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 = 4.0612135 4.0612135 4.0612135 Created orthogonal box = (0.0000000 -44.488365 0.0000000) to (9.0811494 44.488365 9.9479008) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4486896 5.9317820 6.6319338 Created 240 atoms using lattice units in orthogonal box = (0.0000000 -44.488365 0.0000000) to (9.0811494 44.488365 9.9479008) create_atoms CPU = 0.001 seconds 240 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4486896 5.9317820 6.6319338 Created 242 atoms using lattice units in orthogonal box = (0.0000000 -44.488365 0.0000000) to (9.0811494 44.488365 9.9479008) create_atoms CPU = 0.000 seconds 242 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 2 19 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 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 476 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_411898953661_004#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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 2 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 4.979 | 4.979 | 4.979 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1224.1528 0 -1224.1528 10872.732 85 0 -1275.6091 0 -1275.6091 -1557.0507 Loop time of 0.742385 on 1 procs for 85 steps with 476 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1224.15282516425 -1275.60814211697 -1275.60910032371 Force two-norm initial, final = 91.354528 0.093256115 Force max component initial, final = 32.041266 0.012677347 Final line search alpha, max atom move = 1.0000000 0.012677347 Iterations, force evaluations = 85 154 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.72016 | 0.72016 | 0.72016 | 0.0 | 97.01 Neigh | 0.012797 | 0.012797 | 0.012797 | 0.0 | 1.72 Comm | 0.0056221 | 0.0056221 | 0.0056221 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003805 | | | 0.51 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4836.00 ave 4836 max 4836 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: 106496.0 ave 106496 max 106496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106496 Ave neighs/atom = 223.73109 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 2 19 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 85 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.979 | 4.979 | 4.979 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -1275.6091 0 -1275.6091 -1557.0507 8038.013 88 0 -1275.6219 0 -1275.6219 -9.0570826 8021.0445 Loop time of 0.0286013 on 1 procs for 3 steps with 476 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 = -1275.60910032371 -1275.62188526456 -1275.62192447429 Force two-norm initial, final = 14.616788 0.19820995 Force max component initial, final = 11.416235 0.11499956 Final line search alpha, max atom move = 0.0014526249 0.00016705122 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.027558 | 0.027558 | 0.027558 | 0.0 | 96.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021124 | 0.00021124 | 0.00021124 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008322 | | | 2.91 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4762.00 ave 4762 max 4762 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: 106632.0 ave 106632 max 106632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106632 Ave neighs/atom = 224.01681 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 2 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 5.117 | 5.117 | 5.117 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1275.6219 0 -1275.6219 -9.0570826 Loop time of 1.604e-06 on 1 procs for 0 steps with 476 atoms 124.7% 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 | | 1.604e-06 | | |100.00 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4771.00 ave 4771 max 4771 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: 106720.0 ave 106720 max 106720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106720 Ave neighs/atom = 224.20168 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 2 19 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 5.117 | 5.117 | 5.117 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 -1275.6219 -1275.6219 9.08556 88.816757 9.9399527 -9.0570826 -9.0570826 -19.189818 -22.929473 14.948044 2.6037719 327.6293 Loop time of 1.654e-06 on 1 procs for 0 steps with 476 atoms 181.4% 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 | | 1.654e-06 | | |100.00 Nlocal: 476.000 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4771.00 ave 4771 max 4771 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53360.0 ave 53360 max 53360 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106720.0 ave 106720 max 106720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106720 Ave neighs/atom = 224.20168 Neighbor list builds = 0 Dangerous builds = 0 476 -1275.62192447429 eV 2.60377193061975 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01