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 = 2.8602 2.8602 2.8602 Created orthogonal box = (0 -41.6479 0) to (20.8225 41.6479 2.8602) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.5359 3.5359 2.8602 Created 213 atoms create_atoms CPU = 0.00014782 secs 213 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.5359 3.5359 2.8602 Created 213 atoms create_atoms CPU = 4.41074e-05 secs 213 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 32 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 4 atoms, new total = 422 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 4.817 | 4.817 | 4.817 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1764.3279 0 -1764.3279 15932.21 76 0 -1797.2912 0 -1797.2912 -344.14035 Loop time of 1.87588 on 1 procs for 76 steps with 422 atoms 100.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1764.32786454 -1797.28988071 -1797.29120164 Force two-norm initial, final = 69.3141 0.130072 Force max component initial, final = 20.9176 0.0285183 Final line search alpha, max atom move = 1 0.0285183 Iterations, force evaluations = 76 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8712 | 1.8712 | 1.8712 | 0.0 | 99.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.002867 | 0.002867 | 0.002867 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001842 | | | 0.10 Nlocal: 422 ave 422 max 422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2803 ave 2803 max 2803 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: 24242 ave 24242 max 24242 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24242 Ave neighs/atom = 57.4455 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 : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.818 | 4.818 | 4.818 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -1797.2912 0 -1797.2912 -344.14035 4960.8126 80 0 -1797.3143 0 -1797.3143 3827.491 4948.5044 Loop time of 0.067102 on 1 procs for 4 steps with 422 atoms 104.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1797.29120164 -1797.31431425 -1797.31434827 Force two-norm initial, final = 20.3278 0.149393 Force max component initial, final = 17.7942 0.0339277 Final line search alpha, max atom move = 0.00106373 3.609e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.06671 | 0.06671 | 0.06671 | 0.0 | 99.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 9.799e-05 | 9.799e-05 | 9.799e-05 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0002942 | | | 0.44 Nlocal: 422 ave 422 max 422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2819 ave 2819 max 2819 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: 24248 ave 24248 max 24248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24248 Ave neighs/atom = 57.4597 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 8 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 4.955 | 4.955 | 4.955 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1797.3143 0 -1797.3143 3827.491 Loop time of 9.53674e-07 on 1 procs for 0 steps with 422 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: 422 ave 422 max 422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2819 ave 2819 max 2819 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: 24248 ave 24248 max 24248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24248 Ave neighs/atom = 57.4597 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) = 4.955 | 4.955 | 4.955 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 -1797.3143 -1797.3143 20.827952 83.295869 2.8523574 3827.491 3827.491 -0.54355044 11475.304 7.7121599 2.3136017 233.41954 Loop time of 9.53674e-07 on 1 procs for 0 steps with 422 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: 422 ave 422 max 422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2819 ave 2819 max 2819 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 12124 ave 12124 max 12124 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 24248 ave 24248 max 24248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 24248 Ave neighs/atom = 57.4597 Neighbor list builds = 0 Dangerous builds = 0 422 -1797.31434827302 eV 2.31360171497674 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02