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 = 3.68004 3.68004 3.68004 Created orthogonal box = (0 -63.7439 0) to (26.0218 63.7439 9.01423) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.24524 5.52415 6.00949 Created 1202 atoms create_atoms CPU = 0.000599146 secs 1202 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.24524 5.52415 6.00949 Created 1202 atoms create_atoms CPU = 0.000496149 secs 1202 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.86322, bins = 10 45 4 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 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 2384 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.86322, bins = 10 45 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 5.12 | 5.12 | 5.12 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10095.02 0 -10095.02 -113.7304 40 0 -10136.789 0 -10136.789 -13541.003 Loop time of 0.202984 on 1 procs for 40 steps with 2384 atoms 98.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10095.019912 -10136.7810087 -10136.7894422 Force two-norm initial, final = 29.0002 0.317633 Force max component initial, final = 4.91845 0.0603926 Final line search alpha, max atom move = 1 0.0603926 Iterations, force evaluations = 40 68 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19116 | 0.19116 | 0.19116 | 0.0 | 94.18 Neigh | 0.0054109 | 0.0054109 | 0.0054109 | 0.0 | 2.67 Comm | 0.0028481 | 0.0028481 | 0.0028481 | 0.0 | 1.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003564 | | | 1.76 Nlocal: 2384 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6027 ave 6027 max 6027 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: 131480 ave 131480 max 131480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 131480 Ave neighs/atom = 55.151 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 : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.124 | 5.124 | 5.124 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -10136.789 0 -10136.789 -13541.003 29904.435 46 0 -10137.727 0 -10137.727 -2811.7658 29678.307 Loop time of 0.0246148 on 1 procs for 6 steps with 2384 atoms 81.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10136.7894422 -10137.7265085 -10137.7270259 Force two-norm initial, final = 340.042 0.434508 Force max component initial, final = 276.487 0.0605545 Final line search alpha, max atom move = 0.0001933 1.17052e-05 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.022842 | 0.022842 | 0.022842 | 0.0 | 92.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031304 | 0.00031304 | 0.00031304 | 0.0 | 1.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00146 | | | 5.93 Nlocal: 2384 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6031 ave 6031 max 6031 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: 132272 ave 132272 max 132272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132272 Ave neighs/atom = 55.4832 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.86322, bins = 10 45 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 5.262 | 5.262 | 5.262 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10137.727 0 -10137.727 -2811.7658 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2384 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: 2384 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6039 ave 6039 max 6039 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: 132448 ave 132448 max 132448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132448 Ave neighs/atom = 55.557 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) = 5.262 | 5.262 | 5.262 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 -10137.727 -10137.727 25.898105 127.48785 8.9888129 -2811.7658 -2811.7658 0.63467105 -8433.8007 -2.1313953 2.4316513 1044.8765 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2384 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: 2384 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6039 ave 6039 max 6039 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 66224 ave 66224 max 66224 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 132448 ave 132448 max 132448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132448 Ave neighs/atom = 55.557 Neighbor list builds = 0 Dangerous builds = 0 2384 -10137.7270259393 eV 2.43165127750141 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00