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 -35.673230 0.0000000) to (3.5673230 35.673230 3.5673230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5673230 3.5673230 3.5673230 Created 40 atoms using lattice units in orthogonal box = (0.0000000 -35.673230 0.0000000) to (3.5673230 35.673230 3.5673230) create_atoms CPU = 0.000 seconds 40 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5673230 3.5673230 3.5673230 Created 42 atoms using lattice units in orthogonal box = (0.0000000 -35.673230 0.0000000) to (3.5673230 35.673230 3.5673230) create_atoms CPU = 0.000 seconds 42 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 = 2 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 80 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_095610951957_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 2 26 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) = 4.376 | 4.376 | 4.376 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -333.85589 0 -333.85589 18248.893 40 0 -338.01658 0 -338.01658 11793.593 Loop time of 0.215915 on 1 procs for 40 steps with 80 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 = -333.855894220173 -338.016267431733 -338.016584876558 Force two-norm initial, final = 12.642820 0.60922417 Force max component initial, final = 3.7112235 0.16136561 Final line search alpha, max atom move = 0.60210212 0.097158574 Iterations, force evaluations = 40 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21391 | 0.21391 | 0.21391 | 0.0 | 99.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011792 | 0.0011792 | 0.0011792 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008253 | | | 0.38 Nlocal: 80.0000 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1424.00 ave 1424 max 1424 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: 4336.00 ave 4336 max 4336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4336 Ave neighs/atom = 54.200000 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 2 26 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 : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.376 | 4.376 | 4.376 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -338.01658 0 -338.01658 11793.593 907.94031 91 0 -338.76055 0 -338.76055 -1089.7981 935.55403 Loop time of 0.139224 on 1 procs for 51 steps with 80 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -338.016584876558 -338.760308188392 -338.760550950126 Force two-norm initial, final = 19.074341 1.1508088 Force max component initial, final = 19.051496 0.65378695 Final line search alpha, max atom move = 0.0019897601 0.0013008792 Iterations, force evaluations = 51 52 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13448 | 0.13448 | 0.13448 | 0.0 | 96.59 Neigh | 0.0011095 | 0.0011095 | 0.0011095 | 0.0 | 0.80 Comm | 0.00079525 | 0.00079525 | 0.00079525 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002839 | | | 2.04 Nlocal: 80.0000 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1360.00 ave 1360 max 1360 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: 4960.00 ave 4960 max 4960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4960 Ave neighs/atom = 62.000000 Neighbor list builds = 3 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 = 2 27 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) = 4.514 | 4.514 | 4.514 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -338.76055 0 -338.76055 -1089.7981 Loop time of 1.719e-06 on 1 procs for 0 steps with 80 atoms 116.3% 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 | | 1.719e-06 | | |100.00 Nlocal: 80.0000 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1360.00 ave 1360 max 1360 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: 4960.00 ave 4960 max 4960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4960 Ave neighs/atom = 62.000000 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 = 2 27 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) = 4.514 | 4.514 | 4.514 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 -338.76055 -338.76055 3.5368185 74.788998 3.5368642 -1089.7981 -1089.7981 -1046.8166 -1173.6619 -1048.9158 2.5009245 0.039523921 Loop time of 1.343e-06 on 1 procs for 0 steps with 80 atoms 148.9% 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 | | 1.343e-06 | | |100.00 Nlocal: 80.0000 ave 80 max 80 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1360.00 ave 1360 max 1360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 2480.00 ave 2480 max 2480 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 4960.00 ave 4960 max 4960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 4960 Ave neighs/atom = 62.000000 Neighbor list builds = 0 Dangerous builds = 0 80 -338.760550950126 eV 2.50092450031532 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00