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 = 2.8659480 2.8659480 2.8659480 Created orthogonal box = (0.0000000 -34.747773 0.0000000) to (28.371438 34.747773 7.0201103) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0530626 4.0184499 4.6800735 Created 588 atoms using lattice units in orthogonal box = (0.0000000 -34.747773 0.0000000) to (28.371438 34.747773 7.0201103) create_atoms CPU = 0.001 seconds 588 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0530626 4.0184499 4.6800735 Created 590 atoms using lattice units in orthogonal box = (0.0000000 -34.747773 0.0000000) to (28.371438 34.747773 7.0201103) create_atoms CPU = 0.001 seconds 590 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 8 19 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 7.549891471862793 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 1168 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_650279905230_005#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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 8 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 5.049 | 5.049 | 5.049 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2532.6576 0 -2532.6576 331241.97 130 0 -4975.332 0 -4975.332 2180.6158 Loop time of 1.80051 on 1 procs for 130 steps with 1168 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 = -2532.65757045785 -4975.32710120974 -4975.33197958742 Force two-norm initial, final = 4774.6134 0.24797431 Force max component initial, final = 1515.5309 0.063664598 Final line search alpha, max atom move = 1.0000000 0.063664598 Iterations, force evaluations = 130 225 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7366 | 1.7366 | 1.7366 | 0.0 | 96.45 Neigh | 0.04303 | 0.04303 | 0.04303 | 0.0 | 2.39 Comm | 0.010106 | 0.010106 | 0.010106 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01073 | | | 0.60 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5703.00 ave 5703 max 5703 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: 191952.0 ave 191952 max 191952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191952 Ave neighs/atom = 164.34247 Neighbor list builds = 4 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 8 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 130 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.052 | 5.052 | 5.052 Mbytes Step Temp E_pair E_mol TotEng Press Volume 130 0 -4975.332 0 -4975.332 2180.6158 13841.471 136 0 -4975.5666 0 -4975.5666 -13.05477 13860.14 Loop time of 0.0633379 on 1 procs for 6 steps with 1168 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 = -4975.33197958744 -4975.56571815822 -4975.5665790678 Force two-norm initial, final = 82.729863 0.54487430 Force max component initial, final = 80.834502 0.28741206 Final line search alpha, max atom move = 0.00030284555 8.7041463e-05 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.061356 | 0.061356 | 0.061356 | 0.0 | 96.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032466 | 0.00032466 | 0.00032466 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001657 | | | 2.62 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5724.00 ave 5724 max 5724 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: 191948.0 ave 191948 max 191948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191948 Ave neighs/atom = 164.33904 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 8 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 5.190 | 5.190 | 5.190 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4975.5666 0 -4975.5666 -13.05477 Loop time of 1.612e-06 on 1 procs for 0 steps with 1168 atoms 124.1% 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 | | 1.612e-06 | | |100.00 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5730.00 ave 5730 max 5730 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: 191808.0 ave 191808 max 191808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191808 Ave neighs/atom = 164.21918 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 = 7.5498915 ghost atom cutoff = 7.5498915 binsize = 3.7749457, bins = 8 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.549891471862793 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) = 5.190 | 5.190 | 5.190 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 -4975.5666 -4975.5666 28.304191 69.860651 7.0094547 -13.05477 -13.05477 -1.6822092 -4.3088515 -33.173251 2.2687599 930.50724 Loop time of 1.563e-06 on 1 procs for 0 steps with 1168 atoms 128.0% 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 | | 1.563e-06 | | |100.00 Nlocal: 1168.00 ave 1168 max 1168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5730.00 ave 5730 max 5730 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 95904.0 ave 95904 max 95904 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 191808.0 ave 191808 max 191808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 191808 Ave neighs/atom = 164.21918 Neighbor list builds = 0 Dangerous builds = 0 1168 -4975.5663005949 eV 2.26875986911954 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02