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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -41.516379 0.0000000) to (20.758189 41.516379 3.5600001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8842799 4.8842799 3.5600001 Created 271 atoms using lattice units in orthogonal box = (0.0000000 -41.516379 0.0000000) to (20.758189 41.516379 3.5600001) create_atoms CPU = 0.002 seconds 271 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8842799 4.8842799 3.5600001 Created 273 atoms using lattice units in orthogonal box = (0.0000000 -41.516379 0.0000000) to (20.758189 41.516379 3.5600001) create_atoms CPU = 0.001 seconds 273 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 = 6 22 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 544 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 = 6 22 1 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) = 4.528 | 4.528 | 4.528 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2252.3034 0 -2252.3034 63243.74 69 0 -2380.5983 0 -2380.5983 17430.098 Loop time of 1.564 on 1 procs for 69 steps with 544 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 = -2252.30339424042 -2380.59608528037 -2380.5983386824 Force two-norm initial, final = 286.87297 0.23661935 Force max component initial, final = 72.812813 0.062734329 Final line search alpha, max atom move = 1.0000000 0.062734329 Iterations, force evaluations = 69 132 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5214 | 1.5214 | 1.5214 | 0.0 | 97.28 Neigh | 0.012895 | 0.012895 | 0.012895 | 0.0 | 0.82 Comm | 0.017521 | 0.017521 | 0.017521 | 0.0 | 1.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01219 | | | 0.78 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5621.00 ave 5621 max 5621 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: 95382.0 ave 95382 max 95382 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95382 Ave neighs/atom = 175.33456 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 = 6 22 1 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 : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.524 | 4.524 | 4.524 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -2380.5983 0 -2380.5983 17430.098 6136.0508 80 0 -2381.1072 0 -2381.1072 501.19829 6181.8148 Loop time of 0.141772 on 1 procs for 11 steps with 544 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 = -2380.5983386824 -2381.10496354268 -2381.10716788054 Force two-norm initial, final = 131.10799 3.6842291 Force max component initial, final = 116.85947 3.0391089 Final line search alpha, max atom move = 0.00036803129 0.0011184872 Iterations, force evaluations = 11 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13614 | 0.13614 | 0.13614 | 0.0 | 96.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012732 | 0.0012732 | 0.0012732 | 0.0 | 0.90 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00436 | | | 3.08 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5111.00 ave 5111 max 5111 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: 95116.0 ave 95116 max 95116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 95116 Ave neighs/atom = 174.84559 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 = 6 22 1 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) = 4.662 | 4.662 | 4.662 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2381.1072 0 -2381.1072 501.19829 Loop time of 5.994e-06 on 1 procs for 0 steps with 544 atoms 200.2% 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 | | 5.994e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5081.00 ave 5081 max 5081 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: 94932.0 ave 94932 max 94932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94932 Ave neighs/atom = 174.50735 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 = 6 22 1 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) = 4.662 | 4.662 | 4.662 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 -2381.1072 -2381.1072 20.749071 83.865586 3.5524956 501.19829 501.19829 403.45536 795.56369 304.57582 2.3318132 269.12437 Loop time of 6.725e-06 on 1 procs for 0 steps with 544 atoms 237.9% 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 | | 6.725e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5081.00 ave 5081 max 5081 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47466.0 ave 47466 max 47466 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 94932.0 ave 94932 max 94932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94932 Ave neighs/atom = 174.50735 Neighbor list builds = 0 Dangerous builds = 0 544 -2381.10716788054 eV 2.33181321759328 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02