LAMMPS (24 Jan 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.61315 3.61315 3.61315 Created orthogonal box = (0 -37.5525 0) to (26.5511 37.5525 5.10976) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.90025 4.86745 5.10976 Created 440 atoms create_atoms CPU = 0.000650883 secs 440 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.90025 4.86745 5.10976 Created 440 atoms create_atoms CPU = 0.00041604 secs 440 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 = 10.4596 ghost atom cutoff = 10.4596 binsize = 5.22982, bins = 6 15 1 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 10.4596 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 864 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 10.4596 ghost atom cutoff = 10.4596 binsize = 5.22982, bins = 6 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.4596 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) = 5.837 | 5.837 | 5.837 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2924.8716 0 -2924.8716 28463.454 40 0 -2998.9448 0 -2998.9448 5769.934 Loop time of 1.38717 on 1 procs for 40 steps with 864 atoms 67.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2924.87157747 -2998.94290398 -2998.94475624 Force two-norm initial, final = 75.8338 0.164012 Force max component initial, final = 11.025 0.0128961 Final line search alpha, max atom move = 1 0.0128961 Iterations, force evaluations = 40 77 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3779 | 1.3779 | 1.3779 | 0.0 | 99.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0065162 | 0.0065162 | 0.0065162 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002728 | | | 0.20 Nlocal: 864 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9559 ave 9559 max 9559 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: 331136 ave 331136 max 331136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 331136 Ave neighs/atom = 383.259 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.837 | 5.837 | 5.837 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -2998.9448 0 -2998.9448 5769.934 10189.499 44 0 -2999.0214 0 -2999.0214 681.5573 10228.339 Loop time of 0.2701 on 1 procs for 4 steps with 864 atoms 33.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2998.94475624 -2999.02142232 -2999.02144112 Force two-norm initial, final = 53.8615 0.216321 Force max component initial, final = 47.2499 0.0439221 Final line search alpha, max atom move = 0.00165645 7.27548e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26806 | 0.26806 | 0.26806 | 0.0 | 99.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053787 | 0.00053787 | 0.00053787 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001506 | | | 0.56 Nlocal: 864 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9490 ave 9490 max 9490 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: 332752 ave 332752 max 332752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 332752 Ave neighs/atom = 385.13 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 = 10.4596 ghost atom cutoff = 10.4596 binsize = 5.22982, bins = 6 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.4596 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) = 5.974 | 5.974 | 5.974 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2999.0214 0 -2999.0214 681.5573 Loop time of 1.90735e-06 on 1 procs for 0 steps with 864 atoms 157.3% 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 | | 1.907e-06 | | |100.00 Nlocal: 864 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9490 ave 9490 max 9490 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: 332064 ave 332064 max 332064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 332064 Ave neighs/atom = 384.333 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) = 5.974 | 5.974 | 5.974 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 -2999.0214 -2999.0214 26.618852 75.1051 5.1161865 681.5573 681.5573 -6.8975566 2044.8128 6.7566804 2.3730297 458.09958 Loop time of 2.14577e-06 on 1 procs for 0 steps with 864 atoms 139.8% 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 | | 2.146e-06 | | |100.00 Nlocal: 864 ave 864 max 864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9490 ave 9490 max 9490 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 166032 ave 166032 max 166032 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 332064 ave 332064 max 332064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 332064 Ave neighs/atom = 384.333 Neighbor list builds = 0 Dangerous builds = 0 864 -2999.02144111822 eV 2.37302966871323 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01