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 = 3.5181212 3.5181212 3.5181212 Created orthogonal box = (0.0000000 -52.063440 0.0000000) to (42.509621 52.063440 8.6176019) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2409121 4.9923847 5.7450679 Created 1748 atoms using lattice units in orthogonal box = (0.0000000 -52.063440 0.0000000) to (42.509621 52.063440 8.6176019) create_atoms CPU = 0.008 seconds 1748 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2409121 4.9923847 5.7450679 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -52.063440 0.0000000) to (42.509621 52.063440 8.6176019) create_atoms CPU = 0.007 seconds 1756 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 10 24 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 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3504 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_222110751402_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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 10 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 12.22 | 12.22 | 12.22 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13492.788 0 -13492.788 132523.47 50 0 -15304.583 0 -15304.583 7798.3342 Loop time of 9.89801 on 1 procs for 50 steps with 3504 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 = -13492.7876210944 -15304.5689062909 -15304.5834833593 Force two-norm initial, final = 1737.7100 0.39690723 Force max component initial, final = 256.60924 0.039830929 Final line search alpha, max atom move = 1.0000000 0.039830929 Iterations, force evaluations = 50 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.7086 | 9.7086 | 9.7086 | 0.0 | 98.09 Neigh | 0.1213 | 0.1213 | 0.1213 | 0.0 | 1.23 Comm | 0.035269 | 0.035269 | 0.035269 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03282 | | | 0.33 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14309.0 ave 14309 max 14309 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: 865284.0 ave 865284 max 865284 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 865284 Ave neighs/atom = 246.94178 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 10 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.21 | 12.21 | 12.21 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -15304.583 0 -15304.583 7798.3342 38144.903 56 0 -15305.429 0 -15305.429 -170.10936 38322.194 Loop time of 0.928512 on 1 procs for 6 steps with 3504 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 = -15304.5834833592 -15305.4272865143 -15305.4289604502 Force two-norm initial, final = 373.51367 9.1857759 Force max component initial, final = 340.15126 8.5748205 Final line search alpha, max atom move = 7.8910466e-05 0.00067664308 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.9135 | 0.9135 | 0.9135 | 0.0 | 98.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0028382 | 0.0028382 | 0.0028382 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01217 | | | 1.31 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14014.0 ave 14014 max 14014 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: 865488.0 ave 865488 max 865488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 865488 Ave neighs/atom = 247.00000 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 10 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 11.73 | 11.73 | 11.73 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15305.429 0 -15305.429 -170.10936 Loop time of 6.245e-06 on 1 procs for 0 steps with 3504 atoms 192.2% 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 | | 6.245e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14017.0 ave 14017 max 14017 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: 864272.0 ave 864272 max 864272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 864272 Ave neighs/atom = 246.65297 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 10 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 11.73 | 11.73 | 11.73 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 -15305.429 -15305.429 42.494812 104.66596 8.6160653 -170.10936 -170.10936 -358.3717 -17.431421 -134.52495 2.1718836 1350.5671 Loop time of 6.384e-06 on 1 procs for 0 steps with 3504 atoms 313.3% 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 | | 6.384e-06 | | |100.00 Nlocal: 3504.00 ave 3504 max 3504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14017.0 ave 14017 max 14017 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 432136.0 ave 432136 max 432136 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 864272.0 ave 864272 max 864272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 864272 Ave neighs/atom = 246.65297 Neighbor list builds = 0 Dangerous builds = 0 3504 -15305.4289604502 eV 2.17188355843915 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12