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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -42.681261 0.0000000) to (34.846230 42.681261 8.6222058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9780328 4.9355211 5.7481372 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -42.681261 0.0000000) to (34.846230 42.681261 8.6222058) create_atoms CPU = 0.002 seconds 1184 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9780328 4.9355211 5.7481372 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -42.681261 0.0000000) to (34.846230 42.681261 8.6222058) 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 22 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 48 atoms, new total = 2320 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.428 | 6.428 | 6.428 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10188.249 0 -10188.249 -294.58565 76 0 -10262.905 0 -10262.905 -12227.615 Loop time of 2.66288 on 1 procs for 76 steps with 2320 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 = -10188.2488948412 -10262.8967852505 -10262.9053472588 Force two-norm initial, final = 44.409763 0.41178621 Force max component initial, final = 5.5831300 0.039307325 Final line search alpha, max atom move = 1.0000000 0.039307325 Iterations, force evaluations = 76 142 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6143 | 2.6143 | 2.6143 | 0.0 | 98.17 Neigh | 0.026036 | 0.026036 | 0.026036 | 0.0 | 0.98 Comm | 0.0099548 | 0.0099548 | 0.0099548 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01262 | | | 0.47 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8820.00 ave 8820 max 8820 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: 407904.0 ave 407904 max 407904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 407904 Ave neighs/atom = 175.82069 Neighbor list builds = 1 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.431 | 6.431 | 6.431 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -10262.905 0 -10262.905 -12227.615 25647.286 80 0 -10263.303 0 -10263.303 -3351.7626 25524.882 Loop time of 0.130141 on 1 procs for 4 steps with 2320 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 = -10262.9053472591 -10263.3034587183 -10263.3034817414 Force two-norm initial, final = 234.03855 0.69016115 Force max component initial, final = 178.89359 0.31805738 Final line search alpha, max atom move = 0.0016363959 0.00052046779 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1272 | 0.1272 | 0.1272 | 0.0 | 97.74 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00046835 | 0.00046835 | 0.00046835 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002476 | | | 1.90 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8933.00 ave 8933 max 8933 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: 406912.0 ave 406912 max 406912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 406912 Ave neighs/atom = 175.39310 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.569 | 6.569 | 6.569 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10263.303 0 -10263.303 -3351.7626 Loop time of 1.69e-06 on 1 procs for 0 steps with 2320 atoms 177.5% 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 | | 1.69e-06 | | |100.00 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8944.00 ave 8944 max 8944 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: 407264.0 ave 407264 max 407264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 407264 Ave neighs/atom = 175.54483 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 9 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.569 | 6.569 | 6.569 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 -10263.303 -10263.303 34.771523 85.362522 8.5994919 -3351.7626 -3351.7626 -14.157711 -10061.042 19.911616 2.2703594 1413.7092 Loop time of 2.032e-06 on 1 procs for 0 steps with 2320 atoms 196.9% 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 | | 2.032e-06 | | |100.00 Nlocal: 2320.00 ave 2320 max 2320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8944.00 ave 8944 max 8944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 203632.0 ave 203632 max 203632 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 407264.0 ave 407264 max 407264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 407264 Ave neighs/atom = 175.54483 Neighbor list builds = 0 Dangerous builds = 0 2320 -10263.3034817414 eV 2.27035941906504 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03