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 = 3.6583648 3.6583648 3.6583648 Created orthogonal box = (0.0000000 -39.060647 0.0000000) to (22.551675 39.060647 6.3364737) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9346514 5.4821961 6.3364737 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -39.060647 0.0000000) to (22.551675 39.060647 6.3364737) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9346514 5.4821961 6.3364737 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -39.060647 0.0000000) to (22.551675 39.060647 6.3364737) create_atoms CPU = 0.001 seconds 458 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 22 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 910 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_769582363439_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.991 | 4.991 | 4.991 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3303.2001 0 -3303.2001 87308.532 259 0 -3670.3849 0 -3670.3849 -56509.406 Loop time of 3.42478 on 1 procs for 259 steps with 910 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 = -3303.20011906473 -3670.38149091953 -3670.38487777343 Force two-norm initial, final = 837.23871 0.17522711 Force max component initial, final = 365.89729 0.028268982 Final line search alpha, max atom move = 1.0000000 0.028268982 Iterations, force evaluations = 259 492 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.3238 | 3.3238 | 3.3238 | 0.0 | 97.05 Neigh | 0.04828 | 0.04828 | 0.04828 | 0.0 | 1.41 Comm | 0.027134 | 0.027134 | 0.027134 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02561 | | | 0.75 Nlocal: 910.000 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4881.00 ave 4881 max 4881 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: 123976.0 ave 123976 max 123976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 123976 Ave neighs/atom = 136.23736 Neighbor list builds = 6 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 259 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.989 | 4.989 | 4.989 Mbytes Step Temp E_pair E_mol TotEng Press Volume 259 0 -3670.3849 0 -3670.3849 -56509.406 11163.384 284 0 -3679.8746 0 -3679.8746 -18.724694 10715.655 Loop time of 0.206244 on 1 procs for 25 steps with 910 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3670.38487777343 -3679.87237113266 -3679.87457735148 Force two-norm initial, final = 698.74553 4.5027079 Force max component initial, final = 477.00400 2.6892369 Final line search alpha, max atom move = 0.00038151996 0.0010259976 Iterations, force evaluations = 25 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1898 | 0.1898 | 0.1898 | 0.0 | 92.03 Neigh | 0.0083664 | 0.0083664 | 0.0083664 | 0.0 | 4.06 Comm | 0.0013483 | 0.0013483 | 0.0013483 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006728 | | | 3.26 Nlocal: 910.000 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4965.00 ave 4965 max 4965 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: 128304.0 ave 128304 max 128304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128304 Ave neighs/atom = 140.99341 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.127 | 5.127 | 5.127 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3679.8746 0 -3679.8746 -18.724694 Loop time of 2.358e-06 on 1 procs for 0 steps with 910 atoms 212.0% 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 | | 2.358e-06 | | |100.00 Nlocal: 910.000 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4947.00 ave 4947 max 4947 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: 129588.0 ave 129588 max 129588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129588 Ave neighs/atom = 142.40440 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 7 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.127 | 5.127 | 5.127 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 -3679.8746 -3679.8746 22.142317 76.310919 6.3417481 -18.724694 -18.724694 146.20078 200.04743 -402.42229 2.2285319 3273.1614 Loop time of 2.535e-06 on 1 procs for 0 steps with 910 atoms 236.7% 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 | | 2.535e-06 | | |100.00 Nlocal: 910.000 ave 910 max 910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4947.00 ave 4947 max 4947 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 64794.0 ave 64794 max 64794 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 129588.0 ave 129588 max 129588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129588 Ave neighs/atom = 142.40440 Neighbor list builds = 0 Dangerous builds = 0 910 -3679.87457735149 eV 2.22853192661944 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03