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 = 3.63903 3.63903 3.63903 Created orthogonal box = (0 -42.4417 0) to (21.219 42.4417 3.63903) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.99271 4.99271 3.63903 Created 273 atoms create_atoms CPU = 0.000154972 secs 273 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.99271 4.99271 3.63903 Created 273 atoms create_atoms CPU = 7.58171e-05 secs 273 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 ghost atom cutoff = 8 binsize = 4, bins = 6 22 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 540 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 ghost atom cutoff = 8 binsize = 4, bins = 6 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.528 | 4.528 | 4.528 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1828.8295 0 -1828.8295 7955.9457 26 0 -1839.7232 0 -1839.7232 -5222.5895 Loop time of 0.0754559 on 1 procs for 26 steps with 540 atoms 92.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1828.82950925 -1839.72188964 -1839.72315029 Force two-norm initial, final = 35.0396 0.0910044 Force max component initial, final = 11.4556 0.0114468 Final line search alpha, max atom move = 1 0.0114468 Iterations, force evaluations = 26 41 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.071791 | 0.071791 | 0.071791 | 0.0 | 95.14 Neigh | 0.001806 | 0.001806 | 0.001806 | 0.0 | 2.39 Comm | 0.0011954 | 0.0011954 | 0.0011954 | 0.0 | 1.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006638 | | | 0.88 Nlocal: 540 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5620 ave 5620 max 5620 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: 94710 ave 94710 max 94710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94710 Ave neighs/atom = 175.389 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 : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.528 | 4.528 | 4.528 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -1839.7232 0 -1839.7232 -5222.5895 6554.4011 29 0 -1839.7575 0 -1839.7575 -753.5948 6534.0638 Loop time of 0.0109429 on 1 procs for 3 steps with 540 atoms 91.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1839.72315029 -1839.75735677 -1839.75750681 Force two-norm initial, final = 30.3249 0.10468 Force max component initial, final = 23.9602 0.0186639 Final line search alpha, max atom move = 0.00141235 2.636e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.010407 | 0.010407 | 0.010407 | 0.0 | 95.10 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00014782 | 0.00014782 | 0.00014782 | 0.0 | 1.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003879 | | | 3.54 Nlocal: 540 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5620 ave 5620 max 5620 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: 94746 ave 94746 max 94746 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94746 Ave neighs/atom = 175.456 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 ghost atom cutoff = 8 binsize = 4, bins = 6 22 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.666 | 4.666 | 4.666 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1839.7575 0 -1839.7575 -753.5948 Loop time of 0 on 1 procs for 0 steps with 540 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 | | 0 | | | 0.00 Nlocal: 540 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5620 ave 5620 max 5620 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: 94782 ave 94782 max 94782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94782 Ave neighs/atom = 175.522 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) = 4.666 | 4.666 | 4.666 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 -1839.7575 -1839.7575 21.176316 84.883311 3.6350521 -753.5948 -753.5948 0.87818853 -2257.6811 -3.9815105 2.2961428 270.73267 Loop time of 9.53674e-07 on 1 procs for 0 steps with 540 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: 540 ave 540 max 540 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5620 ave 5620 max 5620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47391 ave 47391 max 47391 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 94782 ave 94782 max 94782 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94782 Ave neighs/atom = 175.522 Neighbor list builds = 0 Dangerous builds = 0 540 -1839.75750680888 eV 2.2961428090966 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00