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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -60.968189 0.0000000) to (24.890159 60.968189 8.6222040) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9736381 5.2839097 5.7481360 Created 1197 atoms using lattice units in orthogonal box = (0.0000000 -60.968189 0.0000000) to (24.890159 60.968189 8.6222040) create_atoms CPU = 0.002 seconds 1197 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9736381 5.2839097 5.7481360 Created 1205 atoms using lattice units in orthogonal box = (0.0000000 -60.968189 0.0000000) to (24.890159 60.968189 8.6222040) create_atoms CPU = 0.002 seconds 1205 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 6 29 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 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 2400 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_010613863288_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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 6 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 6.947 | 6.947 | 6.947 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10546.821 0 -10546.821 4697.1879 43 0 -10652.514 0 -10652.514 3454.7843 Loop time of 1.72074 on 1 procs for 43 steps with 2400 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10546.8210394167 -10652.5047030015 -10652.5140106902 Force two-norm initial, final = 35.440073 0.33192481 Force max component initial, final = 4.3098786 0.028089149 Final line search alpha, max atom move = 1.0000000 0.028089149 Iterations, force evaluations = 43 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6292 | 1.6292 | 1.6292 | 0.0 | 94.68 Neigh | 0.072307 | 0.072307 | 0.072307 | 0.0 | 4.20 Comm | 0.0087138 | 0.0087138 | 0.0087138 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0105 | | | 0.61 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10967.0 ave 10967 max 10967 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: 538268.0 ave 538268 max 538268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 538268 Ave neighs/atom = 224.27833 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 6 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.946 | 6.946 | 6.946 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -10652.514 0 -10652.514 3454.7843 26168.525 48 0 -10652.793 0 -10652.793 -12.14556 26219.359 Loop time of 0.197413 on 1 procs for 5 steps with 2400 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 = -10652.5140106902 -10652.7931631652 -10652.7933784648 Force two-norm initial, final = 156.60236 1.0956102 Force max component initial, final = 155.89168 0.80693961 Final line search alpha, max atom move = 0.00022121542 0.00017850748 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19311 | 0.19311 | 0.19311 | 0.0 | 97.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00067434 | 0.00067434 | 0.00067434 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003634 | | | 1.84 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10929.0 ave 10929 max 10929 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: 539490.0 ave 539490 max 539490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 539490 Ave neighs/atom = 224.78750 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 6 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 7.084 | 7.084 | 7.084 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10652.793 0 -10652.793 -12.14556 Loop time of 2.241e-06 on 1 procs for 0 steps with 2400 atoms 223.1% 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 | | 2.241e-06 | | |100.00 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10929.0 ave 10929 max 10929 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: 539310.0 ave 539310 max 539310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 539310 Ave neighs/atom = 224.71250 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 6 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 7.084 | 7.084 | 7.084 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 -10652.793 -10652.793 24.867709 122.38485 8.6150666 -12.14556 -12.14556 32.414369 -19.582511 -49.268538 2.313239 697.41012 Loop time of 2.61e-06 on 1 procs for 0 steps with 2400 atoms 229.9% 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 | | 2.61e-06 | | |100.00 Nlocal: 2400.00 ave 2400 max 2400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10929.0 ave 10929 max 10929 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 269655.0 ave 269655 max 269655 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 539310.0 ave 539310 max 539310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 539310 Ave neighs/atom = 224.71250 Neighbor list builds = 0 Dangerous builds = 0 2400 -10652.7933784648 eV 2.31323898995995 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02