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 = 3.5213918 3.5213918 3.5213918 Created orthogonal box = (0.0000000 -41.066132 0.0000000) to (20.533066 41.066132 3.5213918) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8313096 4.8313096 3.5213918 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -41.066132 0.0000000) to (20.533066 41.066132 3.5213918) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8313096 4.8313096 3.5213918 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -41.066132 0.0000000) to (20.533066 41.066132 3.5213918) create_atoms CPU = 0.000 seconds 274 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 = 7 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 546 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_700541006254_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 = 7 28 2 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) = 4.479 | 4.479 | 4.479 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2114.2957 0 -2114.2957 191323.18 32 0 -2417.6958 0 -2417.6958 19581.881 Loop time of 1.15814 on 1 procs for 32 steps with 546 atoms 98.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2114.2956717705 -2417.69386823583 -2417.69583852225 Force two-norm initial, final = 871.61309 0.18339297 Force max component initial, final = 273.55597 0.027868787 Final line search alpha, max atom move = 1.0000000 0.027868787 Iterations, force evaluations = 32 57 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1534 | 1.1534 | 1.1534 | 0.0 | 99.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0023861 | 0.0023861 | 0.0023861 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002343 | | | 0.20 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3914.00 ave 3914 max 3914 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: 42848.0 ave 42848 max 42848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42848 Ave neighs/atom = 78.476190 Neighbor list builds = 0 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 = 7 28 2 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 : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.479 | 4.479 | 4.479 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -2417.6958 0 -2417.6958 19581.881 5938.5708 46 0 -2418.5845 0 -2418.5845 -24.064789 5999.9101 Loop time of 0.301251 on 1 procs for 14 steps with 546 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 = -2417.69583852225 -2418.58353306917 -2418.58450548437 Force two-norm initial, final = 156.02055 1.3358797 Force max component initial, final = 146.39034 0.80227671 Final line search alpha, max atom move = 0.00046861613 0.00037595981 Iterations, force evaluations = 14 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29494 | 0.29494 | 0.29494 | 0.0 | 97.91 Neigh | 0.0034163 | 0.0034163 | 0.0034163 | 0.0 | 1.13 Comm | 0.00056761 | 0.00056761 | 0.00056761 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002324 | | | 0.77 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3904.00 ave 3904 max 3904 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: 42380.0 ave 42380 max 42380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42380 Ave neighs/atom = 77.619048 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 = 7 28 2 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) = 4.617 | 4.617 | 4.617 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2418.5845 0 -2418.5845 -24.064789 Loop time of 2.014e-06 on 1 procs for 0 steps with 546 atoms 149.0% 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 | | 2.014e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3904.00 ave 3904 max 3904 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: 42380.0 ave 42380 max 42380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42380 Ave neighs/atom = 77.619048 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 = 7 28 2 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) = 4.617 | 4.617 | 4.617 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 -2418.5845 -2418.5845 20.513296 83.201891 3.5154109 -24.064789 -24.064789 -185.09403 217.02472 -104.12505 2.223392 298.81225 Loop time of 1.818e-06 on 1 procs for 0 steps with 546 atoms 220.0% 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 | | 1.818e-06 | | |100.00 Nlocal: 546.000 ave 546 max 546 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3904.00 ave 3904 max 3904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21190.0 ave 21190 max 21190 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 42380.0 ave 42380 max 42380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42380 Ave neighs/atom = 77.619048 Neighbor list builds = 0 Dangerous builds = 0 546 -2418.58450548437 eV 2.22339201507621 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01