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 = 3.61493 3.61493 3.61493 Created orthogonal box = (0 -63.8559 0) to (36.8651 63.8559 6.26123) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.67156 5.73034 6.26123 Created 1249 atoms create_atoms CPU = 0.00074482 secs 1249 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.67156 5.73034 6.26123 Created 1249 atoms create_atoms CPU = 0.000657082 secs 1249 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 34 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 26 atoms, new total = 2472 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.133 | 6.133 | 6.133 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8681.6457 0 -8681.6457 1995.2572 68 0 -8724.8805 0 -8724.8805 -8522.6491 Loop time of 0.876643 on 1 procs for 68 steps with 2472 atoms 100.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8681.64567324 -8724.87185246 -8724.88046998 Force two-norm initial, final = 49.705 0.296871 Force max component initial, final = 9.85147 0.0557569 Final line search alpha, max atom move = 1 0.0557569 Iterations, force evaluations = 68 115 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.82783 | 0.82783 | 0.82783 | 0.0 | 94.43 Neigh | 0.0327 | 0.0327 | 0.0327 | 0.0 | 3.73 Comm | 0.0093088 | 0.0093088 | 0.0093088 | 0.0 | 1.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006808 | | | 0.78 Nlocal: 2472 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10561 ave 10561 max 10561 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: 349136 ave 349136 max 349136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 349136 Ave neighs/atom = 141.236 Neighbor list builds = 3 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 : 68 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.134 | 6.134 | 6.134 Mbytes Step Temp E_pair E_mol TotEng Press Volume 68 0 -8724.8805 0 -8724.8805 -8522.6491 29478.615 72 0 -8725.2343 0 -8725.2343 -1842.6183 29335.21 Loop time of 0.055439 on 1 procs for 4 steps with 2472 atoms 90.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8724.88046998 -8725.23238901 -8725.2342758 Force two-norm initial, final = 200.048 0.351561 Force max component initial, final = 155.738 0.0471415 Final line search alpha, max atom move = 0.000122719 5.78514e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.053387 | 0.053387 | 0.053387 | 0.0 | 96.30 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045609 | 0.00045609 | 0.00045609 | 0.0 | 0.82 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001596 | | | 2.88 Nlocal: 2472 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10627 ave 10627 max 10627 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: 348894 ave 348894 max 348894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 348894 Ave neighs/atom = 141.138 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.272 | 6.272 | 6.272 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8725.2343 0 -8725.2343 -1842.6183 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2472 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: 2472 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10651 ave 10651 max 10651 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: 349452 ave 349452 max 349452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 349452 Ave neighs/atom = 141.364 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) = 6.272 | 6.272 | 6.272 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 -8725.2343 -8725.2343 36.749431 127.71185 6.2503941 -1842.6183 -1842.6183 0.76088295 -5528.7433 0.12751194 2.3225003 1039.3989 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2472 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: 2472 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10651 ave 10651 max 10651 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 174726 ave 174726 max 174726 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 349452 ave 349452 max 349452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 349452 Ave neighs/atom = 141.364 Neighbor list builds = 0 Dangerous builds = 0 2472 -8725.24663579695 eV 2.32250029109465 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01