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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -34.720000 0.0000000) to (28.348761 34.720000 7.0144993) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0498230 4.0152381 4.6763329 Created 588 atoms using lattice units in orthogonal box = (0.0000000 -34.720000 0.0000000) to (28.348761 34.720000 7.0144993) create_atoms CPU = 0.001 seconds 588 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0498230 4.0152381 4.6763329 Created 590 atoms using lattice units in orthogonal box = (0.0000000 -34.720000 0.0000000) to (28.348761 34.720000 7.0144993) create_atoms CPU = 0.001 seconds 590 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 25 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1172 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_856956178669_001#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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.553 | 4.553 | 4.553 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4412.6542 0 -4412.6542 82331.435 79 0 -4995.0704 0 -4995.0704 4834.1286 Loop time of 3.41296 on 1 procs for 79 steps with 1172 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 = -4412.6541520105 -4995.06694741386 -4995.07040177093 Force two-norm initial, final = 860.67194 0.24909145 Force max component initial, final = 255.36848 0.041011008 Final line search alpha, max atom move = 1.0000000 0.041011008 Iterations, force evaluations = 79 138 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3891 | 3.3891 | 3.3891 | 0.0 | 99.30 Neigh | 0.012183 | 0.012183 | 0.012183 | 0.0 | 0.36 Comm | 0.0047224 | 0.0047224 | 0.0047224 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006905 | | | 0.20 Nlocal: 1172.00 ave 1172 max 1172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3574.00 ave 3574 max 3574 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: 68156.0 ave 68156 max 68156 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68156 Ave neighs/atom = 58.153584 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.554 | 4.554 | 4.554 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -4995.0704 0 -4995.0704 4834.1286 13808.308 85 0 -4995.3739 0 -4995.3739 -124.97182 13845.561 Loop time of 0.194412 on 1 procs for 6 steps with 1172 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 = -4995.07040177093 -4995.3701581522 -4995.37390055468 Force two-norm initial, final = 112.68317 2.2513087 Force max component initial, final = 110.32950 1.7688467 Final line search alpha, max atom move = 0.00011922726 0.00021089474 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19289 | 0.19289 | 0.19289 | 0.0 | 99.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022897 | 0.00022897 | 0.00022897 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001292 | | | 0.66 Nlocal: 1172.00 ave 1172 max 1172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3616.00 ave 3616 max 3616 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: 68236.0 ave 68236 max 68236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68236 Ave neighs/atom = 58.221843 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.692 | 4.692 | 4.692 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4995.3739 0 -4995.3739 -124.97182 Loop time of 1.775e-06 on 1 procs for 0 steps with 1172 atoms 112.7% 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 | | 1.775e-06 | | |100.00 Nlocal: 1172.00 ave 1172 max 1172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3613.00 ave 3613 max 3613 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: 68208.0 ave 68208 max 68208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68208 Ave neighs/atom = 58.197952 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.692 | 4.692 | 4.692 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 -4995.3739 -4995.3739 28.320054 69.829844 7.0012472 -124.97182 -124.97182 -204.47959 -139.99748 -30.438401 2.2997179 1173.8503 Loop time of 1.555e-06 on 1 procs for 0 steps with 1172 atoms 128.6% 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 | | 1.555e-06 | | |100.00 Nlocal: 1172.00 ave 1172 max 1172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3613.00 ave 3613 max 3613 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34104.0 ave 34104 max 34104 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 68208.0 ave 68208 max 68208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68208 Ave neighs/atom = 58.197952 Neighbor list builds = 0 Dangerous builds = 0 1172 -4995.37390055468 eV 2.29971787479768 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03