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 = 4.0499858 4.0499858 4.0499858 Created orthogonal box = (0.0000000 -52.493816 0.0000000) to (30.307319 52.493816 7.0147812) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.4944254 6.2492638 7.0147812 Created 672 atoms using lattice units in orthogonal box = (0.0000000 -52.493816 0.0000000) to (30.307319 52.493816 7.0147812) create_atoms CPU = 0.002 seconds 672 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.4944254 6.2492638 7.0147812 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -52.493816 0.0000000) to (30.307319 52.493816 7.0147812) create_atoms CPU = 0.004 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 ghost atom cutoff = 6 binsize = 3, bins = 11 35 3 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1348 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_022920256108_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 ghost atom cutoff = 6 binsize = 3, bins = 11 35 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.603 | 4.603 | 4.603 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4279.1809 0 -4279.1809 27863.212 40 0 -4502.9593 0 -4502.9593 6817.8082 Loop time of 1.46052 on 1 procs for 40 steps with 1348 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 = -4279.18089078616 -4502.95814412098 -4502.95927708958 Force two-norm initial, final = 296.99263 0.60090555 Force max component initial, final = 58.712524 0.11690766 Final line search alpha, max atom move = 1.0000000 0.11690766 Iterations, force evaluations = 40 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4452 | 1.4452 | 1.4452 | 0.0 | 98.95 Neigh | 0.0062021 | 0.0062021 | 0.0062021 | 0.0 | 0.42 Comm | 0.0035119 | 0.0035119 | 0.0035119 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005588 | | | 0.38 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4214.00 ave 4214 max 4214 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: 72576.0 ave 72576 max 72576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72576 Ave neighs/atom = 53.839763 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 ghost atom cutoff = 6 binsize = 3, bins = 11 35 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.603 | 4.603 | 4.603 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -4502.9593 0 -4502.9593 6817.8082 22320.288 53 0 -4503.9605 0 -4503.9605 -3.685036 22550.526 Loop time of 0.289212 on 1 procs for 13 steps with 1348 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 = -4502.95927708959 -4503.95891707805 -4503.96050976875 Force two-norm initial, final = 190.35667 0.72112360 Force max component initial, final = 173.15391 0.15170517 Final line search alpha, max atom move = 0.00024755761 3.7555769e-05 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27919 | 0.27919 | 0.27919 | 0.0 | 96.53 Neigh | 0.0061025 | 0.0061025 | 0.0061025 | 0.0 | 2.11 Comm | 0.00062607 | 0.00062607 | 0.00062607 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003296 | | | 1.14 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4213.00 ave 4213 max 4213 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: 72352.0 ave 72352 max 72352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72352 Ave neighs/atom = 53.673591 Neighbor list builds = 1 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 ghost atom cutoff = 6 binsize = 3, bins = 11 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.741 | 4.741 | 4.741 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4503.9605 0 -4503.9605 -3.685036 Loop time of 1.69e-06 on 1 procs for 0 steps with 1348 atoms 177.5% 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 | | 1.69e-06 | | |100.00 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4225.00 ave 4225 max 4225 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: 72344.0 ave 72344 max 72344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72344 Ave neighs/atom = 53.667656 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 ghost atom cutoff = 6 binsize = 3, bins = 11 36 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 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) = 4.741 | 4.741 | 4.741 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 -4503.9605 -4503.9605 30.252131 106.30024 7.0123964 -3.685036 -3.685036 -4.8121588 -10.913151 4.6702018 2.5636576 1078.0543 Loop time of 1.599e-06 on 1 procs for 0 steps with 1348 atoms 187.6% 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 | | 1.599e-06 | | |100.00 Nlocal: 1348.00 ave 1348 max 1348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4225.00 ave 4225 max 4225 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36172.0 ave 36172 max 36172 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 72344.0 ave 72344 max 72344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 72344 Ave neighs/atom = 53.667656 Neighbor list builds = 0 Dangerous builds = 0 1348 -4503.96050976876 eV 2.56365761913634 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02