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 -49.239597 0.0000000) to (40.203962 49.239597 9.9479008) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7434232 5.6943751 6.6319338 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -49.239597 0.0000000) to (40.203962 49.239597 9.9479008) create_atoms CPU = 0.002 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7434232 5.6943751 6.6319338 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -49.239597 0.0000000) to (40.203962 49.239597 9.9479008) create_atoms CPU = 0.001 seconds 1184 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 = 9 21 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 24 atoms, new total = 2336 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 = 9 21 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) = 6.889 | 6.889 | 6.889 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6055.4569 0 -6055.4569 10203.733 69 0 -6259.6401 0 -6259.6401 -418.3349 Loop time of 2.55328 on 1 procs for 69 steps with 2336 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 = -6055.45692513639 -6259.63545453292 -6259.64006536931 Force two-norm initial, final = 168.20700 0.20082815 Force max component initial, final = 25.144923 0.017419979 Final line search alpha, max atom move = 1.0000000 0.017419979 Iterations, force evaluations = 69 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4734 | 2.4734 | 2.4734 | 0.0 | 96.87 Neigh | 0.056442 | 0.056442 | 0.056442 | 0.0 | 2.21 Comm | 0.010716 | 0.010716 | 0.010716 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01277 | | | 0.50 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9828.00 ave 9828 max 9828 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: 521728.0 ave 521728 max 521728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 521728 Ave neighs/atom = 223.34247 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 = 9 21 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 : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.891 | 6.891 | 6.891 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -6259.6401 0 -6259.6401 -418.3349 39386.264 72 0 -6259.691 0 -6259.691 25.085071 39362.976 Loop time of 0.118103 on 1 procs for 3 steps with 2336 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 = -6259.64006536939 -6259.6909463628 -6259.69102794998 Force two-norm initial, final = 52.433278 1.3676329 Force max component initial, final = 50.127052 1.0854514 Final line search alpha, max atom move = 0.00048491398 0.00052635054 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11546 | 0.11546 | 0.11546 | 0.0 | 97.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00046465 | 0.00046465 | 0.00046465 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002173 | | | 1.84 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10129.0 ave 10129 max 10129 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: 522000.0 ave 522000 max 522000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 522000 Ave neighs/atom = 223.45890 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 = 9 21 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) = 7.029 | 7.029 | 7.029 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6259.691 0 -6259.691 25.085071 Loop time of 1.725e-06 on 1 procs for 0 steps with 2336 atoms 115.9% 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 | | 1.725e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10129.0 ave 10129 max 10129 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: 522016.0 ave 522016 max 522016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 522016 Ave neighs/atom = 223.46575 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 = 9 21 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) = 7.029 | 7.029 | 7.029 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 -6259.691 -6259.691 40.216914 98.563276 9.9303385 25.085071 25.085071 -1.5521049 44.218443 32.588875 2.5571149 1675.259 Loop time of 4.369e-06 on 1 procs for 0 steps with 2336 atoms 251.8% 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 | | 4.369e-06 | | |100.00 Nlocal: 2336.00 ave 2336 max 2336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10129.0 ave 10129 max 10129 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 261008.0 ave 261008 max 261008 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 522016.0 ave 522016 max 522016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 522016 Ave neighs/atom = 223.46575 Neighbor list builds = 0 Dangerous builds = 0 2336 -6259.69102794998 eV 2.557114863588 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03