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 = 4.0398 4.0398 4.0398 Created orthogonal box = (0 -43.7011 0) to (14.5657 43.7011 4.0398) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.60219 5.60219 4.0398 Created 158 atoms create_atoms CPU = 0.000222921 secs 158 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.60219 5.60219 4.0398 Created 158 atoms create_atoms CPU = 8.39233e-05 secs 158 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 3 15 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 11.7794 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 312 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 3 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 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) = 4.91 | 4.91 | 4.91 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -874.53198 0 -874.53198 13867.098 28 0 -895.09012 0 -895.09012 3198.3054 Loop time of 0.154331 on 1 procs for 28 steps with 312 atoms 103.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -874.531981902 -895.089300429 -895.090124029 Force two-norm initial, final = 27.2595 0.0837505 Force max component initial, final = 8.8148 0.0112759 Final line search alpha, max atom move = 1 0.0112759 Iterations, force evaluations = 28 48 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14932 | 0.14932 | 0.14932 | 0.0 | 96.75 Neigh | 0.0022058 | 0.0022058 | 0.0022058 | 0.0 | 1.43 Comm | 0.0021391 | 0.0021391 | 0.0021391 | 0.0 | 1.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006638 | | | 0.43 Nlocal: 312 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6947 ave 6947 max 6947 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: 128724 ave 128724 max 128724 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128724 Ave neighs/atom = 412.577 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 : 28 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.91 | 4.91 | 4.91 Mbytes Step Temp E_pair E_mol TotEng Press Volume 28 0 -895.09012 0 -895.09012 3198.3054 5142.9683 37 0 -895.1672 0 -895.1672 138.00093 5163.4004 Loop time of 0.0410421 on 1 procs for 9 steps with 312 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 = -895.090124029 -895.166805934 -895.167203166 Force two-norm initial, final = 16.9315 0.226827 Force max component initial, final = 16.8073 0.0396034 Final line search alpha, max atom move = 0.0011408 4.51794e-05 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.039303 | 0.039303 | 0.039303 | 0.0 | 95.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045848 | 0.00045848 | 0.00045848 | 0.0 | 1.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001281 | | | 3.12 Nlocal: 312 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6947 ave 6947 max 6947 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: 129068 ave 129068 max 129068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129068 Ave neighs/atom = 413.679 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 = 11.7794 ghost atom cutoff = 11.7794 binsize = 5.88971, bins = 3 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7794 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) = 5.047 | 5.047 | 5.047 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -895.1672 0 -895.1672 138.00093 Loop time of 1.19209e-06 on 1 procs for 0 steps with 312 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: 312 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6968 ave 6968 max 6968 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: 126196 ave 126196 max 126196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126196 Ave neighs/atom = 404.474 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) = 5.047 | 5.047 | 5.047 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 -895.1672 -895.1672 14.499226 87.402282 4.0744426 138.00093 138.00093 7.4798075 415.98609 -9.4631047 2.524594 158.35858 Loop time of 9.53674e-07 on 1 procs for 0 steps with 312 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: 312 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6968 ave 6968 max 6968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63098 ave 63098 max 63098 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 126196 ave 126196 max 126196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126196 Ave neighs/atom = 404.474 Neighbor list builds = 0 Dangerous builds = 0 312 -895.167203165568 eV 2.52459401371704 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00