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 -57.193230 0.0000000) to (20.220860 57.193230 4.9780317) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5147801 6.0659487 4.9780317 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -57.193230 0.0000000) to (20.220860 57.193230 4.9780317) create_atoms CPU = 0.005 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5147801 6.0659487 4.9780317 Created 530 atoms using lattice units in orthogonal box = (0.0000000 -57.193230 0.0000000) to (20.220860 57.193230 4.9780317) create_atoms CPU = 0.005 seconds 530 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 5 28 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1056 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_592013496703_005#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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.472 | 5.472 | 5.472 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4531.3378 0 -4531.3378 29981.303 49 0 -4689.591 0 -4689.591 4660.0772 Loop time of 2.33302 on 1 procs for 49 steps with 1056 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4531.337839501 -4689.58727484767 -4689.59102097815 Force two-norm initial, final = 246.95242 0.20867093 Force max component initial, final = 77.517238 0.048465708 Final line search alpha, max atom move = 1.0000000 0.048465708 Iterations, force evaluations = 49 87 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2684 | 2.2684 | 2.2684 | 0.0 | 97.23 Neigh | 0.033628 | 0.033628 | 0.033628 | 0.0 | 1.44 Comm | 0.018085 | 0.018085 | 0.018085 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01293 | | | 0.55 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8911.00 ave 8911 max 8911 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: 236732.0 ave 236732 max 236732 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236732 Ave neighs/atom = 224.17803 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 5 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.472 | 5.472 | 5.472 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -4689.591 0 -4689.591 4660.0772 11514.151 53 0 -4689.7111 0 -4689.7111 263.51523 11542.477 Loop time of 0.158361 on 1 procs for 4 steps with 1056 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 = -4689.59102097815 -4689.70931149957 -4689.71107174486 Force two-norm initial, final = 77.080816 3.7006465 Force max component initial, final = 74.482181 2.6111551 Final line search alpha, max atom move = 0.00014187055 0.00037044600 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15382 | 0.15382 | 0.15382 | 0.0 | 97.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001166 | 0.001166 | 0.001166 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003378 | | | 2.13 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8925.00 ave 8925 max 8925 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: 236696.0 ave 236696 max 236696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236696 Ave neighs/atom = 224.14394 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.610 | 5.610 | 5.610 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4689.7111 0 -4689.7111 263.51523 Loop time of 6.625e-06 on 1 procs for 0 steps with 1056 atoms 166.0% 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 | | 6.625e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8925.00 ave 8925 max 8925 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: 236560.0 ave 236560 max 236560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236560 Ave neighs/atom = 224.01515 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 5 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.610 | 5.610 | 5.610 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 -4689.7111 -4689.7111 20.204078 114.75112 4.9785522 263.51523 263.51523 71.740275 363.60204 355.20337 2.2947445 338.33026 Loop time of 6.736e-06 on 1 procs for 0 steps with 1056 atoms 282.1% 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 | | 6.736e-06 | | |100.00 Nlocal: 1056.00 ave 1056 max 1056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8925.00 ave 8925 max 8925 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 118280.0 ave 118280 max 118280 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 236560.0 ave 236560 max 236560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236560 Ave neighs/atom = 224.01515 Neighbor list builds = 0 Dangerous builds = 0 1056 -4689.71107174486 eV 2.29474446668213 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03