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 = 4.0500000 4.0500000 4.0500000 Created orthogonal box = (0.0000000 -47.920246 0.0000000) to (58.690076 47.920246 9.9204335) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7074373 6.1611745 6.6136223 Created 1662 atoms using lattice units in orthogonal box = (0.0000000 -47.920246 0.0000000) to (58.690076 47.920246 9.9204335) create_atoms CPU = 0.003 seconds 1662 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7074373 6.1611745 6.6136223 Created 1686 atoms using lattice units in orthogonal box = (0.0000000 -47.920246 0.0000000) to (58.690076 47.920246 9.9204335) create_atoms CPU = 0.002 seconds 1686 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 14 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 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3348 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_664470114311_005#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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 7.001 | 7.001 | 7.001 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11107.05 0 -11107.05 4296.7337 85 0 -11215.273 0 -11215.273 1795.8555 Loop time of 4.24422 on 1 procs for 85 steps with 3348 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 = -11107.0503429231 -11215.2619842994 -11215.2730650668 Force two-norm initial, final = 39.548844 0.25132438 Force max component initial, final = 3.5889078 0.042001503 Final line search alpha, max atom move = 1.0000000 0.042001503 Iterations, force evaluations = 85 137 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.0506 | 4.0506 | 4.0506 | 0.0 | 95.44 Neigh | 0.14821 | 0.14821 | 0.14821 | 0.0 | 3.49 Comm | 0.019377 | 0.019377 | 0.019377 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02606 | | | 0.61 Nlocal: 3348.00 ave 3348 max 3348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11092.0 ave 11092 max 11092 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: 581054.0 ave 581054 max 581054 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 581054 Ave neighs/atom = 173.55257 Neighbor list builds = 4 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 7.000 | 7.000 | 7.000 Mbytes Step Temp E_pair E_mol TotEng Press Volume 85 0 -11215.273 0 -11215.273 1795.8555 55801.305 90 0 -11215.532 0 -11215.532 -21.868548 55930.253 Loop time of 0.217088 on 1 procs for 5 steps with 3348 atoms 94.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11215.2730650667 -11215.5314414893 -11215.5319632224 Force two-norm initial, final = 139.71857 1.3652514 Force max component initial, final = 133.01818 0.82737478 Final line search alpha, max atom move = 0.00025422708 0.00021034108 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21241 | 0.21241 | 0.21241 | 0.0 | 97.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00064257 | 0.00064257 | 0.00064257 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00404 | | | 1.86 Nlocal: 3348.00 ave 3348 max 3348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11068.0 ave 11068 max 11068 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: 581098.0 ave 581098 max 581098 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 581098 Ave neighs/atom = 173.56571 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 7.139 | 7.139 | 7.139 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11215.532 0 -11215.532 -21.868548 Loop time of 2.347e-06 on 1 procs for 0 steps with 3348 atoms 170.4% 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 | | 2.347e-06 | | |100.00 Nlocal: 3348.00 ave 3348 max 3348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11102.0 ave 11102 max 11102 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: 580782.0 ave 580782 max 580782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 580782 Ave neighs/atom = 173.47133 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 7.139 | 7.139 | 7.139 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 -11215.532 -11215.532 58.673412 96.242103 9.9046774 -21.868548 -21.868548 -22.202639 -19.739692 -23.663312 2.5207364 2443.5151 Loop time of 2.426e-06 on 1 procs for 0 steps with 3348 atoms 247.3% 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 | | 2.426e-06 | | |100.00 Nlocal: 3348.00 ave 3348 max 3348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11102.0 ave 11102 max 11102 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 290391.0 ave 290391 max 290391 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 580782.0 ave 580782 max 580782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 580782 Ave neighs/atom = 173.47133 Neighbor list builds = 0 Dangerous builds = 0 3348 -11195.1780831578 eV 2.52073640566777 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05