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 = 3.49194 3.49194 3.49194 Created orthogonal box = (0 -43.055 0) to (15.221 43.055 4.93835) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.60774 4.53174 4.93835 Created 306 atoms create_atoms CPU = 0.000289917 secs 306 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.60774 4.53174 4.93835 Created 306 atoms create_atoms CPU = 0.000157118 secs 306 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 = 6.85342 ghost atom cutoff = 6.85342 binsize = 3.42671, bins = 5 26 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 6.85342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 604 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 = 6.85342 ghost atom cutoff = 6.85342 binsize = 3.42671, bins = 5 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85342 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) = 4.536 | 4.536 | 4.536 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2646.4332 0 -2646.4332 19142.776 23 0 -2671.2445 0 -2671.2445 -1878.1994 Loop time of 0.21303 on 1 procs for 23 steps with 604 atoms 103.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2646.43320901 -2671.24217517 -2671.24452565 Force two-norm initial, final = 52.6262 0.173257 Force max component initial, final = 15.5817 0.0232909 Final line search alpha, max atom move = 0.609387 0.0141932 Iterations, force evaluations = 23 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21079 | 0.21079 | 0.21079 | 0.0 | 98.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014167 | 0.0014167 | 0.0014167 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008247 | | | 0.39 Nlocal: 604 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4692 ave 4692 max 4692 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: 79984 ave 79984 max 79984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 79984 Ave neighs/atom = 132.424 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 : 23 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.536 | 4.536 | 4.536 Mbytes Step Temp E_pair E_mol TotEng Press Volume 23 0 -2671.2445 0 -2671.2445 -1878.1994 6472.5975 24 0 -2671.2466 0 -2671.2466 -2035.6561 6473.1669 Loop time of 0.00971198 on 1 procs for 1 steps with 604 atoms 103.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2671.24452565 -2671.24452565 -2671.24662758 Force two-norm initial, final = 7.04109 0.388479 Force max component initial, final = 5.46946 0.264432 Final line search alpha, max atom move = 0.000182833 4.8347e-05 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0094957 | 0.0094957 | 0.0094957 | 0.0 | 97.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 6.2943e-05 | 6.2943e-05 | 6.2943e-05 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0001533 | | | 1.58 Nlocal: 604 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4692 ave 4692 max 4692 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: 80120 ave 80120 max 80120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80120 Ave neighs/atom = 132.649 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 = 6.85342 ghost atom cutoff = 6.85342 binsize = 3.42671, bins = 5 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85342 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) = 4.674 | 4.674 | 4.674 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2671.2466 0 -2671.2466 -2035.6561 Loop time of 9.53674e-07 on 1 procs for 0 steps with 604 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: 604 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4692 ave 4692 max 4692 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: 80120 ave 80120 max 80120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80120 Ave neighs/atom = 132.649 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) = 4.674 | 4.674 | 4.674 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 -2671.2466 -2671.2466 15.228072 86.110004 4.9364902 -2035.6561 -2035.6561 -55.616473 -5985.9266 -65.42508 2.3289212 219.40087 Loop time of 1.19209e-06 on 1 procs for 0 steps with 604 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: 604 ave 604 max 604 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4692 ave 4692 max 4692 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40060 ave 40060 max 40060 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 80120 ave 80120 max 80120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80120 Ave neighs/atom = 132.649 Neighbor list builds = 0 Dangerous builds = 0 604 -2671.24662757781 eV 2.32892121609299 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00