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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -64.211813 0.0000000) to (45.404609 64.211813 5.0449565) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1660580 5.9455383 5.0449565 Created 1296 atoms using lattice units in orthogonal box = (0.0000000 -64.211813 0.0000000) to (45.404609 64.211813 5.0449565) create_atoms CPU = 0.004 seconds 1296 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1660580 5.9455383 5.0449565 Created 1300 atoms using lattice units in orthogonal box = (0.0000000 -64.211813 0.0000000) to (45.404609 64.211813 5.0449565) create_atoms CPU = 0.003 seconds 1300 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 = 17 46 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 2580 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 17 46 2 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) = 5.313 | 5.313 | 5.313 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10605.132 0 -10605.132 19848.422 184 0 -10896.913 0 -10896.913 41295.641 Loop time of 26.8763 on 1 procs for 184 steps with 2580 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 = -10605.1315904621 -10896.9056008829 -10896.91331059 Force two-norm initial, final = 378.00563 0.50258729 Force max component initial, final = 90.565296 0.066421087 Final line search alpha, max atom move = 1.0000000 0.066421087 Iterations, force evaluations = 184 354 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 26.758 | 26.758 | 26.758 | 0.0 | 99.56 Neigh | 0.025727 | 0.025727 | 0.025727 | 0.0 | 0.10 Comm | 0.043018 | 0.043018 | 0.043018 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04935 | | | 0.18 Nlocal: 2580.00 ave 2580 max 2580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8679.00 ave 8679 max 8679 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: 152912.0 ave 152912 max 152912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 152912 Ave neighs/atom = 59.268217 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 = 17 46 2 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 : 184 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.312 | 5.312 | 5.312 Mbytes Step Temp E_pair E_mol TotEng Press Volume 184 0 -10896.913 0 -10896.913 41295.641 29417.265 195 0 -10902.279 0 -10902.279 -142.57382 29832.786 Loop time of 1.05737 on 1 procs for 11 steps with 2580 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 = -10896.91331059 -10902.2783458524 -10902.2786986642 Force two-norm initial, final = 1318.4834 7.3459291 Force max component initial, final = 827.01130 5.6484636 Final line search alpha, max atom move = 0.00016849688 0.00095174849 Iterations, force evaluations = 11 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0362 | 1.0362 | 1.0362 | 0.0 | 98.00 Neigh | 0.012835 | 0.012835 | 0.012835 | 0.0 | 1.21 Comm | 0.0013156 | 0.0013156 | 0.0013156 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006977 | | | 0.66 Nlocal: 2580.00 ave 2580 max 2580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8665.00 ave 8665 max 8665 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: 147096.0 ave 147096 max 147096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 147096 Ave neighs/atom = 57.013953 Neighbor list builds = 1 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 = 17 47 2 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) = 5.450 | 5.450 | 5.450 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10902.279 0 -10902.279 -142.57382 Loop time of 2.352e-06 on 1 procs for 0 steps with 2580 atoms 127.6% 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 | | 2.352e-06 | | |100.00 Nlocal: 2580.00 ave 2580 max 2580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8665.00 ave 8665 max 8665 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: 146984.0 ave 146984 max 146984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146984 Ave neighs/atom = 56.970543 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 = 17 47 2 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) = 5.450 | 5.450 | 5.450 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 -10902.279 -10902.279 45.651637 129.60475 5.0421589 -142.57382 -142.57382 -146.78729 22.249629 -303.18379 2.4048593 2513.9047 Loop time of 1.0164e-05 on 1 procs for 0 steps with 2580 atoms 49.2% 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 | | 1.016e-05 | | |100.00 Nlocal: 2580.00 ave 2580 max 2580 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8665.00 ave 8665 max 8665 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 73492.0 ave 73492 max 73492 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 146984.0 ave 146984 max 146984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 146984 Ave neighs/atom = 56.970543 Neighbor list builds = 0 Dangerous builds = 0 2580 -10902.2786986642 eV 2.40485933770569 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:28