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 -36.532007 0.0000000) to (8.6100002 36.532007 4.0587930) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7833335 4.0587930 4.0587930 Created 109 atoms using lattice units in orthogonal box = (0.0000000 -36.532007 0.0000000) to (8.6100002 36.532007 4.0587930) create_atoms CPU = 0.001 seconds 109 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7833335 4.0587930 4.0587930 Created 109 atoms using lattice units in orthogonal box = (0.0000000 -36.532007 0.0000000) to (8.6100002 36.532007 4.0587930) create_atoms CPU = 0.001 seconds 109 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 = 3 24 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 6 atoms, new total = 212 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 = 3 24 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) = 4.412 | 4.412 | 4.412 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -896.06392 0 -896.06392 -270.55946 40 0 -901.5526 0 -901.5526 -16705.276 Loop time of 0.113585 on 1 procs for 40 steps with 212 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 = -896.063919154235 -901.551831512956 -901.55259504294 Force two-norm initial, final = 14.786784 0.083789602 Force max component initial, final = 7.9037623 0.015926048 Final line search alpha, max atom move = 1.0000000 0.015926048 Iterations, force evaluations = 40 65 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10653 | 0.10653 | 0.10653 | 0.0 | 93.79 Neigh | 0.002806 | 0.002806 | 0.002806 | 0.0 | 2.47 Comm | 0.0025662 | 0.0025662 | 0.0025662 | 0.0 | 2.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00168 | | | 1.48 Nlocal: 212.000 ave 212 max 212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2517.00 ave 2517 max 2517 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: 13630.0 ave 13630 max 13630 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13630 Ave neighs/atom = 64.292453 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 = 3 24 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 : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.412 | 4.412 | 4.412 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -901.5526 0 -901.5526 -16705.276 2553.3103 46 0 -901.66133 0 -901.66133 -2917.3562 2531.862 Loop time of 0.0163753 on 1 procs for 6 steps with 212 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 = -901.552595042941 -901.661245533287 -901.661329124368 Force two-norm initial, final = 35.739321 0.12787237 Force max component initial, final = 27.761337 0.028962913 Final line search alpha, max atom move = 0.0015665585 4.5372099e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.014755 | 0.014755 | 0.014755 | 0.0 | 90.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033535 | 0.00033535 | 0.00033535 | 0.0 | 2.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001285 | | | 7.85 Nlocal: 212.000 ave 212 max 212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2471.00 ave 2471 max 2471 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: 13680.0 ave 13680 max 13680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13680 Ave neighs/atom = 64.528302 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 = 3 24 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) = 4.550 | 4.550 | 4.550 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -901.66133 0 -901.66133 -2917.3562 Loop time of 2.8e-06 on 1 procs for 0 steps with 212 atoms 107.1% 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 | | 2.8e-06 | | |100.00 Nlocal: 212.000 ave 212 max 212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2480.00 ave 2480 max 2480 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: 13712.0 ave 13712 max 13712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13712 Ave neighs/atom = 64.679245 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 = 3 24 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) = 4.550 | 4.550 | 4.550 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 -901.66133 -901.66133 8.5810113 73.064015 4.0382948 -2917.3562 -2917.3562 -12.036477 -8747.389 7.3568609 2.3521311 221.8722 Loop time of 2.844e-06 on 1 procs for 0 steps with 212 atoms 105.5% 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 | | 2.844e-06 | | |100.00 Nlocal: 212.000 ave 212 max 212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6856.00 ave 6856 max 6856 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 13712.0 ave 13712 max 13712 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13712 Ave neighs/atom = 64.679245 Neighbor list builds = 0 Dangerous builds = 0 212 -901.661307924368 eV 2.35213112431955 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00