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 = 3.63552 3.63552 3.63552 Created orthogonal box = (0 -56.7923 0) to (28.3943 56.7923 3.63552) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.12029 5.12029 3.63552 Created 490 atoms create_atoms CPU = 0.000216961 secs 490 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.12029 5.12029 3.63552 Created 490 atoms create_atoms CPU = 0.000109196 secs 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 10 39 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 5.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 974 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 10 39 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 4.583 | 4.583 | 4.583 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3939.9694 0 -3939.9694 17899.363 79 0 -3987.5629 0 -3987.5629 788.66263 Loop time of 17.9835 on 1 procs for 79 steps with 974 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 = -3939.96936178 -3987.55944026 -3987.56285616 Force two-norm initial, final = 42.0011 0.205812 Force max component initial, final = 12.3383 0.0542745 Final line search alpha, max atom move = 1 0.0542745 Iterations, force evaluations = 79 135 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.971 | 17.971 | 17.971 | 0.0 | 99.93 Neigh | 0.0045509 | 0.0045509 | 0.0045509 | 0.0 | 0.03 Comm | 0.0045137 | 0.0045137 | 0.0045137 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003116 | | | 0.02 Nlocal: 974 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5122 ave 5122 max 5122 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: 74624 ave 74624 max 74624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74624 Ave neighs/atom = 76.616 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 : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.584 | 4.584 | 4.584 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -3987.5629 0 -3987.5629 788.66263 11725.135 82 0 -3987.5882 0 -3987.5882 -1.8509797 11731.826 Loop time of 0.641503 on 1 procs for 3 steps with 974 atoms 101.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3987.56285616 -3987.58786258 -3987.58820585 Force two-norm initial, final = 16.968 2.11319 Force max component initial, final = 13.7226 2.09612 Final line search alpha, max atom move = 0.000356921 0.000748149 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.6409 | 0.6409 | 0.6409 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000139 | 0.000139 | 0.000139 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000463 | | | 0.07 Nlocal: 974 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5094 ave 5094 max 5094 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: 74980 ave 74980 max 74980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74980 Ave neighs/atom = 76.9815 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 10 39 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 4.721 | 4.721 | 4.721 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3987.5882 0 -3987.5882 -1.8509797 Loop time of 1.19209e-06 on 1 procs for 0 steps with 974 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: 974 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5102 ave 5102 max 5102 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: 75008 ave 75008 max 75008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75008 Ave neighs/atom = 77.0103 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) = 4.721 | 4.721 | 4.721 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 -3987.5882 -3987.5882 28.346962 113.5846 3.6436751 -1.8509797 -1.8509797 -285.7826 303.90916 -23.679501 2.3266542 158.23651 Loop time of 1.90735e-06 on 1 procs for 0 steps with 974 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: 974 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5102 ave 5102 max 5102 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37504 ave 37504 max 37504 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75008 ave 75008 max 75008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75008 Ave neighs/atom = 77.0103 Neighbor list builds = 0 Dangerous builds = 0 974 -3426.14405165529 eV 2.32665424874717 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19