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 = 4.0397985 4.0397985 4.0397985 Created orthogonal box = (0.0000000 -49.969547 0.0000000) to (16.656516 49.969547 4.0397985) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8989752 4.8989752 4.0397985 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -49.969547 0.0000000) to (16.656516 49.969547 4.0397985) create_atoms CPU = 0.002 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8989752 4.8989752 4.0397985 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -49.969547 0.0000000) to (16.656516 49.969547 4.0397985) create_atoms CPU = 0.001 seconds 206 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 3 17 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 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 408 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_279544746097_004#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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 3 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 4.933 | 4.933 | 4.933 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1135.5814 0 -1135.5814 13273.878 49 0 -1169.899 0 -1169.899 3918.8002 Loop time of 2.22136 on 1 procs for 49 steps with 408 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 = -1135.58137474883 -1169.89790160433 -1169.898986295 Force two-norm initial, final = 64.577720 0.090204673 Force max component initial, final = 20.448024 0.016896727 Final line search alpha, max atom move = 1.0000000 0.016896727 Iterations, force evaluations = 49 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1751 | 2.1751 | 2.1751 | 0.0 | 97.92 Neigh | 0.021247 | 0.021247 | 0.021247 | 0.0 | 0.96 Comm | 0.016885 | 0.016885 | 0.016885 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008178 | | | 0.37 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7464.00 ave 7464 max 7464 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: 169876.0 ave 169876 max 169876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 169876 Ave neighs/atom = 416.36275 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 3 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.933 | 4.933 | 4.933 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -1169.899 0 -1169.899 3918.8002 6724.7984 55 0 -1169.9659 0 -1169.9659 -53.426435 6759.7617 Loop time of 0.194752 on 1 procs for 6 steps with 408 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 = -1169.89898629499 -1169.9657656153 -1169.96590240893 Force two-norm initial, final = 30.348688 0.69570179 Force max component initial, final = 24.129772 0.47090465 Final line search alpha, max atom move = 0.00077481582 0.00036486437 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18934 | 0.18934 | 0.18934 | 0.0 | 97.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013958 | 0.0013958 | 0.0013958 | 0.0 | 0.72 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004016 | | | 2.06 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7495.00 ave 7495 max 7495 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: 170136.0 ave 170136 max 170136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 170136 Ave neighs/atom = 417.00000 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 3 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 5.072 | 5.072 | 5.072 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1169.9659 0 -1169.9659 -53.426435 Loop time of 6.575e-06 on 1 procs for 0 steps with 408 atoms 152.1% 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 | | 6.575e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7513.00 ave 7513 max 7513 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: 165004.0 ave 165004 max 165004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165004 Ave neighs/atom = 404.42157 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 3 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 5.072 | 5.072 | 5.072 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 -1169.9659 -1169.9659 16.635326 100.45347 4.0451544 -53.426435 -53.426435 -111.47028 53.70004 -102.50906 2.5551246 251.56123 Loop time of 6.775e-06 on 1 procs for 0 steps with 408 atoms 295.2% 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 | | 6.775e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7513.00 ave 7513 max 7513 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 82502.0 ave 82502 max 82502 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 165004.0 ave 165004 max 165004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 165004 Ave neighs/atom = 404.42157 Neighbor list builds = 0 Dangerous builds = 0 408 -1169.96590240893 eV 2.55512456331743 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02