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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -46.805186 0.0000000) to (27.022987 46.805186 6.2546061) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7906401 5.5720460 6.2546061 Created 672 atoms using lattice units in orthogonal box = (0.0000000 -46.805186 0.0000000) to (27.022987 46.805186 6.2546061) create_atoms CPU = 0.002 seconds 672 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7906401 5.5720460 6.2546061 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -46.805186 0.0000000) to (27.022987 46.805186 6.2546061) create_atoms CPU = 0.002 seconds 676 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 9 30 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 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1344 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_343168101490_001#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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.065 | 5.065 | 5.065 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5257.1852 0 -5257.1852 63390.946 179 0 -5688.0031 0 -5688.0031 7531.3459 Loop time of 21.8601 on 1 procs for 179 steps with 1344 atoms 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5257.18520890006 -5687.99762321081 -5688.00312168311 Force two-norm initial, final = 592.42344 0.25169250 Force max component initial, final = 133.06284 0.030832885 Final line search alpha, max atom move = 1.0000000 0.030832885 Iterations, force evaluations = 179 331 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 21.768 | 21.768 | 21.768 | 0.0 | 99.58 Neigh | 0.038033 | 0.038033 | 0.038033 | 0.0 | 0.17 Comm | 0.02604 | 0.02604 | 0.02604 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0285 | | | 0.13 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5489.00 ave 5489 max 5489 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: 116200.0 ave 116200 max 116200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116200 Ave neighs/atom = 86.458333 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 9 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 179 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.066 | 5.066 | 5.066 Mbytes Step Temp E_pair E_mol TotEng Press Volume 179 0 -5688.0031 0 -5688.0031 7531.3459 15821.851 183 0 -5688.2118 0 -5688.2118 123.82879 15889.885 Loop time of 0.397663 on 1 procs for 4 steps with 1344 atoms 99.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5688.00312168314 -5688.21111498562 -5688.21180699555 Force two-norm initial, final = 133.97884 3.5768406 Force max component initial, final = 96.683530 3.2490438 Final line search alpha, max atom move = 0.00015773136 0.00051247609 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39572 | 0.39572 | 0.39572 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027597 | 0.00027597 | 0.00027597 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001668 | | | 0.42 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5459.00 ave 5459 max 5459 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: 116464.0 ave 116464 max 116464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116464 Ave neighs/atom = 86.654762 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.203 | 5.203 | 5.203 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5688.2118 0 -5688.2118 123.82879 Loop time of 2.208e-06 on 1 procs for 0 steps with 1344 atoms 181.2% 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 | | 2.208e-06 | | |100.00 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5448.00 ave 5448 max 5448 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: 116320.0 ave 116320 max 116320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116320 Ave neighs/atom = 86.547619 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 = 6.4 ghost atom cutoff = 6.4 binsize = 3.2, bins = 9 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.4 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) = 5.203 | 5.203 | 5.203 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 -5688.2118 -5688.2118 27.009482 93.798904 6.2720102 123.82879 123.82879 -80.64806 328.26074 123.8737 2.2836055 1252.6957 Loop time of 2.871e-06 on 1 procs for 0 steps with 1344 atoms 243.8% 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 | | 2.871e-06 | | |100.00 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5448.00 ave 5448 max 5448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 58160.0 ave 58160 max 58160 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 116320.0 ave 116320 max 116320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 116320 Ave neighs/atom = 86.547619 Neighbor list builds = 0 Dangerous builds = 0 1344 -5688.21180699555 eV 2.28360551451161 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:22