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 = 3.3024436 3.3024436 3.3024436 Created orthogonal box = (0.0000000 -43.185053 0.0000000) to (20.357629 43.185053 4.6703605) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2858167 5.3034276 4.6703605 Created 228 atoms using lattice units in orthogonal box = (0.0000000 -43.185053 0.0000000) to (20.357629 43.185053 4.6703605) create_atoms CPU = 0.002 seconds 228 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2858167 5.3034276 4.6703605 Created 230 atoms using lattice units in orthogonal box = (0.0000000 -43.185053 0.0000000) to (20.357629 43.185053 4.6703605) create_atoms CPU = 0.002 seconds 230 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 7 27 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 452 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_072689718616_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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 7 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.455 | 4.455 | 4.455 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3280.9551 0 -3280.9551 15717.437 44 0 -3356.6492 0 -3356.6492 -7456.5845 Loop time of 2.27338 on 1 procs for 44 steps with 452 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3280.95505667663 -3356.64709392497 -3356.64917366454 Force two-norm initial, final = 129.86791 0.14347017 Force max component initial, final = 45.284847 0.020769742 Final line search alpha, max atom move = 1.0000000 0.020769742 Iterations, force evaluations = 44 71 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2564 | 2.2564 | 2.2564 | 0.0 | 99.25 Neigh | 0.0050529 | 0.0050529 | 0.0050529 | 0.0 | 0.22 Comm | 0.0059716 | 0.0059716 | 0.0059716 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006004 | | | 0.26 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2972.00 ave 2972 max 2972 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: 26892.0 ave 26892 max 26892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26892 Ave neighs/atom = 59.495575 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 7 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.455 | 4.455 | 4.455 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -3356.6492 0 -3356.6492 -7456.5845 8211.8509 48 0 -3356.743 0 -3356.743 -186.52993 8180.7795 Loop time of 0.24443 on 1 procs for 4 steps with 452 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 = -3356.64917366454 -3356.74255573415 -3356.74299112067 Force two-norm initial, final = 69.059361 1.7847126 Force max component initial, final = 54.186361 1.4836938 Final line search alpha, max atom move = 0.00033910615 0.00050312969 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.24198 | 0.24198 | 0.24198 | 0.0 | 99.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005275 | 0.0005275 | 0.0005275 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001926 | | | 0.79 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2948.00 ave 2948 max 2948 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: 26728.0 ave 26728 max 26728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26728 Ave neighs/atom = 59.132743 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.593 | 4.593 | 4.593 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3356.743 0 -3356.743 -186.52993 Loop time of 6.105e-06 on 1 procs for 0 steps with 452 atoms 196.6% 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 | | 6.105e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2948.00 ave 2948 max 2948 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: 27160.0 ave 27160 max 27160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27160 Ave neighs/atom = 60.088496 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.593 | 4.593 | 4.593 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 -3356.743 -3356.743 20.358107 86.126582 4.6657353 -186.52993 -186.52993 -127.73756 -141.56387 -290.28837 2.6216882 424.87893 Loop time of 6.164e-06 on 1 procs for 0 steps with 452 atoms 308.2% 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 | | 6.164e-06 | | |100.00 Nlocal: 452.000 ave 452 max 452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2948.00 ave 2948 max 2948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13580.0 ave 13580 max 13580 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 27160.0 ave 27160 max 27160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 27160 Ave neighs/atom = 60.088496 Neighbor list builds = 0 Dangerous builds = 0 452 -3356.74299112067 eV 2.62168820998901 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03