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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -41.695480 0.0000000) to (20.847740 41.695480 2.8636573) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5401823 3.5401823 2.8636573 Created 212 atoms using lattice units in orthogonal box = (0.0000000 -41.695480 0.0000000) to (20.847740 41.695480 2.8636573) create_atoms CPU = 0.002 seconds 212 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5401823 3.5401823 2.8636573 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -41.695480 0.0000000) to (20.847740 41.695480 2.8636573) create_atoms CPU = 0.001 seconds 213 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 30 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 425 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_856956178669_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.438 | 4.438 | 4.438 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1753.0451 0 -1753.0451 45045.556 37 0 -1813.8294 0 -1813.8294 12073.011 Loop time of 1.69007 on 1 procs for 37 steps with 425 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 = -1753.04510555752 -1813.82804544958 -1813.8294160856 Force two-norm initial, final = 148.58929 0.13831326 Force max component initial, final = 94.069416 0.033014244 Final line search alpha, max atom move = 1.0000000 0.033014244 Iterations, force evaluations = 37 65 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6806 | 1.6806 | 1.6806 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0047807 | 0.0047807 | 0.0047807 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004718 | | | 0.28 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2905.00 ave 2905 max 2905 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: 24838.0 ave 24838 max 24838 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24838 Ave neighs/atom = 58.442353 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.438 | 4.438 | 4.438 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -1813.8294 0 -1813.8294 12073.011 4978.5057 50 0 -1814.2726 0 -1814.2726 1.0729525 5012.3576 Loop time of 0.40485 on 1 procs for 13 steps with 425 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 = -1813.82941608559 -1814.27183004655 -1814.27260452467 Force two-norm initial, final = 81.316375 0.39006459 Force max component initial, final = 76.475082 0.092960945 Final line search alpha, max atom move = 0.00057922432 5.3845240e-05 Iterations, force evaluations = 13 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39559 | 0.39559 | 0.39559 | 0.0 | 97.71 Neigh | 0.0042234 | 0.0042234 | 0.0042234 | 0.0 | 1.04 Comm | 0.0011943 | 0.0011943 | 0.0011943 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003846 | | | 0.95 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2889.00 ave 2889 max 2889 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: 24626.0 ave 24626 max 24626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24626 Ave neighs/atom = 57.943529 Neighbor list builds = 1 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.576 | 4.576 | 4.576 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1814.2726 0 -1814.2726 1.0729525 Loop time of 6.415e-06 on 1 procs for 0 steps with 425 atoms 171.5% 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 | | 6.415e-06 | | |100.00 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2889.00 ave 2889 max 2889 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: 24626.0 ave 24626 max 24626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24626 Ave neighs/atom = 57.943529 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 8 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.576 | 4.576 | 4.576 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 -1814.2726 -1814.2726 20.858192 84.425379 2.8463766 1.0729525 1.0729525 26.073608 -30.083121 7.2283707 2.3197712 265.60228 Loop time of 6.656e-06 on 1 procs for 0 steps with 425 atoms 240.4% 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 | | 6.656e-06 | | |100.00 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2889.00 ave 2889 max 2889 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12313.0 ave 12313 max 12313 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 24626.0 ave 24626 max 24626 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24626 Ave neighs/atom = 57.943529 Neighbor list builds = 0 Dangerous builds = 0 425 -1814.27260452467 eV 2.31977123237553 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02