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 = 3.6150127 3.6150127 3.6150127 Created orthogonal box = (0.0000000 -68.207923 0.0000000) to (34.103961 68.207923 3.6150127) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9814775 4.9814775 3.6150127 Created 712 atoms using lattice units in orthogonal box = (0.0000000 -68.207923 0.0000000) to (34.103961 68.207923 3.6150127) create_atoms CPU = 0.003 seconds 712 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9814775 4.9814775 3.6150127 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -68.207923 0.0000000) to (34.103961 68.207923 3.6150127) create_atoms CPU = 0.002 seconds 714 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 = 10 39 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 0 atoms, new total = 1426 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_028979335952_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 = 10 39 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) = 5.106 | 5.106 | 5.106 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4950.6079 0 -4950.6079 19982.775 83 0 -5027.7784 0 -5027.7784 7014.8053 Loop time of 33.0911 on 1 procs for 83 steps with 1426 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 = -4950.60794801973 -5027.77381406469 -5027.77843298324 Force two-norm initial, final = 78.955129 0.21862247 Force max component initial, final = 22.213156 0.036125645 Final line search alpha, max atom move = 1.0000000 0.036125645 Iterations, force evaluations = 83 153 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 33.006 | 33.006 | 33.006 | 0.0 | 99.74 Neigh | 0.024368 | 0.024368 | 0.024368 | 0.0 | 0.07 Comm | 0.033735 | 0.033735 | 0.033735 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02714 | | | 0.08 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9659.00 ave 9659 max 9659 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: 189784.0 ave 189784 max 189784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189784 Ave neighs/atom = 133.08836 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 ghost atom cutoff = 7 binsize = 3.5, bins = 10 39 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 : 83 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.106 | 5.106 | 5.106 Mbytes Step Temp E_pair E_mol TotEng Press Volume 83 0 -5027.7784 0 -5027.7784 7014.8053 16818.198 88 0 -5028.0366 0 -5028.0366 -109.97215 16902.289 Loop time of 1.45475 on 1 procs for 5 steps with 1426 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 = -5027.77843298323 -5028.03475960478 -5028.03664749032 Force two-norm initial, final = 135.82463 2.8752410 Force max component initial, final = 104.59008 2.7718538 Final line search alpha, max atom move = 0.00010586309 0.00029343701 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4487 | 1.4487 | 1.4487 | 0.0 | 99.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014344 | 0.0014344 | 0.0014344 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004658 | | | 0.32 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9664.00 ave 9664 max 9664 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: 189704.0 ave 189704 max 189704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189704 Ave neighs/atom = 133.03226 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 = 10 40 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) = 5.244 | 5.244 | 5.244 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5028.0366 0 -5028.0366 -109.97215 Loop time of 6.375e-06 on 1 procs for 0 steps with 1426 atoms 188.2% 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 | | 6.375e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9654.00 ave 9654 max 9654 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: 189596.0 ave 189596 max 189596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189596 Ave neighs/atom = 132.95652 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 = 10 40 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) = 5.244 | 5.244 | 5.244 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 -5028.0366 -5028.0366 34.076598 136.92655 3.6224435 -109.97215 -109.97215 -262.53462 -68.47433 1.092507 2.2677329 424.97664 Loop time of 7.246e-06 on 1 procs for 0 steps with 1426 atoms 317.4% 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 | | 7.246e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9654.00 ave 9654 max 9654 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 94798.0 ave 94798 max 94798 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 189596.0 ave 189596 max 189596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 189596 Ave neighs/atom = 132.95652 Neighbor list builds = 0 Dangerous builds = 0 1426 -5028.03664749031 eV 2.2677329487185 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:35