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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -33.004535 0.0000000) to (40.418282 33.004535 7.7074639) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1441449 4.8002020 5.1383093 Created 662 atoms using lattice units in orthogonal box = (0.0000000 -33.004535 0.0000000) to (40.418282 33.004535 7.7074639) create_atoms CPU = 0.004 seconds 662 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1441449 4.8002020 5.1383093 Created 662 atoms using lattice units in orthogonal box = (0.0000000 -33.004535 0.0000000) to (40.418282 33.004535 7.7074639) create_atoms CPU = 0.003 seconds 662 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 23 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1316 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.587 | 4.587 | 4.587 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8798.8422 0 -8798.8422 23558.683 59 0 -8900.5659 0 -8900.5659 7704.1261 Loop time of 5.88638 on 1 procs for 59 steps with 1316 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8798.84218136855 -8900.55878491023 -8900.56594112217 Force two-norm initial, final = 44.908890 0.78481410 Force max component initial, final = 6.4505374 0.26171114 Final line search alpha, max atom move = 0.39181130 0.10254138 Iterations, force evaluations = 59 81 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.8338 | 5.8338 | 5.8338 | 0.0 | 99.11 Neigh | 0.029627 | 0.029627 | 0.029627 | 0.0 | 0.50 Comm | 0.0085016 | 0.0085016 | 0.0085016 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0145 | | | 0.25 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3849.00 ave 3849 max 3849 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: 75312.0 ave 75312 max 75312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75312 Ave neighs/atom = 57.227964 Neighbor list builds = 2 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 59 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.586 | 4.586 | 4.586 Mbytes Step Temp E_pair E_mol TotEng Press Volume 59 0 -8900.5659 0 -8900.5659 7704.1261 20563.307 63 0 -8900.8029 0 -8900.8029 3336.7764 20596.978 Loop time of 0.422652 on 1 procs for 4 steps with 1316 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8900.56594112217 -8900.79765020619 -8900.80285775046 Force two-norm initial, final = 138.32759 5.9604629 Force max component initial, final = 138.30196 4.9297000 Final line search alpha, max atom move = 6.7967884e-05 0.00033506127 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41952 | 0.41952 | 0.41952 | 0.0 | 99.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053507 | 0.00053507 | 0.00053507 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002597 | | | 0.61 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3859.00 ave 3859 max 3859 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: 75270.0 ave 75270 max 75270 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75270 Ave neighs/atom = 57.196049 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.724 | 4.724 | 4.724 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8900.8029 0 -8900.8029 3336.7764 Loop time of 6.244e-06 on 1 procs for 0 steps with 1316 atoms 176.2% 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 | | 6.244e-06 | | |100.00 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3888.00 ave 3888 max 3888 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: 75238.0 ave 75238 max 75238 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75238 Ave neighs/atom = 57.171733 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.724 | 4.724 | 4.724 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 -8900.8029 -8900.8029 40.552605 66.009071 7.6945127 3336.7764 3336.7764 384.74081 9373.1136 252.47478 2.2878734 1978.7223 Loop time of 6.765e-06 on 1 procs for 0 steps with 1316 atoms 295.6% 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 | | 6.765e-06 | | |100.00 Nlocal: 1316.00 ave 1316 max 1316 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3888.00 ave 3888 max 3888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37619.0 ave 37619 max 37619 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75238.0 ave 75238 max 75238 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75238 Ave neighs/atom = 57.171733 Neighbor list builds = 0 Dangerous builds = 0 1316 -8900.80285775046 eV 2.28787344265484 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06