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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -44.805806 0.0000000) to (10.560000 44.805806 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8666667 4.9780318 4.9780318 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -44.805806 0.0000000) to (10.560000 44.805806 4.9780318) create_atoms CPU = 0.002 seconds 218 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8666667 4.9780318 4.9780318 Created 218 atoms using lattice units in orthogonal box = (0.0000000 -44.805806 0.0000000) to (10.560000 44.805806 4.9780318) create_atoms CPU = 0.002 seconds 218 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 3 22 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 428 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_103383163946_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 3 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.540 | 4.540 | 4.540 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1891.0793 0 -1891.0793 1637.7031 39 0 -1897.568 0 -1897.568 -8974.6073 Loop time of 0.871374 on 1 procs for 39 steps with 428 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 = -1891.07927885658 -1897.5665865473 -1897.56799383281 Force two-norm initial, final = 11.083965 0.12335514 Force max component initial, final = 3.1682923 0.018897889 Final line search alpha, max atom move = 1.0000000 0.018897889 Iterations, force evaluations = 39 75 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.85517 | 0.85517 | 0.85517 | 0.0 | 98.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0099334 | 0.0099334 | 0.0099334 | 0.0 | 1.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006273 | | | 0.72 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5539.00 ave 5539 max 5539 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: 95340.0 ave 95340 max 95340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95340 Ave neighs/atom = 222.75701 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 3 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.540 | 4.540 | 4.540 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -1897.568 0 -1897.568 -8974.6073 4710.7046 42 0 -1897.5886 0 -1897.5886 -4375.7785 4698.3531 Loop time of 0.076436 on 1 procs for 3 steps with 428 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 = -1897.56799383281 -1897.58854495507 -1897.58857511856 Force two-norm initial, final = 21.845383 0.13778373 Force max component initial, final = 16.883710 0.029546547 Final line search alpha, max atom move = 0.0019676011 5.8135820e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.073254 | 0.073254 | 0.073254 | 0.0 | 95.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00077654 | 0.00077654 | 0.00077654 | 0.0 | 1.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002406 | | | 3.15 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5494.00 ave 5494 max 5494 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: 95912.0 ave 95912 max 95912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95912 Ave neighs/atom = 224.09346 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 3 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.678 | 4.678 | 4.678 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1897.5886 0 -1897.5886 -4375.7785 Loop time of 6.235e-06 on 1 procs for 0 steps with 428 atoms 208.5% 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 | | 6.235e-06 | | |100.00 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5503.00 ave 5503 max 5503 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: 95944.0 ave 95944 max 95944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95944 Ave neighs/atom = 224.16822 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 3 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.678 | 4.678 | 4.678 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 -1897.5886 -1897.5886 10.548699 89.611612 4.9702982 -4375.7785 -4375.7785 -10.06483 -13120.374 3.1033616 2.3239099 169.75328 Loop time of 6.956e-06 on 1 procs for 0 steps with 428 atoms 301.9% 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 | | 6.956e-06 | | |100.00 Nlocal: 428.000 ave 428 max 428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5503.00 ave 5503 max 5503 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47972.0 ave 47972 max 47972 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 95944.0 ave 95944 max 95944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95944 Ave neighs/atom = 224.16822 Neighbor list builds = 0 Dangerous builds = 0 428 -1885.93357169936 eV 2.32390988041225 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01