LAMMPS (7 Aug 2019) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:93) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 2.8665 2.8665 2.8665 Created orthogonal box = (0 -54.0879 0) to (27.0425 54.0879 2.8665) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.95003 3.95003 2.8665 Created 357 atoms create_atoms CPU = 0.000231981 secs 357 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.95003 3.95003 2.8665 Created 357 atoms create_atoms CPU = 0.000119209 secs 357 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.86322, bins = 10 38 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 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 707 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.86322, bins = 10 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.52 | 4.52 | 4.52 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2999.9968 0 -2999.9968 8218.2637 72 0 -3038.6247 0 -3038.6247 -4546.9599 Loop time of 0.107953 on 1 procs for 72 steps with 707 atoms 101.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2999.99681192 -3038.62171833 -3038.62467821 Force two-norm initial, final = 52.8504 0.215435 Force max component initial, final = 18.4793 0.0451664 Final line search alpha, max atom move = 1 0.0451664 Iterations, force evaluations = 72 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.099396 | 0.099396 | 0.099396 | 0.0 | 92.07 Neigh | 0.002799 | 0.002799 | 0.002799 | 0.0 | 2.59 Comm | 0.0035944 | 0.0035944 | 0.0035944 | 0.0 | 3.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002164 | | | 2.00 Nlocal: 707 ave 707 max 707 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4873 ave 4873 max 4873 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 42128 ave 42128 max 42128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42128 Ave neighs/atom = 59.587 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:168) Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.521 | 4.521 | 4.521 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -3038.6247 0 -3038.6247 -4546.9599 8385.4975 77 0 -3038.7231 0 -3038.7231 1312.9596 8358.5047 Loop time of 0.00704813 on 1 procs for 5 steps with 707 atoms 141.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3038.62467821 -3038.72210564 -3038.72313887 Force two-norm initial, final = 49.2054 2.11744 Force max component initial, final = 47.6205 1.91626 Final line search alpha, max atom move = 0.000272564 0.000522304 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0061538 | 0.0061538 | 0.0061538 | 0.0 | 87.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00019264 | 0.00019264 | 0.00019264 | 0.0 | 2.73 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007017 | | | 9.96 Nlocal: 707 ave 707 max 707 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4868 ave 4868 max 4868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 42032 ave 42032 max 42032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 42032 Ave neighs/atom = 59.4512 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.86322, bins = 10 38 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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/newton bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.672 | 4.672 | 4.672 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3038.7231 0 -3038.7231 1312.9596 Loop time of 1.90735e-06 on 1 procs for 0 steps with 707 atoms 0.0% 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 | | 1.907e-06 | | |100.00 Nlocal: 707 ave 707 max 707 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4868 ave 4868 max 4868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 43326 ave 43326 max 43326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43326 Ave neighs/atom = 61.2815 Neighbor list builds = 0 Dangerous builds = 0 Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.672 | 4.672 | 4.672 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 -3038.7231 -3038.7231 27.076368 108.17576 2.8536994 1312.9596 1312.9596 367.77287 3405.6865 165.41937 2.2802758 235.18699 Loop time of 1.19209e-06 on 1 procs for 0 steps with 707 atoms 0.0% 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 | | 1.192e-06 | | |100.00 Nlocal: 707 ave 707 max 707 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4868 ave 4868 max 4868 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21663 ave 21663 max 21663 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 43326 ave 43326 max 43326 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43326 Ave neighs/atom = 61.2815 Neighbor list builds = 0 Dangerous builds = 0 707 -3038.7231388727 eV 2.28027582813339 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00