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 = 3.45246 3.45246 3.45246 Created orthogonal box = (0 -56.0994 0) to (11.4505 56.0994 8.45678) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.20479 5.09963 5.63785 Created 530 atoms create_atoms CPU = 0.000252962 secs 530 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.20479 5.09963 5.63785 Created 530 atoms create_atoms CPU = 0.000156879 secs 530 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 = 7.95414 ghost atom cutoff = 7.95414 binsize = 3.97707, bins = 3 29 3 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 7.95414 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 1046 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 = 7.95414 ghost atom cutoff = 7.95414 binsize = 3.97707, bins = 3 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.95414 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) = 5.548 | 5.548 | 5.548 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4683.2329 0 -4683.2329 -5079.1165 55 0 -4696.2887 0 -4696.2887 -16739.966 Loop time of 0.47625 on 1 procs for 55 steps with 1046 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4683.23288685 -4696.28418753 -4696.28866073 Force two-norm initial, final = 29.6872 0.210658 Force max component initial, final = 12.0285 0.0450975 Final line search alpha, max atom move = 1 0.0450975 Iterations, force evaluations = 55 106 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.46193 | 0.46193 | 0.46193 | 0.0 | 96.99 Neigh | 0.0065448 | 0.0065448 | 0.0065448 | 0.0 | 1.37 Comm | 0.004782 | 0.004782 | 0.004782 | 0.0 | 1.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002996 | | | 0.63 Nlocal: 1046 ave 1046 max 1046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7498 ave 7498 max 7498 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: 208036 ave 208036 max 208036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208036 Ave neighs/atom = 198.887 Neighbor list builds = 1 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 : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.548 | 5.548 | 5.548 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -4696.2887 0 -4696.2887 -16739.966 10864.712 58 0 -4696.4755 0 -4696.4755 -2760.6935 10827.464 Loop time of 0.032974 on 1 procs for 3 steps with 1046 atoms 91.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4696.28866073 -4696.4745476 -4696.47550284 Force two-norm initial, final = 151.037 0.249989 Force max component initial, final = 114.804 0.0541119 Final line search alpha, max atom move = 0.00022067 1.19409e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.031831 | 0.031831 | 0.031831 | 0.0 | 96.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026226 | 0.00026226 | 0.00026226 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008812 | | | 2.67 Nlocal: 1046 ave 1046 max 1046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7498 ave 7498 max 7498 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: 208076 ave 208076 max 208076 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208076 Ave neighs/atom = 198.925 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 = 7.95414 ghost atom cutoff = 7.95414 binsize = 3.97707, bins = 3 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.95414 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) = 5.686 | 5.686 | 5.686 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4696.4755 0 -4696.4755 -2760.6935 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1046 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 | | 9.537e-07 | | |100.00 Nlocal: 1046 ave 1046 max 1046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7498 ave 7498 max 7498 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: 208132 ave 208132 max 208132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208132 Ave neighs/atom = 198.979 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) = 5.686 | 5.686 | 5.686 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 -4696.4755 -4696.4755 11.426283 112.19871 8.4456655 -2760.6935 -2760.6935 -1.5354737 -8277.4636 -3.0814979 2.1811451 386.59521 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1046 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: 1046 ave 1046 max 1046 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7498 ave 7498 max 7498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 104066 ave 104066 max 104066 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 208132 ave 208132 max 208132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208132 Ave neighs/atom = 198.979 Neighbor list builds = 0 Dangerous builds = 0 1046 -4696.47550284082 eV 2.18114514340839 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00