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 = 4.03208 4.03208 4.03208 Created orthogonal box = (0 -41.9067 0) to (29.6296 41.9067 5.70223) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.58436 5.43182 5.70223 Created 439 atoms create_atoms CPU = 0.000362873 secs 439 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.58436 5.43182 5.70223 Created 439 atoms create_atoms CPU = 0.00019908 secs 439 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 8 23 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 7.55805 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 15 atoms, new total = 863 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 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) = 4.958 | 4.958 | 4.958 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2847.2281 0 -2847.2281 15981.196 37 0 -2891.0524 0 -2891.0524 2545.4041 Loop time of 0.235422 on 1 procs for 37 steps with 863 atoms 101.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2847.22810701 -2891.05018166 -2891.05240555 Force two-norm initial, final = 44.6467 0.121338 Force max component initial, final = 6.5885 0.0146134 Final line search alpha, max atom move = 1 0.0146134 Iterations, force evaluations = 37 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23162 | 0.23162 | 0.23162 | 0.0 | 98.38 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0022426 | 0.0022426 | 0.0022426 | 0.0 | 0.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001562 | | | 0.66 Nlocal: 863 ave 863 max 863 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4881 ave 4881 max 4881 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: 113542 ave 113542 max 113542 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113542 Ave neighs/atom = 131.567 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 : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.958 | 4.958 | 4.958 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -2891.0524 0 -2891.0524 2545.4041 14160.671 40 0 -2891.1188 0 -2891.1188 -778.04409 14217.997 Loop time of 0.0131009 on 1 procs for 3 steps with 863 atoms 76.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2891.05240555 -2891.11802446 -2891.1188154 Force two-norm initial, final = 46.5094 1.17468 Force max component initial, final = 35.6185 1.09274 Final line search alpha, max atom move = 0.000222494 0.000243127 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.012623 | 0.012623 | 0.012623 | 0.0 | 96.35 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012255 | 0.00012255 | 0.00012255 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000355 | | | 2.71 Nlocal: 863 ave 863 max 863 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4878 ave 4878 max 4878 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: 110184 ave 110184 max 110184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 110184 Ave neighs/atom = 127.676 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 = 7.55805 ghost atom cutoff = 7.55805 binsize = 3.77903, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.55805 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) = 5.096 | 5.096 | 5.096 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2891.1188 0 -2891.1188 -778.04409 Loop time of 9.53674e-07 on 1 procs for 0 steps with 863 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: 863 ave 863 max 863 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4878 ave 4878 max 4878 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: 102772 ave 102772 max 102772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102772 Ave neighs/atom = 119.087 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) = 5.096 | 5.096 | 5.096 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 -2891.1188 -2891.1188 29.697958 83.81333 5.7121384 -778.04409 -778.04409 46.305332 -2257.0867 -123.35089 2.6487299 532.33774 Loop time of 2.14577e-06 on 1 procs for 0 steps with 863 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: 863 ave 863 max 863 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4878 ave 4878 max 4878 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 51386 ave 51386 max 51386 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 102772 ave 102772 max 102772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 102772 Ave neighs/atom = 119.087 Neighbor list builds = 0 Dangerous builds = 0 863 -2891.11881539984 eV 2.64872987388369 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00