LAMMPS (24 Jan 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6063 3.6063 3.6063 Created orthogonal box = (0 -58.5991 0) to (11.9608 58.5991 8.8336) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.43671 5.32686 5.88907 Created 530 atoms create_atoms CPU = 0.00105906 secs 530 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.43671 5.32686 5.88907 Created 530 atoms create_atoms CPU = 0.00101805 secs 530 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 = 11.9775 ghost atom cutoff = 11.9775 binsize = 5.98874, bins = 2 20 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 11.9775 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 13 atoms, new total = 1047 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.9775 ghost atom cutoff = 11.9775 binsize = 5.98874, bins = 2 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.9775 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) = 7.273 | 7.273 | 7.273 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4333.8346 0 -4333.8346 5940.562 74 0 -4378.6804 0 -4378.6804 -8374.7729 Loop time of 3.00583 on 1 procs for 74 steps with 1047 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4333.8346146 -4378.6761031 -4378.68039105 Force two-norm initial, final = 51.7229 0.310713 Force max component initial, final = 11.8853 0.0571339 Final line search alpha, max atom move = 1 0.0571339 Iterations, force evaluations = 74 130 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9374 | 2.9374 | 2.9374 | 0.0 | 97.72 Neigh | 0.048168 | 0.048168 | 0.048168 | 0.0 | 1.60 Comm | 0.014811 | 0.014811 | 0.014811 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005436 | | | 0.18 Nlocal: 1047 ave 1047 max 1047 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13131 ave 13131 max 13131 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: 643976 ave 643976 max 643976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 643976 Ave neighs/atom = 615.068 Neighbor list builds = 2 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : metal Current step : 74 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.274 | 7.274 | 7.274 Mbytes Step Temp E_pair E_mol TotEng Press Volume 74 0 -4378.6804 0 -4378.6804 -8374.7729 12382.751 77 0 -4378.7913 0 -4378.7913 -2019.9229 12336.29 Loop time of 0.10909 on 1 procs for 3 steps with 1047 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4378.68039105 -4378.79117993 -4378.79133658 Force two-norm initial, final = 83.4749 0.343884 Force max component initial, final = 61.3869 0.0778076 Final line search alpha, max atom move = 0.000608483 4.73447e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10728 | 0.10728 | 0.10728 | 0.0 | 98.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052786 | 0.00052786 | 0.00052786 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001283 | | | 1.18 Nlocal: 1047 ave 1047 max 1047 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13243 ave 13243 max 13243 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: 642932 ave 642932 max 642932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 642932 Ave neighs/atom = 614.071 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 = 11.9775 ghost atom cutoff = 11.9775 binsize = 5.98874, bins = 2 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.9775 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) = 7.413 | 7.413 | 7.413 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4378.7913 0 -4378.7913 -2019.9229 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1047 atoms 209.7% 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: 1047 ave 1047 max 1047 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13448 ave 13448 max 13448 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: 644922 ave 644922 max 644922 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 644922 Ave neighs/atom = 615.971 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) = 7.413 | 7.413 | 7.413 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 -4378.7913 -4378.7913 11.937633 117.19818 8.8175009 -2019.9229 -2019.9229 3.3869663 -6057.5671 -5.588547 2.260734 443.80121 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1047 atoms 157.3% 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 | | 1.907e-06 | | |100.00 Nlocal: 1047 ave 1047 max 1047 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13448 ave 13448 max 13448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 322461 ave 322461 max 322461 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 644922 ave 644922 max 644922 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 644922 Ave neighs/atom = 615.971 Neighbor list builds = 0 Dangerous builds = 0 1047 -4378.79133657569 eV 2.26073404957957 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03