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 -41.533207 0.0000000) to (29.368412 41.533207 5.1123844) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4497595 5.6636192 5.1123844 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -41.533207 0.0000000) to (29.368412 41.533207 5.1123844) create_atoms CPU = 0.003 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4497595 5.6636192 5.1123844 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -41.533207 0.0000000) to (29.368412 41.533207 5.1123844) create_atoms CPU = 0.003 seconds 532 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 = 7 20 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 8.4527 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1048 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 = 7 20 2 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) = 5.421 | 5.421 | 5.421 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3586.0835 0 -3586.0835 18498.323 56 0 -3694.6748 0 -3694.6748 -2988.6903 Loop time of 2.43653 on 1 procs for 56 steps with 1048 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3586.08351998933 -3694.67136987765 -3694.67481504241 Force two-norm initial, final = 157.01398 0.17928508 Force max component initial, final = 36.209908 0.025481834 Final line search alpha, max atom move = 1.0000000 0.025481834 Iterations, force evaluations = 56 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3439 | 2.3439 | 2.3439 | 0.0 | 96.20 Neigh | 0.06102 | 0.06102 | 0.06102 | 0.0 | 2.50 Comm | 0.017336 | 0.017336 | 0.017336 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01428 | | | 0.59 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7351.00 ave 7351 max 7351 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: 211320.0 ave 211320 max 211320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211320 Ave neighs/atom = 201.64122 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 = 7 20 2 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 : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.421 | 5.421 | 5.421 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -3694.6748 0 -3694.6748 -2988.6903 12471.809 61 0 -3694.7291 0 -3694.7291 9.2649244 12444.586 Loop time of 0.195126 on 1 procs for 5 steps with 1048 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 = -3694.67481504237 -3694.72901720041 -3694.72912604263 Force two-norm initial, final = 43.325018 0.53890318 Force max component initial, final = 36.239236 0.36280589 Final line search alpha, max atom move = 0.00053241286 0.00019316252 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18982 | 0.18982 | 0.18982 | 0.0 | 97.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011934 | 0.0011934 | 0.0011934 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004117 | | | 2.11 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7378.00 ave 7378 max 7378 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: 211160.0 ave 211160 max 211160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211160 Ave neighs/atom = 201.48855 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 = 7 20 2 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) = 5.559 | 5.559 | 5.559 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3694.7291 0 -3694.7291 9.2649244 Loop time of 6.655e-06 on 1 procs for 0 steps with 1048 atoms 195.3% 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 | | 6.655e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7378.00 ave 7378 max 7378 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: 211536.0 ave 211536 max 211536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211536 Ave neighs/atom = 201.84733 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 = 7 20 2 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) = 5.559 | 5.559 | 5.559 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 -3694.7291 -3694.7291 29.262497 83.127412 5.1159324 9.2649244 9.2649244 -37.591355 18.644316 46.741812 2.3108606 452.7629 Loop time of 6.906e-06 on 1 procs for 0 steps with 1048 atoms 260.6% 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 | | 6.906e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7378.00 ave 7378 max 7378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105768.0 ave 105768 max 105768 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 211536.0 ave 211536 max 211536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211536 Ave neighs/atom = 201.84733 Neighbor list builds = 0 Dangerous builds = 0 1048 -3694.72912604263 eV 2.31086059285058 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03