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 = 3.6200000 3.6200000 3.6200000 Created orthogonal box = (0.0000000 -57.007817 0.0000000) to (34.910016 57.007817 8.8671528) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6306477 5.5168855 5.9114352 Created 1486 atoms using lattice units in orthogonal box = (0.0000000 -57.007817 0.0000000) to (34.910016 57.007817 8.8671528) create_atoms CPU = 0.007 seconds 1486 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6306477 5.5168855 5.9114352 Created 1492 atoms using lattice units in orthogonal box = (0.0000000 -57.007817 0.0000000) to (34.910016 57.007817 8.8671528) create_atoms CPU = 0.006 seconds 1492 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 12 39 3 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2978 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_313717476091_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 12 39 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.580 | 5.580 | 5.580 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9519.7798 0 -9519.7798 96226.033 31 0 -10507.847 0 -10507.847 4865.8115 Loop time of 7.00779 on 1 procs for 31 steps with 2978 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 = -9519.77977991428 -10507.8363410947 -10507.8465023748 Force two-norm initial, final = 1983.5405 1.8210644 Force max component initial, final = 429.25028 0.69001812 Final line search alpha, max atom move = 0.52177377 0.36003335 Iterations, force evaluations = 31 62 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.9779 | 6.9779 | 6.9779 | 0.0 | 99.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.01147 | 0.01147 | 0.01147 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0184 | | | 0.26 Nlocal: 2978.00 ave 2978 max 2978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7367.00 ave 7367 max 7367 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: 232102.0 ave 232102 max 232102 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 232102 Ave neighs/atom = 77.938885 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 12 39 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 31 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.580 | 5.580 | 5.580 Mbytes Step Temp E_pair E_mol TotEng Press Volume 31 0 -10507.847 0 -10507.847 4865.8115 35293.818 37 0 -10508.351 0 -10508.351 -53.414211 35421.285 Loop time of 0.860093 on 1 procs for 6 steps with 2978 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 = -10507.8465023748 -10508.3506141301 -10508.3508928246 Force two-norm initial, final = 226.52131 3.4278657 Force max component initial, final = 211.76577 2.1384047 Final line search alpha, max atom move = 0.00019803071 0.00042346981 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.85168 | 0.85168 | 0.85168 | 0.0 | 99.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014745 | 0.0014745 | 0.0014745 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006934 | | | 0.81 Nlocal: 2978.00 ave 2978 max 2978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7336.00 ave 7336 max 7336 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: 230992.0 ave 230992 max 230992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230992 Ave neighs/atom = 77.566152 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 12 39 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.718 | 5.718 | 5.718 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10508.351 0 -10508.351 -53.414211 Loop time of 6.475e-06 on 1 procs for 0 steps with 2978 atoms 216.2% 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 | | 6.475e-06 | | |100.00 Nlocal: 2978.00 ave 2978 max 2978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7336.00 ave 7336 max 7336 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: 230884.0 ave 230884 max 230884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230884 Ave neighs/atom = 77.529886 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 12 39 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.718 | 5.718 | 5.718 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 -10508.351 -10508.351 34.903866 114.59487 8.8557551 -53.414211 -53.414211 -74.204313 10.56173 -96.60005 2.2032376 1076.7168 Loop time of 8.69e-06 on 1 procs for 0 steps with 2978 atoms 0.0% 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 | | 8.69e-06 | | |100.00 Nlocal: 2978.00 ave 2978 max 2978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7336.00 ave 7336 max 7336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115442.0 ave 115442 max 115442 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 230884.0 ave 230884 max 230884 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 230884 Ave neighs/atom = 77.529886 Neighbor list builds = 0 Dangerous builds = 0 2978 -10508.3508928246 eV 2.20323757753771 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08