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 = 3.61315 3.61315 3.61315 Created orthogonal box = (0 -47.2517 0) to (22.2729 47.2517 5.10976) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.68904 5.80239 5.10976 Created 462 atoms create_atoms CPU = 0.000398874 secs 462 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.68904 5.80239 5.10976 Created 462 atoms create_atoms CPU = 0.00027585 secs 462 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 = 10.4596 ghost atom cutoff = 10.4596 binsize = 5.22982, bins = 5 19 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 10.4596 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 912 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 = 10.4596 ghost atom cutoff = 10.4596 binsize = 5.22982, bins = 5 19 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.4596 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) = 5.862 | 5.862 | 5.862 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3102.6692 0 -3102.6692 21786.566 22 0 -3165.9478 0 -3165.9478 5326.4231 Loop time of 0.271679 on 1 procs for 22 steps with 912 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3102.66918618 -3165.94468337 -3165.94780355 Force two-norm initial, final = 74.5445 0.204604 Force max component initial, final = 13.9192 0.0184719 Final line search alpha, max atom move = 1 0.0184719 Iterations, force evaluations = 22 40 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26858 | 0.26858 | 0.26858 | 0.0 | 98.86 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021107 | 0.0021107 | 0.0021107 | 0.0 | 0.78 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009928 | | | 0.37 Nlocal: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9838 ave 9838 max 9838 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: 348984 ave 348984 max 348984 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 348984 Ave neighs/atom = 382.658 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 : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.862 | 5.862 | 5.862 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -3165.9478 0 -3165.9478 5326.4231 10755.37 24 0 -3165.9579 0 -3165.9579 3950.8129 10765.966 Loop time of 0.041039 on 1 procs for 2 steps with 912 atoms 97.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3165.94780355 -3165.95713085 -3165.95793133 Force two-norm initial, final = 20.4982 0.54007 Force max component initial, final = 19.1083 0.474705 Final line search alpha, max atom move = 0.000340365 0.000161573 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.039982 | 0.039982 | 0.039982 | 0.0 | 97.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002923 | 0.0002923 | 0.0002923 | 0.0 | 0.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007646 | | | 1.86 Nlocal: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9838 ave 9838 max 9838 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: 349244 ave 349244 max 349244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 349244 Ave neighs/atom = 382.943 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 = 10.4596 ghost atom cutoff = 10.4596 binsize = 5.22982, bins = 5 19 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.4596 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 | 6 | 6 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3165.9579 0 -3165.9579 3950.8129 Loop time of 9.53674e-07 on 1 procs for 0 steps with 912 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: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9838 ave 9838 max 9838 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: 349088 ave 349088 max 349088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 349088 Ave neighs/atom = 382.772 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 | 6 | 6 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 -3165.9579 -3165.9579 22.269737 94.503312 5.1155331 3950.8129 3950.8129 70.634764 11802.655 -20.851516 2.2840263 532.00491 Loop time of 9.53674e-07 on 1 procs for 0 steps with 912 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: 912 ave 912 max 912 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9838 ave 9838 max 9838 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 174544 ave 174544 max 174544 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 349088 ave 349088 max 349088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 349088 Ave neighs/atom = 382.772 Neighbor list builds = 0 Dangerous builds = 0 912 -3165.95793132974 eV 2.28402626004413 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00