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 = 2.86385 2.86385 2.86385 Created orthogonal box = (0 -46.5349 0) to (9.49831 46.5349 7.01497) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.31741 4.23018 4.67665 Created 266 atoms create_atoms CPU = 0.00026083 secs 266 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.31741 4.23018 4.67665 Created 266 atoms create_atoms CPU = 0.000119925 secs 266 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 = 11.9775 ghost atom cutoff = 11.9775 binsize = 5.98874, bins = 2 16 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 11.9775 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 522 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 = 11.9775 ghost atom cutoff = 11.9775 binsize = 5.98874, bins = 2 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.9775 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) = 5.883 | 5.883 | 5.883 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2126.3807 0 -2126.3807 8378.5205 116 0 -2169.5129 0 -2169.5129 -12591.673 Loop time of 1.8154 on 1 procs for 116 steps with 522 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2126.38074344 -2169.5107556 -2169.51287535 Force two-norm initial, final = 97.1853 0.204501 Force max component initial, final = 47.4423 0.0313463 Final line search alpha, max atom move = 1 0.0313463 Iterations, force evaluations = 116 223 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7806 | 1.7806 | 1.7806 | 0.0 | 98.08 Neigh | 0.015958 | 0.015958 | 0.015958 | 0.0 | 0.88 Comm | 0.014403 | 0.014403 | 0.014403 | 0.0 | 0.79 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004461 | | | 0.25 Nlocal: 522 ave 522 max 522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9781 ave 9781 max 9781 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: 314108 ave 314108 max 314108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 314108 Ave neighs/atom = 601.739 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 : 116 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.883 | 5.883 | 5.883 Mbytes Step Temp E_pair E_mol TotEng Press Volume 116 0 -2169.5129 0 -2169.5129 -12591.673 6201.272 124 0 -2169.8682 0 -2169.8682 776.45019 6151.5837 Loop time of 0.060931 on 1 procs for 8 steps with 522 atoms 114.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2169.51287535 -2169.8675509 -2169.86823898 Force two-norm initial, final = 101.649 0.451839 Force max component initial, final = 94.9574 0.0847325 Final line search alpha, max atom move = 0.000244176 2.06896e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.059326 | 0.059326 | 0.059326 | 0.0 | 97.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004642 | 0.0004642 | 0.0004642 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001141 | | | 1.87 Nlocal: 522 ave 522 max 522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9802 ave 9802 max 9802 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: 314180 ave 314180 max 314180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 314180 Ave neighs/atom = 601.877 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 = 11.9775 ghost atom cutoff = 11.9775 binsize = 5.98874, bins = 2 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.9775 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) = 6.021 | 6.021 | 6.021 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2169.8682 0 -2169.8682 776.45019 Loop time of 9.53674e-07 on 1 procs for 0 steps with 522 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: 522 ave 522 max 522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9810 ave 9810 max 9810 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: 315412 ave 315412 max 315412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 315412 Ave neighs/atom = 604.238 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) = 6.021 | 6.021 | 6.021 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 -2169.8682 -2169.8682 9.4889362 93.069789 6.9656345 776.45019 776.45019 -17.528321 2368.7922 -21.91333 2.3378908 626.87966 Loop time of 1.90735e-06 on 1 procs for 0 steps with 522 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: 522 ave 522 max 522 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9810 ave 9810 max 9810 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 157706 ave 157706 max 157706 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 315412 ave 315412 max 315412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 315412 Ave neighs/atom = 604.238 Neighbor list builds = 0 Dangerous builds = 0 522 -2169.86823897961 eV 2.33789077043235 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01