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 = 2.8665000 2.8665000 2.8665000 Created orthogonal box = (0.0000000 -36.484589 0.0000000) to (25.798500 36.484589 4.0538432) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7775001 4.9546973 4.0538432 Created 324 atoms using lattice units in orthogonal box = (0.0000000 -36.484589 0.0000000) to (25.798500 36.484589 4.0538432) create_atoms CPU = 0.001 seconds 324 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7775001 4.9546973 4.0538432 Created 326 atoms using lattice units in orthogonal box = (0.0000000 -36.484589 0.0000000) to (25.798500 36.484589 4.0538432) create_atoms CPU = 0.001 seconds 326 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, 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 7.673367000244601 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 642 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_960699513424_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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 4.915 | 4.915 | 4.915 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 84402.452 0 84402.452 63868674 122 0 -2732.4376 0 -2732.4376 -4223.469 Loop time of 1.13116 on 1 procs for 122 steps with 642 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = 84402.45228507 -2732.43522017044 -2732.43759934943 Force two-norm initial, final = 555970.69 0.25110409 Force max component initial, final = 194901.02 0.046697928 Final line search alpha, max atom move = 1.0000000 0.046697928 Iterations, force evaluations = 122 229 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0957 | 1.0957 | 1.0957 | 0.0 | 96.87 Neigh | 0.018573 | 0.018573 | 0.018573 | 0.0 | 1.64 Comm | 0.0098486 | 0.0098486 | 0.0098486 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00701 | | | 0.62 Nlocal: 642.000 ave 642 max 642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5543.00 ave 5543 max 5543 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: 106320.0 ave 106320 max 106320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106320 Ave neighs/atom = 165.60748 Neighbor list builds = 3 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 7 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 122 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.915 | 4.915 | 4.915 Mbytes Step Temp E_pair E_mol TotEng Press Volume 122 0 -2732.4376 0 -2732.4376 -4223.469 7631.3411 126 0 -2732.4928 0 -2732.4928 12.269546 7613.1018 Loop time of 0.034616 on 1 procs for 4 steps with 642 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 = -2732.43759934942 -2732.49274657919 -2732.49283359786 Force two-norm initial, final = 43.811668 0.44648938 Force max component initial, final = 40.682445 0.17167640 Final line search alpha, max atom move = 0.00066132697 0.00011353423 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.033257 | 0.033257 | 0.033257 | 0.0 | 96.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026057 | 0.00026057 | 0.00026057 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001098 | | | 3.17 Nlocal: 642.000 ave 642 max 642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5543.00 ave 5543 max 5543 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: 106444.0 ave 106444 max 106444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106444 Ave neighs/atom = 165.80062 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 7 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 5.053 | 5.053 | 5.053 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2732.4928 0 -2732.4928 12.269546 Loop time of 1.787e-06 on 1 procs for 0 steps with 642 atoms 111.9% 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 | | 1.787e-06 | | |100.00 Nlocal: 642.000 ave 642 max 642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5543.00 ave 5543 max 5543 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: 106504.0 ave 106504 max 106504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106504 Ave neighs/atom = 165.89408 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 7 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 5.053 | 5.053 | 5.053 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 -2732.4928 -2732.4928 25.815825 72.780761 4.0519029 12.269546 12.269546 36.153543 33.577495 -32.9224 2.3132226 466.02169 Loop time of 1.393e-06 on 1 procs for 0 steps with 642 atoms 215.4% 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 | | 1.393e-06 | | |100.00 Nlocal: 642.000 ave 642 max 642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5543.00 ave 5543 max 5543 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 53252.0 ave 53252 max 53252 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 106504.0 ave 106504 max 106504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 106504 Ave neighs/atom = 165.89408 Neighbor list builds = 0 Dangerous builds = 0 642 -2732.49283359787 eV 2.31322256686134 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01