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 = 3.51812 3.51812 3.51812 Created orthogonal box = (0 -57.1662 0) to (11.6683 57.1662 8.6176) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.30377 5.19661 5.74507 Created 530 atoms create_atoms CPU = 0.000282764 secs 530 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.30377 5.19661 5.74507 Created 530 atoms create_atoms CPU = 0.000172138 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1048 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.996 | 5.996 | 5.996 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4551.2937 0 -4551.2937 13238.514 47 0 -4580.3491 0 -4580.3491 -5488.6794 Loop time of 0.82124 on 1 procs for 47 steps with 1048 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 = -4551.29366454 -4580.34521005 -4580.34907015 Force two-norm initial, final = 84.8388 0.190872 Force max component initial, final = 27.6093 0.0287421 Final line search alpha, max atom move = 1 0.0287421 Iterations, force evaluations = 47 86 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.81218 | 0.81218 | 0.81218 | 0.0 | 98.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0062084 | 0.0062084 | 0.0062084 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002856 | | | 0.35 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9415 ave 9415 max 9415 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: 334564 ave 334564 max 334564 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 334564 Ave neighs/atom = 319.24 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 : 47 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.996 | 5.996 | 5.996 Mbytes Step Temp E_pair E_mol TotEng Press Volume 47 0 -4580.3491 0 -4580.3491 -5488.6794 11496.43 49 0 -4580.3865 0 -4580.3865 -1586.0845 11470.624 Loop time of 0.0406461 on 1 procs for 2 steps with 1048 atoms 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4580.34907015 -4580.38558287 -4580.3864754 Force two-norm initial, final = 46.9632 0.265628 Force max component initial, final = 34.9087 0.133637 Final line search alpha, max atom move = 0.000190878 2.55083e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.039639 | 0.039639 | 0.039639 | 0.0 | 97.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025058 | 0.00025058 | 0.00025058 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007567 | | | 1.86 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9409 ave 9409 max 9409 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: 337704 ave 337704 max 337704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 337704 Ave neighs/atom = 322.237 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 3 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.134 | 6.134 | 6.134 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4580.3865 0 -4580.3865 -1586.0845 Loop time of 1.90735e-06 on 1 procs for 0 steps with 1048 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 | | 1.907e-06 | | |100.00 Nlocal: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9415 ave 9415 max 9415 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: 338192 ave 338192 max 338192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338192 Ave neighs/atom = 322.702 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) = 6.134 | 6.134 | 6.134 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 -4580.3865 -4580.3865 11.655808 114.33244 8.6074629 -1586.0845 -1586.0845 -18.645929 -4754.6934 15.08601 2.1751749 401.69249 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1048 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: 1048 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9415 ave 9415 max 9415 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 169096 ave 169096 max 169096 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 338192 ave 338192 max 338192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 338192 Ave neighs/atom = 322.702 Neighbor list builds = 0 Dangerous builds = 0 1048 -4580.38647539896 eV 2.17517487143779 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01