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 = 3.6149590 3.6149590 3.6149590 Created orthogonal box = (0.0000000 -69.158237 0.0000000) to (39.928527 69.158237 6.2612926) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8910941 5.2907941 6.2612926 Created 1464 atoms using lattice units in orthogonal box = (0.0000000 -69.158237 0.0000000) to (39.928527 69.158237 6.2612926) create_atoms CPU = 0.009 seconds 1464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8910941 5.2907941 6.2612926 Created 1466 atoms using lattice units in orthogonal box = (0.0000000 -69.158237 0.0000000) to (39.928527 69.158237 6.2612926) create_atoms CPU = 0.009 seconds 1466 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 11 36 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 7.715751993501819 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2926 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_759493141826_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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 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) = 6.993 | 6.993 | 6.993 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9890.3093 0 -9890.3093 30827.431 81 0 -10334.353 0 -10334.353 7346.0264 Loop time of 7.69986 on 1 procs for 81 steps with 2926 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9890.30927476533 -10334.343165416 -10334.3534889955 Force two-norm initial, final = 595.68149 0.34293343 Force max component initial, final = 164.31340 0.058951537 Final line search alpha, max atom move = 0.68657640 0.040474734 Iterations, force evaluations = 81 140 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.3349 | 7.3349 | 7.3349 | 0.0 | 95.26 Neigh | 0.272 | 0.272 | 0.272 | 0.0 | 3.53 Comm | 0.047681 | 0.047681 | 0.047681 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04532 | | | 0.59 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12074.0 ave 12074 max 12074 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: 503560.0 ave 503560 max 503560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 503560 Ave neighs/atom = 172.09843 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.992 | 6.992 | 6.992 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -10334.353 0 -10334.353 7346.0264 34579.698 86 0 -10334.88 0 -10334.88 -46.173559 34762.741 Loop time of 0.352645 on 1 procs for 5 steps with 2926 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 = -10334.3534889956 -10334.8798917379 -10334.8803739658 Force two-norm initial, final = 286.37551 3.4840097 Force max component initial, final = 224.60470 3.4378173 Final line search alpha, max atom move = 0.00010474957 0.00036010989 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34264 | 0.34264 | 0.34264 | 0.0 | 97.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020958 | 0.0020958 | 0.0020958 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007912 | | | 2.24 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12048.0 ave 12048 max 12048 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: 505072.0 ave 505072 max 505072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 505072 Ave neighs/atom = 172.61517 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 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) = 7.131 | 7.131 | 7.131 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10334.88 0 -10334.88 -46.173559 Loop time of 6.234e-06 on 1 procs for 0 steps with 2926 atoms 240.6% 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 | | 6.234e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12048.0 ave 12048 max 12048 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: 502632.0 ave 502632 max 502632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 502632 Ave neighs/atom = 171.78127 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 = 7.715752 ghost atom cutoff = 7.715752 binsize = 3.857876, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715751993501819 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) = 7.131 | 7.131 | 7.131 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 -10334.88 -10334.88 39.938552 138.8872 6.2669967 -46.173559 -46.173559 -158.485 19.571621 0.39270272 2.3274942 1008.811 Loop time of 6.786e-06 on 1 procs for 0 steps with 2926 atoms 353.7% 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 | | 6.786e-06 | | |100.00 Nlocal: 2926.00 ave 2926 max 2926 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12048.0 ave 12048 max 12048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 251316.0 ave 251316 max 251316 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 502632.0 ave 502632 max 502632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 502632 Ave neighs/atom = 171.78127 Neighbor list builds = 0 Dangerous builds = 0 2926 -10334.8803739658 eV 2.3274941806154 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:09