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 = 4.0320734 4.0320734 4.0320734 Created orthogonal box = (0.0000000 -49.873993 0.0000000) to (16.624664 49.873993 4.0320734) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8896072 4.8896072 4.0320734 Created 204 atoms using lattice units in orthogonal box = (0.0000000 -49.873993 0.0000000) to (16.624664 49.873993 4.0320734) create_atoms CPU = 0.002 seconds 204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8896072 4.8896072 4.0320734 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -49.873993 0.0000000) to (16.624664 49.873993 4.0320734) create_atoms CPU = 0.001 seconds 206 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 5 26 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 410 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 4.465 | 4.465 | 4.465 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1335.7726 0 -1335.7726 12827.09 54 0 -1373.2497 0 -1373.2497 8126.1432 Loop time of 0.586621 on 1 procs for 54 steps with 410 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 = -1335.77259734884 -1373.24839422957 -1373.24968242672 Force two-norm initial, final = 29.935675 0.097234627 Force max component initial, final = 6.6989343 0.018225340 Final line search alpha, max atom move = 1.0000000 0.018225340 Iterations, force evaluations = 54 97 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.56418 | 0.56418 | 0.56418 | 0.0 | 96.17 Neigh | 0.0069982 | 0.0069982 | 0.0069982 | 0.0 | 1.19 Comm | 0.0087118 | 0.0087118 | 0.0087118 | 0.0 | 1.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006734 | | | 1.15 Nlocal: 410.000 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4135.00 ave 4135 max 4135 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: 53928.0 ave 53928 max 53928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53928 Ave neighs/atom = 131.53171 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.465 | 4.465 | 4.465 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -1373.2497 0 -1373.2497 8126.1432 6686.2938 62 0 -1373.4493 0 -1373.4493 -200.77735 6754.5941 Loop time of 0.0607196 on 1 procs for 8 steps with 410 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 = -1373.24968242672 -1373.44868287175 -1373.44925080957 Force two-norm initial, final = 59.941913 1.7902137 Force max component initial, final = 43.665892 1.3266493 Final line search alpha, max atom move = 0.00043324480 0.00057476393 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.057049 | 0.057049 | 0.057049 | 0.0 | 93.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00085693 | 0.00085693 | 0.00085693 | 0.0 | 1.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002814 | | | 4.63 Nlocal: 410.000 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4140.00 ave 4140 max 4140 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: 53932.0 ave 53932 max 53932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53932 Ave neighs/atom = 131.54146 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 4.604 | 4.604 | 4.604 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1373.4493 0 -1373.4493 -200.77735 Loop time of 5.863e-06 on 1 procs for 0 steps with 410 atoms 187.6% 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 | | 5.863e-06 | | |100.00 Nlocal: 410.000 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4130.00 ave 4130 max 4130 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: 53860.0 ave 53860 max 53860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53860 Ave neighs/atom = 131.36585 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 4.604 | 4.604 | 4.604 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 -1373.4493 -1373.4493 16.646874 100.49477 4.0375982 -200.77735 -200.77735 -280.58474 -6.6375111 -315.10981 2.6095826 227.14049 Loop time of 6.926e-06 on 1 procs for 0 steps with 410 atoms 259.9% 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 | | 6.926e-06 | | |100.00 Nlocal: 410.000 ave 410 max 410 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4130.00 ave 4130 max 4130 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26930.0 ave 26930 max 26930 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 53860.0 ave 53860 max 53860 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53860 Ave neighs/atom = 131.36585 Neighbor list builds = 0 Dangerous builds = 0 410 -1373.44925080957 eV 2.60958263546823 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00