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 = 4.0397985 4.0397985 4.0397985 Created orthogonal box = (0.0000000 -45.705102 0.0000000) to (4.0397985 45.705102 5.7131378) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0397985 5.7131378 5.7131378 Created 64 atoms using lattice units in orthogonal box = (0.0000000 -45.705102 0.0000000) to (4.0397985 45.705102 5.7131378) create_atoms CPU = 0.001 seconds 64 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0397985 5.7131378 5.7131378 Created 66 atoms using lattice units in orthogonal box = (0.0000000 -45.705102 0.0000000) to (4.0397985 45.705102 5.7131378) create_atoms CPU = 0.000 seconds 66 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 1 16 1 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 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 128 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_279544746097_004#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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 1 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 4.527 | 4.527 | 4.527 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -369.70765 0 -369.70765 -0.0097116782 1 0 -369.70765 0 -369.70765 -0.0097116783 Loop time of 0.009311 on 1 procs for 1 steps with 128 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 = -369.707654340017 -369.707654340017 -369.707654340014 Force two-norm initial, final = 7.4017361e-08 2.2765958e-08 Force max component initial, final = 3.2750151e-08 1.0763090e-08 Final line search alpha, max atom move = 1.0000000 1.0763090e-08 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0090943 | 0.0090943 | 0.0090943 | 0.0 | 97.67 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012568 | 0.00012568 | 0.00012568 | 0.0 | 1.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 9.105e-05 | | | 0.98 Nlocal: 128.000 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5378.00 ave 5378 max 5378 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: 54784.0 ave 54784 max 54784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54784 Ave neighs/atom = 428.00000 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 1 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.527 | 4.527 | 4.527 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -369.70765 0 -369.70765 -0.0097116783 2109.7407 2 0 -369.70765 0 -369.70765 -5.5287526e-07 2109.7406 Loop time of 0.00961465 on 1 procs for 1 steps with 128 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 = -369.707654340014 -369.707654340014 -369.707654340045 Force two-norm initial, final = 2.2150287e-05 5.2576044e-08 Force max component initial, final = 1.2872031e-05 3.7990110e-08 Final line search alpha, max atom move = 1.0000000 3.7990110e-08 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0090933 | 0.0090933 | 0.0090933 | 0.0 | 94.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0001189 | 0.0001189 | 0.0001189 | 0.0 | 1.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004025 | | | 4.19 Nlocal: 128.000 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5378.00 ave 5378 max 5378 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: 54784.0 ave 54784 max 54784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54784 Ave neighs/atom = 428.00000 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 1 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 4.665 | 4.665 | 4.665 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -369.70765 0 -369.70765 -5.5284318e-07 Loop time of 1.955e-06 on 1 procs for 0 steps with 128 atoms 153.5% 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 | | 1.955e-06 | | |100.00 Nlocal: 128.000 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5378.00 ave 5378 max 5378 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: 54784.0 ave 54784 max 54784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54784 Ave neighs/atom = 428.00000 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 = 11.77941 ghost atom cutoff = 11.77941 binsize = 5.889705, bins = 1 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.77941 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) = 4.665 | 4.665 | 4.665 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 -369.70765 -369.70765 4.0397984 91.410204 5.7131377 -5.5284318e-07 -5.5284318e-07 6.7177205e-06 -2.8850359e-05 2.0474109e-05 2.8565689 1.4916751e-16 Loop time of 2.529e-06 on 1 procs for 0 steps with 128 atoms 237.2% 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 | | 2.529e-06 | | |100.00 Nlocal: 128.000 ave 128 max 128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5378.00 ave 5378 max 5378 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27392.0 ave 27392 max 27392 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 54784.0 ave 54784 max 54784 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54784 Ave neighs/atom = 428.00000 Neighbor list builds = 0 Dangerous builds = 0 128 -369.707654340045 eV 2.856568868666 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00