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 = 3.61115 3.61115 3.61115 Created orthogonal box = (0 -69.089 0) to (39.8865 69.089 6.2547) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.88489 5.28522 6.2547 Created 1466 atoms create_atoms CPU = 0.000618935 secs 1466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.88489 5.28522 6.2547 Created 1466 atoms create_atoms CPU = 0.000511885 secs 1466 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 15 52 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 26 atoms, new total = 2906 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 15 52 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 6.41 | 6.41 | 6.41 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12245.456 0 -12245.456 571.84206 47 0 -12309.725 0 -12309.725 -8122.5159 Loop time of 5.67329 on 1 procs for 47 steps with 2906 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12245.4557755 -12309.7140827 -12309.7249513 Force two-norm initial, final = 53.8625 0.464388 Force max component initial, final = 10.2956 0.082222 Final line search alpha, max atom move = 0.937625 0.0770934 Iterations, force evaluations = 47 81 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6637 | 5.6637 | 5.6637 | 0.0 | 99.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0043223 | 0.0043223 | 0.0043223 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005257 | | | 0.09 Nlocal: 2906 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7670 ave 7670 max 7670 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: 155812 ave 155812 max 155812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 155812 Ave neighs/atom = 53.6173 Neighbor list builds = 0 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 : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.41 | 6.41 | 6.41 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -12309.725 0 -12309.725 -8122.5159 34472.384 50 0 -12309.926 0 -12309.926 -3197.6175 34368.441 Loop time of 0.436305 on 1 procs for 3 steps with 2906 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 = -12309.7249513 -12309.9229731 -12309.9260411 Force two-norm initial, final = 176.27 0.540054 Force max component initial, final = 145.964 0.0949839 Final line search alpha, max atom move = 7.45982e-05 7.08563e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43475 | 0.43475 | 0.43475 | 0.0 | 99.64 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028014 | 0.00028014 | 0.00028014 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001271 | | | 0.29 Nlocal: 2906 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7693 ave 7693 max 7693 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: 156736 ave 156736 max 156736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156736 Ave neighs/atom = 53.9353 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 15 52 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 6.548 | 6.548 | 6.548 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12309.926 0 -12309.926 -3197.6175 Loop time of 2.14577e-06 on 1 procs for 0 steps with 2906 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 | | 2.146e-06 | | |100.00 Nlocal: 2906 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7693 ave 7693 max 7693 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: 156748 ave 156748 max 156748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156748 Ave neighs/atom = 53.9394 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) = 6.548 | 6.548 | 6.548 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 -12309.926 -12309.926 39.799126 138.17806 6.2495279 -3197.6175 -3197.6175 1.0729219 -9593.6983 -0.22708935 2.2922265 777.43669 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2906 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: 2906 ave 2906 max 2906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7693 ave 7693 max 7693 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78374 ave 78374 max 78374 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 156748 ave 156748 max 156748 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156748 Ave neighs/atom = 53.9394 Neighbor list builds = 0 Dangerous builds = 0 2906 -12309.9260411189 eV 2.29222648812032 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06