784 | 0.0 | 1.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001977 | | | 5.28 Nlocal: 1064.00 ave 1064 max 1064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6354.00 ave 6354 max 6354 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: 69240.0 ave 69240 max 69240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69240 Ave neighs/atom = 65.075188 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.752 | 4.752 | 4.752 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4538.8748 0 -4538.8748 431.28718 Loop time of 3.194e-06 on 1 procs for 0 steps with 1064 atoms 125.2% 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 | | 3.194e-06 | | |100.00 Nlocal: 1064.00 ave 1064 max 1064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6373.00 ave 6373 max 6373 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: 69348.0 ave 69348 max 69348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69348 Ave neighs/atom = 65.176692 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.752 | 4.752 | 4.752 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 -4538.8748 -4538.8748 33.187526 93.973592 4.0484991 431.28718 431.28718 465.93014 826.38027 1.5511176 2.2760118 452.7737 Loop time of 3.2e-06 on 1 procs for 0 steps with 1064 atoms 187.5% 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 | | 3.2e-06 | | |100.00 Nlocal: 1064.00 ave 1064 max 1064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6373.00 ave 6373 max 6373 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34287.0 ave 34287 max 34287 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69348.0 ave 69348 max 69348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69348 Ave neighs/atom = 65.176692 Neighbor list builds = 0 Dangerous builds = 0 1064 -4538.87470310603 eV 2.27601184768259 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01