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 = 2.8603420 2.8603420 2.8603420 Created orthogonal box = (0.0000000 -40.856716 0.0000000) to (28.888038 40.856716 4.0451344) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.5314570 3.6047519 4.0451344 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -40.856716 0.0000000) to (28.888038 40.856716 4.0451344) create_atoms CPU = 0.001 seconds 410 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.5314570 3.6047519 4.0451344 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -40.856716 0.0000000) to (28.888038 40.856716 4.0451344) create_atoms CPU = 0.001 seconds 410 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 = 8 21 2 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 4 atoms, new total = 816 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 = 8 21 2 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) = 4.960 | 4.960 | 4.960 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3424.3567 0 -3424.3567 32122.069 437 0 -3561.926 0 -3561.926 5079.5661 Loop time of 5.38299 on 1 procs for 437 steps with 816 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 = -3424.35673281765 -3561.92240812613 -3561.92596559788 Force two-norm initial, final = 70.191180 0.31034669 Force max component initial, final = 15.048755 0.11857513 Final line search alpha, max atom move = 0.75202331 0.089171263 Iterations, force evaluations = 437 820 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.207 | 5.207 | 5.207 | 0.0 | 96.73 Neigh | 0.10505 | 0.10505 | 0.10505 | 0.0 | 1.95 Comm | 0.040601 | 0.040601 | 0.040601 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03032 | | | 0.56 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6689.00 ave 6689 max 6689 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: 130982.0 ave 130982 max 130982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130982 Ave neighs/atom = 160.51716 Neighbor list builds = 13 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 = 8 21 2 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 : 437 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.960 | 4.960 | 4.960 Mbytes Step Temp E_pair E_mol TotEng Press Volume 437 0 -3561.926 0 -3561.926 5079.5661 9548.7046 441 0 -3562.1658 0 -3562.1658 -8081.7039 9599.9414 Loop time of 0.0447476 on 1 procs for 4 steps with 816 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 = -3561.92596559787 -3562.16418877768 -3562.16580958269 Force two-norm initial, final = 128.34330 0.49940303 Force max component initial, final = 93.467993 0.077403338 Final line search alpha, max atom move = 0.00019856735 1.5369776e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.043108 | 0.043108 | 0.043108 | 0.0 | 96.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031134 | 0.00031134 | 0.00031134 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001328 | | | 2.97 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6669.00 ave 6669 max 6669 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: 130910.0 ave 130910 max 130910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 130910 Ave neighs/atom = 160.42892 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 = 8 21 2 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) = 5.098 | 5.098 | 5.098 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3562.1658 0 -3562.1658 -8081.7039 Loop time of 1.775e-06 on 1 procs for 0 steps with 816 atoms 169.0% 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: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6664.00 ave 6664 max 6664 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: 129916.0 ave 129916 max 129916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129916 Ave neighs/atom = 159.21078 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 = 8 21 2 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) = 5.098 | 5.098 | 5.098 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 -3562.1658 -3562.1658 28.978572 81.713431 4.0541345 -8081.7039 -8081.7039 -4.1799363 -24249.546 8.6143431 2.2826189 5186.2035 Loop time of 1.882e-06 on 1 procs for 0 steps with 816 atoms 159.4% 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 | | 1.882e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6664.00 ave 6664 max 6664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 64958.0 ave 64958 max 64958 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 129916.0 ave 129916 max 129916 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129916 Ave neighs/atom = 159.21078 Neighbor list builds = 0 Dangerous builds = 0 816 -3562.16580958269 eV 2.28261894160851 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05