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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -72.270467 0.0000000) to (41.723293 72.270467 6.2429061) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6046214 5.7525861 6.2429061 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -72.270467 0.0000000) to (41.723293 72.270467 6.2429061) create_atoms CPU = 0.004 seconds 1610 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6046214 5.7525861 6.2429061 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -72.270467 0.0000000) to (41.723293 72.270467 6.2429061) create_atoms CPU = 0.003 seconds 1610 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 14 49 3 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 34 atoms, new total = 3186 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_492310898779_001#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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 14 49 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.834 | 5.834 | 5.834 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13448.731 0 -13448.731 -2756.5277 469 0 -13521.367 0 -13521.367 -19459.414 Loop time of 102.472 on 1 procs for 469 steps with 3186 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13448.7310597628 -13521.3544241459 -13521.3672063051 Force two-norm initial, final = 28.546608 0.41299365 Force max component initial, final = 5.4451163 0.086115592 Final line search alpha, max atom move = 1.0000000 0.086115592 Iterations, force evaluations = 469 923 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 101.95 | 101.95 | 101.95 | 0.0 | 99.49 Neigh | 0.27975 | 0.27975 | 0.27975 | 0.0 | 0.27 Comm | 0.10316 | 0.10316 | 0.10316 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1386 | | | 0.14 Nlocal: 3186.00 ave 3186 max 3186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9807.00 ave 9807 max 9807 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: 212508.0 ave 212508 max 212508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212508 Ave neighs/atom = 66.700565 Neighbor list builds = 15 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 14 49 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 469 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.832 | 5.832 | 5.832 Mbytes Step Temp E_pair E_mol TotEng Press Volume 469 0 -13521.367 0 -13521.367 -19459.414 37649.241 506 0 -13551.328 0 -13551.328 10634.919 36900.572 Loop time of 4.64716 on 1 procs for 37 steps with 3186 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13521.3672063052 -13551.3270216706 -13551.3280984299 Force two-norm initial, final = 1586.7390 3.3902127 Force max component initial, final = 1583.9403 1.0731289 Final line search alpha, max atom move = 0.00010196588 0.00010942253 Iterations, force evaluations = 37 40 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.6022 | 4.6022 | 4.6022 | 0.0 | 99.03 Neigh | 0.018362 | 0.018362 | 0.018362 | 0.0 | 0.40 Comm | 0.0035765 | 0.0035765 | 0.0035765 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02302 | | | 0.50 Nlocal: 3186.00 ave 3186 max 3186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9831.00 ave 9831 max 9831 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: 211760.0 ave 211760 max 211760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211760 Ave neighs/atom = 66.465788 Neighbor list builds = 1 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 14 49 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.970 | 5.970 | 5.970 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13551.328 0 -13551.328 10634.919 Loop time of 2.296e-06 on 1 procs for 0 steps with 3186 atoms 174.2% 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 | | 2.296e-06 | | |100.00 Nlocal: 3186.00 ave 3186 max 3186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9849.00 ave 9849 max 9849 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: 211464.0 ave 211464 max 211464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211464 Ave neighs/atom = 66.372881 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 14 49 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.970 | 5.970 | 5.970 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 -13551.328 -13551.328 40.269888 144.54093 6.3395995 10634.919 10634.919 -44.97084 31957.185 -7.4584423 2.180058 3179.355 Loop time of 2.105e-06 on 1 procs for 0 steps with 3186 atoms 237.5% 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 | | 2.105e-06 | | |100.00 Nlocal: 3186.00 ave 3186 max 3186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9849.00 ave 9849 max 9849 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 105732.0 ave 105732 max 105732 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 211464.0 ave 211464 max 211464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 211464 Ave neighs/atom = 66.372881 Neighbor list builds = 0 Dangerous builds = 0 3186 -13551.3280984299 eV 2.18005802056019 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:47