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 = 3.7004755 3.7004755 3.7004755 Created orthogonal box = (0.0000000 -39.855341 0.0000000) to (19.927671 39.855341 3.7004755) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8101274 4.8101274 3.7004755 Created 232 atoms using lattice units in orthogonal box = (0.0000000 -39.855341 0.0000000) to (19.927671 39.855341 3.7004755) create_atoms CPU = 0.000 seconds 232 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8101274 4.8101274 3.7004755 Created 234 atoms using lattice units in orthogonal box = (0.0000000 -39.855341 0.0000000) to (19.927671 39.855341 3.7004755) create_atoms CPU = 0.000 seconds 234 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 6 21 1 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 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 460 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_466808877130_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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 4.490 | 4.490 | 4.490 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1704.8382 0 -1704.8382 48110.516 116 0 -1831.5353 0 -1831.5353 -4369.0343 Loop time of 0.846699 on 1 procs for 116 steps with 460 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1704.83820411118 -1831.53389552151 -1831.53527629272 Force two-norm initial, final = 289.80111 0.14602996 Force max component initial, final = 101.22436 0.027876274 Final line search alpha, max atom move = 1.0000000 0.027876274 Iterations, force evaluations = 116 222 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.8273 | 0.8273 | 0.8273 | 0.0 | 97.71 Neigh | 0.0043239 | 0.0043239 | 0.0043239 | 0.0 | 0.51 Comm | 0.0085542 | 0.0085542 | 0.0085542 | 0.0 | 1.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006524 | | | 0.77 Nlocal: 460.000 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4460.00 ave 4460 max 4460 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: 67248.0 ave 67248 max 67248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67248 Ave neighs/atom = 146.19130 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 6 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 116 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.490 | 4.490 | 4.490 Mbytes Step Temp E_pair E_mol TotEng Press Volume 116 0 -1831.5353 0 -1831.5353 -4369.0343 5878.0139 523 0 -1842.5513 0 -1842.5513 663.20548 5479.8317 Loop time of 2.17028 on 1 procs for 407 steps with 460 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 = -1831.53527629272 -1842.54968494679 -1842.55128523856 Force two-norm initial, final = 93.956316 5.3831256 Force max component initial, final = 70.549085 2.6104066 Final line search alpha, max atom move = 0.00028208373 0.00073635323 Iterations, force evaluations = 407 474 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0252 | 2.0252 | 2.0252 | 0.0 | 93.31 Neigh | 0.047352 | 0.047352 | 0.047352 | 0.0 | 2.18 Comm | 0.017754 | 0.017754 | 0.017754 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.07999 | | | 3.69 Nlocal: 460.000 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4490.00 ave 4490 max 4490 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: 74776.0 ave 74776 max 74776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74776 Ave neighs/atom = 162.55652 Neighbor list builds = 11 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 6 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 4.627 | 4.627 | 4.627 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1842.5513 0 -1842.5513 663.20548 Loop time of 2.032e-06 on 1 procs for 0 steps with 460 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: 460.000 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4490.00 ave 4490 max 4490 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: 74840.0 ave 74840 max 74840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74840 Ave neighs/atom = 162.69565 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 = 7.8 ghost atom cutoff = 7.8 binsize = 3.9, bins = 6 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.8 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) = 4.627 | 4.627 | 4.627 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 -1842.5513 -1842.5513 20.85249 67.612194 3.8867292 663.20548 663.20548 797.91916 647.38077 544.31653 2.2341816 326.76076 Loop time of 2.172e-06 on 1 procs for 0 steps with 460 atoms 230.2% 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 | | 2.172e-06 | | |100.00 Nlocal: 460.000 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4490.00 ave 4490 max 4490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37420.0 ave 37420 max 37420 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74840.0 ave 74840 max 74840 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74840 Ave neighs/atom = 162.69565 Neighbor list builds = 0 Dangerous builds = 0 460 -1842.55128523856 eV 2.23418157874445 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03