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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -50.095735 0.0000000) to (23.615356 50.095735 5.7275651) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9456929 6.8758852 5.7275651 Created 407 atoms using lattice units in orthogonal box = (0.0000000 -50.095735 0.0000000) to (23.615356 50.095735 5.7275651) create_atoms CPU = 0.004 seconds 407 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9456929 6.8758852 5.7275651 Created 411 atoms using lattice units in orthogonal box = (0.0000000 -50.095735 0.0000000) to (23.615356 50.095735 5.7275651) create_atoms CPU = 0.003 seconds 411 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 6 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 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 816 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_826591359508_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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 4.971 | 4.971 | 4.971 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2688.447 0 -2688.447 6981.2459 48 0 -2735.3289 0 -2735.3289 3134.5376 Loop time of 1.29575 on 1 procs for 48 steps with 816 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 = -2688.44703004744 -2735.32676537683 -2735.32894415959 Force two-norm initial, final = 36.555697 0.11904918 Force max component initial, final = 7.9010698 0.019019690 Final line search alpha, max atom move = 1.0000000 0.019019690 Iterations, force evaluations = 48 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2408 | 1.2408 | 1.2408 | 0.0 | 95.76 Neigh | 0.034114 | 0.034114 | 0.034114 | 0.0 | 2.63 Comm | 0.011078 | 0.011078 | 0.011078 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009751 | | | 0.75 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5326.00 ave 5326 max 5326 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: 115912.0 ave 115912 max 115912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 115912 Ave neighs/atom = 142.04902 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 48 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.971 | 4.971 | 4.971 Mbytes Step Temp E_pair E_mol TotEng Press Volume 48 0 -2735.3289 0 -2735.3289 3134.5376 13551.747 56 0 -2735.5487 0 -2735.5487 -0.19236808 13605.201 Loop time of 0.161176 on 1 procs for 8 steps with 816 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 = -2735.3289441596 -2735.54756537615 -2735.54866049575 Force two-norm initial, final = 62.886588 0.22834382 Force max component initial, final = 60.227866 0.074598463 Final line search alpha, max atom move = 0.00036520158 2.7243477e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15561 | 0.15561 | 0.15561 | 0.0 | 96.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0013072 | 0.0013072 | 0.0013072 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004255 | | | 2.64 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5347.00 ave 5347 max 5347 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: 114944.0 ave 114944 max 114944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114944 Ave neighs/atom = 140.86275 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 5.109 | 5.109 | 5.109 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2735.5487 0 -2735.5487 -0.19236808 Loop time of 6.816e-06 on 1 procs for 0 steps with 816 atoms 161.4% 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 | | 6.816e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5323.00 ave 5323 max 5323 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: 114804.0 ave 114804 max 114804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114804 Ave neighs/atom = 140.69118 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 5.109 | 5.109 | 5.109 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 -2735.5487 -2735.5487 23.539255 100.94418 5.7257315 -0.19236808 -0.19236808 7.7860758 0.41887599 -8.7820561 2.7269268 567.90328 Loop time of 7.227e-06 on 1 procs for 0 steps with 816 atoms 221.4% 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 | | 7.227e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5323.00 ave 5323 max 5323 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 57402.0 ave 57402 max 57402 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 114804.0 ave 114804 max 114804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 114804 Ave neighs/atom = 140.69118 Neighbor list builds = 0 Dangerous builds = 0 816 -2735.54866049575 eV 2.72692684001787 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02