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 = 4.0310361 4.0310361 4.0310361 Created orthogonal box = (0.0000000 -62.966797 0.0000000) to (31.483398 62.966797 4.0310361) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6773341 5.6773341 4.0310361 Created 488 atoms using lattice units in orthogonal box = (0.0000000 -62.966797 0.0000000) to (31.483398 62.966797 4.0310361) create_atoms CPU = 0.001 seconds 488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6773341 5.6773341 4.0310361 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -62.966797 0.0000000) to (31.483398 62.966797 4.0310361) create_atoms CPU = 0.001 seconds 490 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 9 33 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 978 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_699137396381_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 9 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.001 | 5.001 | 5.001 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3203.8176 0 -3203.8176 11797.719 90 0 -3280.3442 0 -3280.3442 2832.941 Loop time of 1.05992 on 1 procs for 90 steps with 978 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3203.8175569422 -3280.34115420462 -3280.34416794114 Force two-norm initial, final = 42.793010 0.15708536 Force max component initial, final = 6.5894535 0.041569683 Final line search alpha, max atom move = 1.0000000 0.041569683 Iterations, force evaluations = 90 166 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0246 | 1.0246 | 1.0246 | 0.0 | 96.67 Neigh | 0.014881 | 0.014881 | 0.014881 | 0.0 | 1.40 Comm | 0.010957 | 0.010957 | 0.010957 | 0.0 | 1.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009454 | | | 0.89 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6368.00 ave 6368 max 6368 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: 129296.0 ave 129296 max 129296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129296 Ave neighs/atom = 132.20450 Neighbor list builds = 2 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 9 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 90 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.994 | 4.994 | 4.994 Mbytes Step Temp E_pair E_mol TotEng Press Volume 90 0 -3280.3442 0 -3280.3442 2832.941 15982.323 96 0 -3280.4982 0 -3280.4982 -86.115915 16043.981 Loop time of 0.0522172 on 1 procs for 6 steps with 978 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 = -3280.34416794113 -3280.49783102726 -3280.49817725092 Force two-norm initial, final = 61.514819 1.7763251 Force max component initial, final = 55.011362 1.5186220 Final line search alpha, max atom move = 0.00039600490 0.00060138175 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.049748 | 0.049748 | 0.049748 | 0.0 | 95.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00044518 | 0.00044518 | 0.00044518 | 0.0 | 0.85 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002024 | | | 3.88 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6363.00 ave 6363 max 6363 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: 129236.0 ave 129236 max 129236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129236 Ave neighs/atom = 132.14315 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 9 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.132 | 5.132 | 5.132 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3280.4982 0 -3280.4982 -86.115915 Loop time of 1.823e-06 on 1 procs for 0 steps with 978 atoms 219.4% 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 | | 1.823e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6368.00 ave 6368 max 6368 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: 129068.0 ave 129068 max 129068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129068 Ave neighs/atom = 131.97137 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 9 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.132 | 5.132 | 5.132 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 -3280.4982 -3280.4982 31.406614 126.57914 4.035793 -86.115915 -86.115915 -151.28205 -18.971196 -88.094496 2.59574 200.75026 Loop time of 2.205e-06 on 1 procs for 0 steps with 978 atoms 181.4% 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 | | 2.205e-06 | | |100.00 Nlocal: 978.000 ave 978 max 978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6368.00 ave 6368 max 6368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 64534.0 ave 64534 max 64534 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 129068.0 ave 129068 max 129068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129068 Ave neighs/atom = 131.97137 Neighbor list builds = 0 Dangerous builds = 0 978 -3280.49817725092 eV 2.59573995438802 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01