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 = 3.98756 3.98756 3.98756 Created orthogonal box = (0 -39.8796 0) to (19.9378 39.8796 3.98756) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.58258 5.58258 3.98756 Created 202 atoms create_atoms CPU = 0.000213861 secs 202 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.58258 5.58258 3.98756 Created 202 atoms create_atoms CPU = 9.29832e-05 secs 202 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 5 20 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 398 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 5 20 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.471 | 4.471 | 4.471 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1323.8364 0 -1323.8364 12116.999 67 0 -1343.7708 0 -1343.7708 -804.05152 Loop time of 0.164177 on 1 procs for 67 steps with 398 atoms 97.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1323.83639237 -1343.76959963 -1343.77083552 Force two-norm initial, final = 20.4725 0.0911399 Force max component initial, final = 7.06594 0.0201439 Final line search alpha, max atom move = 1 0.0201439 Iterations, force evaluations = 67 116 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1581 | 0.1581 | 0.1581 | 0.0 | 96.30 Neigh | 0.001771 | 0.001771 | 0.001771 | 0.0 | 1.08 Comm | 0.0027971 | 0.0027971 | 0.0027971 | 0.0 | 1.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00151 | | | 0.92 Nlocal: 398 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3952 ave 3952 max 3952 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: 55056 ave 55056 max 55056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55056 Ave neighs/atom = 138.332 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 : 67 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.471 | 4.471 | 4.471 Mbytes Step Temp E_pair E_mol TotEng Press Volume 67 0 -1343.7708 0 -1343.7708 -804.05152 6341.1006 71 0 -1343.7892 0 -1343.7892 -86.398745 6336.1213 Loop time of 0.00878501 on 1 procs for 4 steps with 398 atoms 113.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1343.77083552 -1343.78834544 -1343.7892364 Force two-norm initial, final = 9.22452 1.9006 Force max component initial, final = 9.05624 1.64405 Final line search alpha, max atom move = 0.000560336 0.000921218 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0082271 | 0.0082271 | 0.0082271 | 0.0 | 93.65 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00013828 | 0.00013828 | 0.00013828 | 0.0 | 1.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004196 | | | 4.78 Nlocal: 398 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3872 ave 3872 max 3872 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: 54936 ave 54936 max 54936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54936 Ave neighs/atom = 138.03 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 5 20 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.608 | 4.608 | 4.608 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1343.7892 0 -1343.7892 -86.398745 Loop time of 9.53674e-07 on 1 procs for 0 steps with 398 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: 398 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3887 ave 3887 max 3887 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: 55044 ave 55044 max 55044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55044 Ave neighs/atom = 138.302 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) = 4.608 | 4.608 | 4.608 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 -1343.7892 -1343.7892 19.870034 79.759146 3.9980145 -86.398745 -86.398745 238.70341 -914.7098 416.81015 2.535649 187.31125 Loop time of 9.53674e-07 on 1 procs for 0 steps with 398 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: 398 ave 398 max 398 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3887 ave 3887 max 3887 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27522 ave 27522 max 27522 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 55044 ave 55044 max 55044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 55044 Ave neighs/atom = 138.302 Neighbor list builds = 0 Dangerous builds = 0 398 -623.409236402742 eV 2.53564902059376 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00