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 -55.726933 0.0000000) to (27.861683 55.726933 3.5673230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0242379 5.0242379 3.5673230 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -55.726933 0.0000000) to (27.861683 55.726933 3.5673230) create_atoms CPU = 0.002 seconds 490 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0242379 5.0242379 3.5673230 Created 490 atoms using lattice units in orthogonal box = (0.0000000 -55.726933 0.0000000) to (27.861683 55.726933 3.5673230) create_atoms CPU = 0.002 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 40 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 16 atoms, new total = 964 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 = 10 40 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) = 4.575 | 4.575 | 4.575 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4035.0126 0 -4035.0126 -3514.5757 119 0 -4070.0485 0 -4070.0485 18121.862 Loop time of 14.6086 on 1 procs for 119 steps with 964 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 = -4035.01257386224 -4070.04545309392 -4070.04853289911 Force two-norm initial, final = 34.126957 0.18183093 Force max component initial, final = 9.7142597 0.026943493 Final line search alpha, max atom move = 1.0000000 0.026943493 Iterations, force evaluations = 119 226 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.531 | 14.531 | 14.531 | 0.0 | 99.47 Neigh | 0.021432 | 0.021432 | 0.021432 | 0.0 | 0.15 Comm | 0.02815 | 0.02815 | 0.02815 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02761 | | | 0.19 Nlocal: 964.000 ave 964 max 964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5214.00 ave 5214 max 5214 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: 56688.0 ave 56688 max 56688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56688 Ave neighs/atom = 58.804979 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 10 40 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 : 119 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.585 | 4.585 | 4.585 Mbytes Step Temp E_pair E_mol TotEng Press Volume 119 0 -4070.0485 0 -4070.0485 18121.862 11077.581 137 0 -4072.705 0 -4072.705 5510.5271 11198.332 Loop time of 1.24963 on 1 procs for 18 steps with 964 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 = -4070.04853289911 -4072.7033488846 -4072.70498704621 Force two-norm initial, final = 304.07732 7.5946733 Force max component initial, final = 284.07878 6.3783530 Final line search alpha, max atom move = 0.00072964444 0.0046539298 Iterations, force evaluations = 18 19 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2378 | 1.2378 | 1.2378 | 0.0 | 99.05 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.002376 | 0.002376 | 0.002376 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009461 | | | 0.76 Nlocal: 964.000 ave 964 max 964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5737.00 ave 5737 max 5737 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: 57536.0 ave 57536 max 57536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 57536 Ave neighs/atom = 59.684647 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 = 11 40 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) = 4.723 | 4.723 | 4.723 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4072.705 0 -4072.705 5510.5271 Loop time of 6.305e-06 on 1 procs for 0 steps with 964 atoms 190.3% 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 | | 6.305e-06 | | |100.00 Nlocal: 964.000 ave 964 max 964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5694.00 ave 5694 max 5694 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: 56132.0 ave 56132 max 56132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56132 Ave neighs/atom = 58.228216 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 = 11 40 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) = 4.723 | 4.723 | 4.723 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 -4072.705 -4072.705 28.347523 111.45387 3.5444028 5510.5271 5510.5271 -420.45861 16045.334 906.70545 2.3209316 175.04523 Loop time of 6.876e-06 on 1 procs for 0 steps with 964 atoms 276.3% 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 | | 6.876e-06 | | |100.00 Nlocal: 964.000 ave 964 max 964 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5694.00 ave 5694 max 5694 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 28066.0 ave 28066 max 28066 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 56132.0 ave 56132 max 56132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 56132 Ave neighs/atom = 58.228216 Neighbor list builds = 0 Dangerous builds = 0 964 -4072.70498704621 eV 2.32093162885286 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:16