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 = 3.6784521 3.6784521 3.6784521 Created orthogonal box = (0.0000000 -51.760410 0.0000000) to (12.200046 51.760410 5.2021169) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.5454753 6.2739891 5.2021169 Created 264 atoms using lattice units in orthogonal box = (0.0000000 -51.760410 0.0000000) to (12.200046 51.760410 5.2021169) create_atoms CPU = 0.003 seconds 264 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.5454753 6.2739891 5.2021169 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -51.760410 0.0000000) to (12.200046 51.760410 5.2021169) create_atoms CPU = 0.003 seconds 266 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 4 34 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 530 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 4 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.506 | 4.506 | 4.506 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2109.8816 0 -2109.8816 46017.911 226 0 -2235.7448 0 -2235.7448 -26875.825 Loop time of 1.90292 on 1 procs for 226 steps with 530 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 = -2109.88156662288 -2235.74265312118 -2235.74483441613 Force two-norm initial, final = 113.72570 0.15701852 Force max component initial, final = 38.488204 0.041375953 Final line search alpha, max atom move = 1.0000000 0.041375953 Iterations, force evaluations = 226 433 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7702 | 1.7702 | 1.7702 | 0.0 | 93.03 Neigh | 0.054785 | 0.054785 | 0.054785 | 0.0 | 2.88 Comm | 0.042007 | 0.042007 | 0.042007 | 0.0 | 2.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03589 | | | 1.89 Nlocal: 530.000 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3474.00 ave 3474 max 3474 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: 38816.0 ave 38816 max 38816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38816 Ave neighs/atom = 73.237736 Neighbor list builds = 7 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 4 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 226 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.505 | 4.505 | 4.505 Mbytes Step Temp E_pair E_mol TotEng Press Volume 226 0 -2235.7448 0 -2235.7448 -26875.825 6570.0589 256 0 -2239.5097 0 -2239.5097 5.5589408 6419.6914 Loop time of 0.148641 on 1 procs for 30 steps with 530 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 = -2235.74483441613 -2239.50789718423 -2239.50969080382 Force two-norm initial, final = 256.38369 1.1951796 Force max component initial, final = 248.18746 0.35205829 Final line search alpha, max atom move = 0.00030500784 0.00010738054 Iterations, force evaluations = 30 31 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12874 | 0.12874 | 0.12874 | 0.0 | 86.61 Neigh | 0.0075973 | 0.0075973 | 0.0075973 | 0.0 | 5.11 Comm | 0.0026653 | 0.0026653 | 0.0026653 | 0.0 | 1.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00964 | | | 6.49 Nlocal: 530.000 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3508.00 ave 3508 max 3508 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: 39128.0 ave 39128 max 39128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39128 Ave neighs/atom = 73.826415 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 4 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.643 | 4.643 | 4.643 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2239.5097 0 -2239.5097 5.5589408 Loop time of 6.365e-06 on 1 procs for 0 steps with 530 atoms 188.5% 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 | | 6.365e-06 | | |100.00 Nlocal: 530.000 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3508.00 ave 3508 max 3508 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: 39136.0 ave 39136 max 39136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39136 Ave neighs/atom = 73.841509 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 4 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 4.643 | 4.643 | 4.643 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 -2239.5097 -2239.5097 12.155981 104.55673 5.0509393 5.5589408 5.5589408 -10.740304 -57.893438 85.310565 2.3581168 401.16768 Loop time of 6.926e-06 on 1 procs for 0 steps with 530 atoms 245.5% 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 | | 6.926e-06 | | |100.00 Nlocal: 530.000 ave 530 max 530 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3508.00 ave 3508 max 3508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19568.0 ave 19568 max 19568 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39136.0 ave 39136 max 39136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39136 Ave neighs/atom = 73.841509 Neighbor list builds = 0 Dangerous builds = 0 530 -2239.50963780382 eV 2.35811677975914 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02