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 = 3.6584 3.6584 3.6584 Created orthogonal box = (0 -42.6676 0) to (15.084 42.6676 5.17377) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.21105 6.27411 5.17377 Created 274 atoms create_atoms CPU = 0.000217915 secs 274 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.21105 6.27411 5.17377 Created 274 atoms create_atoms CPU = 0.000144005 secs 274 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 542 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 5 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.523 | 4.523 | 4.523 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2088.4483 0 -2088.4483 6257.6121 341 0 -2122.7003 0 -2122.7003 -56031.942 Loop time of 1.18075 on 1 procs for 341 steps with 542 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2088.44833458 -2122.69828315 -2122.70033217 Force two-norm initial, final = 24.0436 0.147123 Force max component initial, final = 6.6743 0.0148515 Final line search alpha, max atom move = 1 0.0148515 Iterations, force evaluations = 341 671 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1385 | 1.1385 | 1.1385 | 0.0 | 96.43 Neigh | 0.01384 | 0.01384 | 0.01384 | 0.0 | 1.17 Comm | 0.018473 | 0.018473 | 0.018473 | 0.0 | 1.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009884 | | | 0.84 Nlocal: 542 ave 542 max 542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4442 ave 4442 max 4442 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: 74088 ave 74088 max 74088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74088 Ave neighs/atom = 136.694 Neighbor list builds = 7 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 : 341 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 341 0 -2122.7003 0 -2122.7003 -56031.942 6659.6504 401 0 -2130.2939 0 -2130.2939 -31876.91 6626.5955 Loop time of 0.10166 on 1 procs for 60 steps with 542 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 = -2122.70033217 -2130.29220808 -2130.29390508 Force two-norm initial, final = 317.682 2.23869 Force max component initial, final = 317.664 1.33039 Final line search alpha, max atom move = 0.000658363 0.000875879 Iterations, force evaluations = 60 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.095485 | 0.095485 | 0.095485 | 0.0 | 93.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0014625 | 0.0014625 | 0.0014625 | 0.0 | 1.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004712 | | | 4.64 Nlocal: 542 ave 542 max 542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4442 ave 4442 max 4442 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: 74108 ave 74108 max 74108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74108 Ave neighs/atom = 136.731 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 4 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.656 | 4.656 | 4.656 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2130.2939 0 -2130.2939 -31876.91 Loop time of 2.14577e-06 on 1 procs for 0 steps with 542 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: 542 ave 542 max 542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3945 ave 3945 max 3945 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: 74900 ave 74900 max 74900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74900 Ave neighs/atom = 138.192 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) = 4.656 | 4.656 | 4.656 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 -2130.2939 -2130.2939 14.389763 85.335247 5.3964525 -31876.91 -31876.91 171.62461 -95466.848 -335.50575 2.3872228 1052.1905 Loop time of 9.53674e-07 on 1 procs for 0 steps with 542 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: 542 ave 542 max 542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3945 ave 3945 max 3945 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37450 ave 37450 max 37450 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74900 ave 74900 max 74900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74900 Ave neighs/atom = 138.192 Neighbor list builds = 0 Dangerous builds = 0 542 -2130.29390507889 eV 2.3872228378226 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01