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 = 3.99461 3.99461 3.99461 Created orthogonal box = (0 -47.2688 0) to (57.8874 47.2688 9.78475) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6157 6.07691 6.52317 Created 1684 atoms create_atoms CPU = 0.000555992 secs 1684 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6157 6.07691 6.52317 Created 1684 atoms create_atoms CPU = 0.000439167 secs 1684 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 = 7.6001 ghost atom cutoff = 7.6001 binsize = 3.80005, bins = 16 25 3 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 7.6001 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 56 atoms, new total = 3312 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 = 7.6001 ghost atom cutoff = 7.6001 binsize = 3.80005, bins = 16 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6001 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) = 6.505 | 6.505 | 6.505 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10802.292 0 -10802.292 1278.7001 62 0 -10851.827 0 -10851.827 -4624.0328 Loop time of 2.52282 on 1 procs for 62 steps with 3312 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 = -10802.2919833 -10851.8185946 -10851.8268293 Force two-norm initial, final = 23.9412 0.190041 Force max component initial, final = 2.49152 0.019029 Final line search alpha, max atom move = 1 0.019029 Iterations, force evaluations = 62 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4854 | 2.4854 | 2.4854 | 0.0 | 98.51 Neigh | 0.022664 | 0.022664 | 0.022664 | 0.0 | 0.90 Comm | 0.0069082 | 0.0069082 | 0.0069082 | 0.0 | 0.27 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007896 | | | 0.31 Nlocal: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9184 ave 9184 max 9184 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: 429590 ave 429590 max 429590 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 429590 Ave neighs/atom = 129.707 Neighbor list builds = 2 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 : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.505 | 6.505 | 6.505 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -10851.827 0 -10851.827 -4624.0328 53547.426 67 0 -10852.285 0 -10852.285 -1652.8238 53150.875 Loop time of 0.115687 on 1 procs for 5 steps with 3312 atoms 95.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10851.8268293 -10852.2850932 -10852.2851064 Force two-norm initial, final = 173.401 0.254213 Force max component initial, final = 132.457 0.0611617 Final line search alpha, max atom move = 0.00194112 0.000118722 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11391 | 0.11391 | 0.11391 | 0.0 | 98.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035238 | 0.00035238 | 0.00035238 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001426 | | | 1.23 Nlocal: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9183 ave 9183 max 9183 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: 430890 ave 430890 max 430890 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 430890 Ave neighs/atom = 130.1 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 = 7.6001 ghost atom cutoff = 7.6001 binsize = 3.80005, bins = 16 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6001 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) = 6.642 | 6.642 | 6.642 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10852.285 0 -10852.285 -1652.8238 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3312 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: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9199 ave 9199 max 9199 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: 431894 ave 431894 max 431894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 431894 Ave neighs/atom = 130.403 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) = 6.642 | 6.642 | 6.642 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 -10852.285 -10852.285 57.657114 94.537676 9.7510774 -1652.8238 -1652.8238 -1.7498738 -4958.5587 1.8373098 2.6301164 2026.6717 Loop time of 1.19209e-06 on 1 procs for 0 steps with 3312 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: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9199 ave 9199 max 9199 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 215947 ave 215947 max 215947 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 431894 ave 431894 max 431894 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 431894 Ave neighs/atom = 130.403 Neighbor list builds = 0 Dangerous builds = 0 3312 -10852.2851063651 eV 2.63011642700235 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02