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 = 3.6150017 3.6150017 3.6150017 Created orthogonal box = (0.0000000 -62.194841 0.0000000) to (31.097420 62.194841 3.6150017) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0428249 5.0428249 3.6150017 Created 592 atoms using lattice units in orthogonal box = (0.0000000 -62.194841 0.0000000) to (31.097420 62.194841 3.6150017) create_atoms CPU = 0.003 seconds 592 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0428249 5.0428249 3.6150017 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -62.194841 0.0000000) to (31.097420 62.194841 3.6150017) create_atoms CPU = 0.002 seconds 594 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 8 30 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 1184 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_592013496703_005#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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.479 | 5.479 | 5.479 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3948.1971 0 -3948.1971 30834.602 71 0 -4181.1288 0 -4181.1288 4337.9582 Loop time of 3.85316 on 1 procs for 71 steps with 1184 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 = -3948.1970764937 -4181.12488707758 -4181.12878260986 Force two-norm initial, final = 276.67661 0.19493628 Force max component initial, final = 72.319555 0.032005593 Final line search alpha, max atom move = 1.0000000 0.032005593 Iterations, force evaluations = 71 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.7351 | 3.7351 | 3.7351 | 0.0 | 96.93 Neigh | 0.0637 | 0.0637 | 0.0637 | 0.0 | 1.65 Comm | 0.033417 | 0.033417 | 0.033417 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02099 | | | 0.54 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10906.0 ave 10906 max 10906 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: 244208.0 ave 244208 max 244208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 244208 Ave neighs/atom = 206.25676 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.491 | 5.491 | 5.491 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -4181.1288 0 -4181.1288 4337.9582 13983.543 75 0 -4181.2396 0 -4181.2396 -21.357815 14027.122 Loop time of 0.178765 on 1 procs for 4 steps with 1184 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 = -4181.12878260986 -4181.23950614233 -4181.23961574892 Force two-norm initial, final = 75.064644 0.51526849 Force max component initial, final = 63.518343 0.39412847 Final line search alpha, max atom move = 0.00084742987 0.00033399624 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17306 | 0.17306 | 0.17306 | 0.0 | 96.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0016189 | 0.0016189 | 0.0016189 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004083 | | | 2.28 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11260.0 ave 11260 max 11260 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: 240256.0 ave 240256 max 240256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240256 Ave neighs/atom = 202.91892 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 8 30 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.629 | 5.629 | 5.629 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4181.2396 0 -4181.2396 -21.357815 Loop time of 6.656e-06 on 1 procs for 0 steps with 1184 atoms 180.3% 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 | | 6.656e-06 | | |100.00 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11266.0 ave 11266 max 11266 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: 238744.0 ave 238744 max 238744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238744 Ave neighs/atom = 201.64189 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 = 8.4527 ghost atom cutoff = 8.4527 binsize = 4.22635, bins = 8 30 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4527 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) = 5.629 | 5.629 | 5.629 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 -4181.2396 -4181.2396 31.065019 124.76749 3.6190577 -21.357815 -21.357815 -28.059348 -45.154046 9.1399497 2.3063463 283.93152 Loop time of 8.229e-06 on 1 procs for 0 steps with 1184 atoms 218.7% 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 | | 8.229e-06 | | |100.00 Nlocal: 1184.00 ave 1184 max 1184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11266.0 ave 11266 max 11266 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 119372.0 ave 119372 max 119372 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 238744.0 ave 238744 max 238744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238744 Ave neighs/atom = 201.64189 Neighbor list builds = 0 Dangerous builds = 0 1184 -4181.23961574892 eV 2.30634627957781 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04