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 = 4.0499992 4.0499992 4.0499992 Created orthogonal box = (0.0000000 -43.811489 0.0000000) to (14.602480 43.811489 4.0499992) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6163383 5.6163383 4.0499992 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -43.811489 0.0000000) to (14.602480 43.811489 4.0499992) create_atoms CPU = 0.001 seconds 158 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6163383 5.6163383 4.0499992 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -43.811489 0.0000000) to (14.602480 43.811489 4.0499992) create_atoms CPU = 0.001 seconds 158 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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 26 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 308 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_262519520678_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.430 | 4.430 | 4.430 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1025.0272 0 -1025.0272 -1172.6999 18 0 -1028.8566 0 -1028.8566 -6067.6375 Loop time of 1.17273 on 1 procs for 18 steps with 308 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1025.02722796562 -1028.85612385037 -1028.85659547967 Force two-norm initial, final = 6.8870581 0.056419959 Force max component initial, final = 2.0824231 0.0095379111 Final line search alpha, max atom move = 1.0000000 0.0095379111 Iterations, force evaluations = 18 31 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1686 | 1.1686 | 1.1686 | 0.0 | 99.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020859 | 0.0020859 | 0.0020859 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00208 | | | 0.18 Nlocal: 308.000 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2837.00 ave 2837 max 2837 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: 23808.0 ave 23808 max 23808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23808 Ave neighs/atom = 77.298701 Neighbor list builds = 0 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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 18 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.430 | 4.430 | 4.430 Mbytes Step Temp E_pair E_mol TotEng Press Volume 18 0 -1028.8566 0 -1028.8566 -6067.6375 5182.0256 23 0 -1028.9159 0 -1028.9159 -1120.4438 5148.2168 Loop time of 0.302165 on 1 procs for 5 steps with 308 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1028.85659547967 -1028.91578447706 -1028.91592489872 Force two-norm initial, final = 25.365387 0.066765073 Force max component initial, final = 18.749116 0.010653819 Final line search alpha, max atom move = 0.0018830145 2.0061296e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29993 | 0.29993 | 0.29993 | 0.0 | 99.26 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00051768 | 0.00051768 | 0.00051768 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001717 | | | 0.57 Nlocal: 308.000 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2837.00 ave 2837 max 2837 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: 24184.0 ave 24184 max 24184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24184 Ave neighs/atom = 78.519481 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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.567 | 4.567 | 4.567 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1028.9159 0 -1028.9159 -1120.4438 Loop time of 6.475e-06 on 1 procs for 0 steps with 308 atoms 169.9% 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 | | 6.475e-06 | | |100.00 Nlocal: 308.000 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2837.00 ave 2837 max 2837 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: 25096.0 ave 25096 max 25096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25096 Ave neighs/atom = 81.480519 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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 4.567 | 4.567 | 4.567 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 -1028.9159 -1028.9159 14.563624 87.622978 4.0343107 -1120.4438 -1120.4438 -2.9424909 -3358.6393 0.25046987 2.4974826 202.85026 Loop time of 6.455e-06 on 1 procs for 0 steps with 308 atoms 232.4% 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 | | 6.455e-06 | | |100.00 Nlocal: 308.000 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2837.00 ave 2837 max 2837 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12548.0 ave 12548 max 12548 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 25096.0 ave 25096 max 25096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 25096 Ave neighs/atom = 81.480519 Neighbor list builds = 0 Dangerous builds = 0 308 -1028.91592489872 eV 2.49748262584259 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02