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 = 3.49213 3.49213 3.49213 Created orthogonal box = (0 -40.4278 0) to (28.5843 40.4278 4.93861) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.54621 6.03348 4.93861 Created 538 atoms create_atoms CPU = 0.000442982 secs 538 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.54621 6.03348 4.93861 Created 538 atoms create_atoms CPU = 0.000319004 secs 538 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 8 21 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 7.998 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 1066 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 8 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 5.419 | 5.419 | 5.419 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3513.9996 0 -3513.9996 6887.1705 49 0 -3534.9103 0 -3534.9103 -4063.136 Loop time of 0.357255 on 1 procs for 49 steps with 1066 atoms 100.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3513.99963804 -3534.90704956 -3534.91031129 Force two-norm initial, final = 30.1214 0.144437 Force max component initial, final = 9.90917 0.018933 Final line search alpha, max atom move = 1 0.018933 Iterations, force evaluations = 49 82 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34075 | 0.34075 | 0.34075 | 0.0 | 95.38 Neigh | 0.010427 | 0.010427 | 0.010427 | 0.0 | 2.92 Comm | 0.0037899 | 0.0037899 | 0.0037899 | 0.0 | 1.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002293 | | | 0.64 Nlocal: 1066 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6950 ave 6950 max 6950 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: 212360 ave 212360 max 212360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212360 Ave neighs/atom = 199.212 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 : 49 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.419 | 5.419 | 5.419 Mbytes Step Temp E_pair E_mol TotEng Press Volume 49 0 -3534.9103 0 -3534.9103 -4063.136 11414.124 53 0 -3534.9864 0 -3534.9864 -185.54946 11370.779 Loop time of 0.024092 on 1 procs for 4 steps with 1066 atoms 124.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3534.91031129 -3534.98392296 -3534.98637839 Force two-norm initial, final = 47.4467 1.30371 Force max component initial, final = 40.4385 1.10084 Final line search alpha, max atom move = 0.00017536 0.000193042 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.023239 | 0.023239 | 0.023239 | 0.0 | 96.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00023127 | 0.00023127 | 0.00023127 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006213 | | | 2.58 Nlocal: 1066 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6934 ave 6934 max 6934 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: 212256 ave 212256 max 212256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212256 Ave neighs/atom = 199.114 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 = 7.998 ghost atom cutoff = 7.998 binsize = 3.999, bins = 8 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.998 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) = 5.557 | 5.557 | 5.557 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3534.9864 0 -3534.9864 -185.54946 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1066 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: 1066 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6950 ave 6950 max 6950 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: 212480 ave 212480 max 212480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212480 Ave neighs/atom = 199.325 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) = 5.557 | 5.557 | 5.557 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 -3534.9864 -3534.9864 28.486437 80.855582 4.9367606 -185.54946 -185.54946 -154.58 -306.12056 -95.947809 2.2829566 523.83592 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1066 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: 1066 ave 1066 max 1066 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6950 ave 6950 max 6950 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 106240 ave 106240 max 106240 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 212480 ave 212480 max 212480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 212480 Ave neighs/atom = 199.325 Neighbor list builds = 0 Dangerous builds = 0 1066 -3489.97598656448 eV 2.28295661672823 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00