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 = 3.17012 3.17012 3.17012 Created orthogonal box = (0 -41.5789 0) to (29.3985 41.5789 4.48323) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.46949 5.31783 4.48323 Created 345 atoms create_atoms CPU = 0.000354052 secs 345 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.46949 5.31783 4.48323 Created 345 atoms create_atoms CPU = 0.000201941 secs 345 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 = 7.2 ghost atom cutoff = 7.2 binsize = 3.6, bins = 9 24 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 7.2 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 687 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 = 7.2 ghost atom cutoff = 7.2 binsize = 3.6, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.2 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) = 4.517 | 4.517 | 4.517 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7309.9493 0 -7309.9493 26755.135 77 0 -7428.9933 0 -7428.9933 3811.2776 Loop time of 16.1266 on 1 procs for 77 steps with 687 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7309.94932056 -7428.98698587 -7428.99329204 Force two-norm initial, final = 109.602 0.256963 Force max component initial, final = 20.6044 0.0352435 Final line search alpha, max atom move = 1 0.0352435 Iterations, force evaluations = 77 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.115 | 16.115 | 16.115 | 0.0 | 99.93 Neigh | 0.0053101 | 0.0053101 | 0.0053101 | 0.0 | 0.03 Comm | 0.0038905 | 0.0038905 | 0.0038905 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002428 | | | 0.02 Nlocal: 687 ave 687 max 687 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4710 ave 4710 max 4710 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: 75200 ave 75200 max 75200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75200 Ave neighs/atom = 109.461 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 : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.523 | 4.523 | 4.523 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -7428.9933 0 -7428.9933 3811.2776 10960.222 79 0 -7429.0157 0 -7429.0157 2687.3199 10964.898 Loop time of 0.490978 on 1 procs for 2 steps with 687 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7428.99329204 -7429.01109103 -7429.01567152 Force two-norm initial, final = 29.7134 6.45224 Force max component initial, final = 29.4143 6.11601 Final line search alpha, max atom move = 7.66188e-05 0.000468601 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.49053 | 0.49053 | 0.49053 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00010586 | 0.00010586 | 0.00010586 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003412 | | | 0.07 Nlocal: 687 ave 687 max 687 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4714 ave 4714 max 4714 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: 75246 ave 75246 max 75246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75246 Ave neighs/atom = 109.528 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 = 7.2 ghost atom cutoff = 7.2 binsize = 3.6, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.2 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) = 4.661 | 4.661 | 4.661 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7429.0157 0 -7429.0157 2687.3199 Loop time of 9.53674e-07 on 1 procs for 0 steps with 687 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: 687 ave 687 max 687 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4714 ave 4714 max 4714 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: 75246 ave 75246 max 75246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75246 Ave neighs/atom = 109.528 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) = 4.661 | 4.661 | 4.661 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 -7429.0157 -7429.0157 29.434191 83.157852 4.4797032 2687.3199 2687.3199 894.74808 6869.5919 297.61969 2.4659015 420.70555 Loop time of 2.14577e-06 on 1 procs for 0 steps with 687 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: 687 ave 687 max 687 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4714 ave 4714 max 4714 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37623 ave 37623 max 37623 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 75246 ave 75246 max 75246 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 75246 Ave neighs/atom = 109.528 Neighbor list builds = 0 Dangerous builds = 0 687 -4526.13423115463 eV 2.46590153681482 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:17