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 = 3.61496 3.61496 3.61496 Created orthogonal box = (0 -58.2931 0) to (29.1447 58.2931 3.61496) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.93219 4.93219 3.61496 Created 521 atoms create_atoms CPU = 0.000285149 secs 521 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.93219 4.93219 3.61496 Created 521 atoms create_atoms CPU = 0.00016284 secs 521 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 = 8.39534 ghost atom cutoff = 8.39534 binsize = 4.19767, bins = 7 28 1 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 8.39534 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 1032 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 = 8.39534 ghost atom cutoff = 8.39534 binsize = 4.19767, bins = 7 28 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.39534 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) = 5.447 | 5.447 | 5.447 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3628.7883 0 -3628.7883 2108.1269 24 0 -3642.7421 0 -3642.7421 -2403.3879 Loop time of 0.192356 on 1 procs for 24 steps with 1032 atoms 104.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3628.78825397 -3642.73884776 -3642.74210607 Force two-norm initial, final = 28.8186 0.174158 Force max component initial, final = 9.21199 0.0297336 Final line search alpha, max atom move = 1 0.0297336 Iterations, force evaluations = 24 41 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.18475 | 0.18475 | 0.18475 | 0.0 | 96.05 Neigh | 0.0038271 | 0.0038271 | 0.0038271 | 0.0 | 1.99 Comm | 0.0026157 | 0.0026157 | 0.0026157 | 0.0 | 1.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001161 | | | 0.60 Nlocal: 1032 ave 1032 max 1032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10110 ave 10110 max 10110 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: 205832 ave 205832 max 205832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205832 Ave neighs/atom = 199.45 Neighbor list builds = 1 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 : 24 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.447 | 5.447 | 5.447 Mbytes Step Temp E_pair E_mol TotEng Press Volume 24 0 -3642.7421 0 -3642.7421 -2403.3879 12283.18 26 0 -3642.765 0 -3642.765 310.65844 12259.111 Loop time of 0.0224199 on 1 procs for 2 steps with 1032 atoms 89.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3642.74210607 -3642.76345876 -3642.76503978 Force two-norm initial, final = 31.7243 0.318612 Force max component initial, final = 24.1167 0.197471 Final line search alpha, max atom move = 0.000328354 6.48405e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.021538 | 0.021538 | 0.021538 | 0.0 | 96.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002346 | 0.0002346 | 0.0002346 | 0.0 | 1.05 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006473 | | | 2.89 Nlocal: 1032 ave 1032 max 1032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10098 ave 10098 max 10098 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: 205818 ave 205818 max 205818 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205818 Ave neighs/atom = 199.436 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 = 8.39534 ghost atom cutoff = 8.39534 binsize = 4.19767, bins = 7 28 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.39534 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) = 5.585 | 5.585 | 5.585 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3642.765 0 -3642.765 310.65844 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1032 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: 1032 ave 1032 max 1032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10098 ave 10098 max 10098 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: 205830 ave 205830 max 205830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205830 Ave neighs/atom = 199.448 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) = 5.585 | 5.585 | 5.585 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 -3642.765 -3642.765 29.134678 116.58619 3.6091226 310.65844 310.65844 25.799142 883.20126 22.974919 2.3063225 399.62308 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1032 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: 1032 ave 1032 max 1032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10098 ave 10098 max 10098 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 102915 ave 102915 max 102915 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 205830 ave 205830 max 205830 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 205830 Ave neighs/atom = 199.448 Neighbor list builds = 0 Dangerous builds = 0 1032 -3642.76503977958 eV 2.30632245138682 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00