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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -42.727094 0.0000000) to (52.329789 42.727094 8.8453488) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9805474 5.4934835 5.8968992 Created 1671 atoms using lattice units in orthogonal box = (0.0000000 -42.727094 0.0000000) to (52.329789 42.727094 8.8453488) create_atoms CPU = 0.003 seconds 1671 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9805474 5.4934835 5.8968992 Created 1695 atoms using lattice units in orthogonal box = (0.0000000 -42.727094 0.0000000) to (52.329789 42.727094 8.8453488) create_atoms CPU = 0.002 seconds 1695 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 16 26 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3366 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_110119204723_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.503 | 6.503 | 6.503 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13463.275 0 -13463.275 61246.61 552 0 -14268.053 0 -14268.053 8327.5352 Loop time of 243.266 on 1 procs for 552 steps with 3366 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13463.274803557 -14268.039697312 -14268.0531600591 Force two-norm initial, final = 465.45061 0.43717052 Force max component initial, final = 40.874250 0.097979639 Final line search alpha, max atom move = 1.0000000 0.097979639 Iterations, force evaluations = 552 1067 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 242.56 | 242.56 | 242.56 | 0.0 | 99.71 Neigh | 0.38366 | 0.38366 | 0.38366 | 0.0 | 0.16 Comm | 0.14145 | 0.14145 | 0.14145 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1772 | | | 0.07 Nlocal: 3366.00 ave 3366 max 3366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9034.00 ave 9034 max 9034 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: 406766.0 ave 406766 max 406766 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 406766 Ave neighs/atom = 120.84551 Neighbor list builds = 13 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 16 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 552 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.500 | 6.500 | 6.500 Mbytes Step Temp E_pair E_mol TotEng Press Volume 552 0 -14268.053 0 -14268.053 8327.5352 39554.628 561 0 -14270.314 0 -14270.314 11.049426 39744.437 Loop time of 2.43552 on 1 procs for 9 steps with 3366 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 = -14268.053160059 -14270.3121024106 -14270.313895799 Force two-norm initial, final = 503.02211 0.99918617 Force max component initial, final = 395.52650 0.32520756 Final line search alpha, max atom move = 0.00011147556 3.6252696e-05 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4282 | 2.4282 | 2.4282 | 0.0 | 99.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00092334 | 0.00092334 | 0.00092334 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006377 | | | 0.26 Nlocal: 3366.00 ave 3366 max 3366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9069.00 ave 9069 max 9069 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: 407942.0 ave 407942 max 407942 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 407942 Ave neighs/atom = 121.19489 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.638 | 6.638 | 6.638 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14270.314 0 -14270.314 11.049426 Loop time of 2.282e-06 on 1 procs for 0 steps with 3366 atoms 175.3% 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 | | 2.282e-06 | | |100.00 Nlocal: 3366.00 ave 3366 max 3366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9033.00 ave 9033 max 9033 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: 396632.0 ave 396632 max 396632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 396632 Ave neighs/atom = 117.83482 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 16 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 6.638 | 6.638 | 6.638 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 -14270.314 -14270.314 51.992166 85.828173 8.9065308 11.049426 11.049426 13.025175 10.308179 9.814924 2.2524709 12811.511 Loop time of 2.522e-06 on 1 procs for 0 steps with 3366 atoms 237.9% 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 | | 2.522e-06 | | |100.00 Nlocal: 3366.00 ave 3366 max 3366 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9033.00 ave 9033 max 9033 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 198316.0 ave 198316 max 198316 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 396632.0 ave 396632 max 396632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 396632 Ave neighs/atom = 117.83482 Neighbor list builds = 0 Dangerous builds = 0 3366 -14270.313895799 eV 2.25247086417179 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:04:06