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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -36.383266 0.0000000) to (18.189849 36.383266 3.5673230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.1976576 4.1976576 3.5673230 Created 209 atoms using lattice units in orthogonal box = (0.0000000 -36.383266 0.0000000) to (18.189849 36.383266 3.5673230) create_atoms CPU = 0.002 seconds 209 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.1976576 4.1976576 3.5673230 Created 209 atoms using lattice units in orthogonal box = (0.0000000 -36.383266 0.0000000) to (18.189849 36.383266 3.5673230) create_atoms CPU = 0.001 seconds 209 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 = 7 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 413 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 7 26 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) = 4.440 | 4.440 | 4.440 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1708.0183 0 -1708.0183 22991.532 42 0 -1737.0453 0 -1737.0453 20886.15 Loop time of 2.67574 on 1 procs for 42 steps with 413 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 = -1708.01830816315 -1737.04383638772 -1737.04528929434 Force two-norm initial, final = 43.318524 0.40054006 Force max component initial, final = 12.930492 0.15247831 Final line search alpha, max atom move = 0.70049793 0.10681074 Iterations, force evaluations = 42 87 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6588 | 2.6588 | 2.6588 | 0.0 | 99.37 Neigh | 0.0045619 | 0.0045619 | 0.0045619 | 0.0 | 0.17 Comm | 0.006227 | 0.006227 | 0.006227 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006127 | | | 0.23 Nlocal: 413.000 ave 413 max 413 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2667.00 ave 2667 max 2667 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: 23554.0 ave 23554 max 23554 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23554 Ave neighs/atom = 57.031477 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 7 26 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 : 42 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.440 | 4.440 | 4.440 Mbytes Step Temp E_pair E_mol TotEng Press Volume 42 0 -1737.0453 0 -1737.0453 20886.15 4721.7524 82 0 -1739.3044 0 -1739.3044 -4438.0261 4851.4331 Loop time of 1.2931 on 1 procs for 40 steps with 413 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1737.04528929434 -1739.30347491465 -1739.30441966966 Force two-norm initial, final = 88.223406 3.0237535 Force max component initial, final = 87.606893 1.8788705 Final line search alpha, max atom move = 0.00021475109 0.00040348949 Iterations, force evaluations = 40 44 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2786 | 1.2786 | 1.2786 | 0.0 | 98.88 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.002848 | 0.002848 | 0.002848 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01163 | | | 0.90 Nlocal: 413.000 ave 413 max 413 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2655.00 ave 2655 max 2655 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: 23540.0 ave 23540 max 23540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23540 Ave neighs/atom = 56.997579 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 = 7 26 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) = 4.577 | 4.577 | 4.577 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1739.3044 0 -1739.3044 -4438.0261 Loop time of 7.918e-06 on 1 procs for 0 steps with 413 atoms 0.0% 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 | | 7.918e-06 | | |100.00 Nlocal: 413.000 ave 413 max 413 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2607.00 ave 2607 max 2607 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: 24188.0 ave 24188 max 24188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24188 Ave neighs/atom = 58.566586 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 = 7 26 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) = 4.577 | 4.577 | 4.577 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 -1739.3044 -1739.3044 18.853779 72.766532 3.5362255 -4438.0261 -4438.0261 629.23269 -14558.395 615.08435 2.2764864 203.13603 Loop time of 6.595e-06 on 1 procs for 0 steps with 413 atoms 242.6% 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 | | 6.595e-06 | | |100.00 Nlocal: 413.000 ave 413 max 413 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2607.00 ave 2607 max 2607 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12094.0 ave 12094 max 12094 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 24188.0 ave 24188 max 24188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24188 Ave neighs/atom = 58.566586 Neighbor list builds = 0 Dangerous builds = 0 413 -1739.30441966966 eV 2.27648639055684 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04