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 = 4.03299 4.03299 4.03299 Created orthogonal box = (0 -43.4406 0) to (21.7183 43.4406 4.03299) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.24235 5.24235 4.03299 Created 233 atoms create_atoms CPU = 0.000169039 secs 233 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.24235 5.24235 4.03299 Created 233 atoms create_atoms CPU = 5.10216e-05 secs 233 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 4 13 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 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 460 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 4 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 5.75 | 5.75 | 5.75 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1308.5153 0 -1308.5153 7960.5244 76 0 -1333.0297 0 -1333.0297 -2048.5386 Loop time of 1.18863 on 1 procs for 76 steps with 460 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1308.51534645 -1333.02861329 -1333.02970957 Force two-norm initial, final = 30.464 0.104246 Force max component initial, final = 8.80894 0.0233481 Final line search alpha, max atom move = 1 0.0233481 Iterations, force evaluations = 76 141 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.17 | 1.17 | 1.17 | 0.0 | 98.44 Neigh | 0.006402 | 0.006402 | 0.006402 | 0.0 | 0.54 Comm | 0.0095823 | 0.0095823 | 0.0095823 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002617 | | | 0.22 Nlocal: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9875 ave 9875 max 9875 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: 305678 ave 305678 max 305678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 305678 Ave neighs/atom = 664.517 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 : 76 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.75 | 5.75 | 5.75 Mbytes Step Temp E_pair E_mol TotEng Press Volume 76 0 -1333.0297 0 -1333.0297 -2048.5386 7609.9055 83 0 -1333.0865 0 -1333.0865 -231.65557 7590.7888 Loop time of 0.0800641 on 1 procs for 7 steps with 460 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 = -1333.02970957 -1333.08629563 -1333.08645909 Force two-norm initial, final = 21.6537 0.700435 Force max component initial, final = 21.3003 0.649964 Final line search alpha, max atom move = 0.000747196 0.00048565 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.07824 | 0.07824 | 0.07824 | 0.0 | 97.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049567 | 0.00049567 | 0.00049567 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001328 | | | 1.66 Nlocal: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9888 ave 9888 max 9888 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: 306036 ave 306036 max 306036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306036 Ave neighs/atom = 665.296 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 4 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 5.888 | 5.888 | 5.888 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1333.0865 0 -1333.0865 -231.65557 Loop time of 9.53674e-07 on 1 procs for 0 steps with 460 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: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9888 ave 9888 max 9888 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: 306212 ave 306212 max 306212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306212 Ave neighs/atom = 665.678 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) = 5.888 | 5.888 | 5.888 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 -1333.0865 -1333.0865 21.596548 86.881297 4.0455378 -231.65557 -231.65557 -136.41773 -592.32637 33.777372 2.55385 336.94723 Loop time of 2.14577e-06 on 1 procs for 0 steps with 460 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 | | 2.146e-06 | | |100.00 Nlocal: 460 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9888 ave 9888 max 9888 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 153106 ave 153106 max 153106 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 306212 ave 306212 max 306212 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 306212 Ave neighs/atom = 665.678 Neighbor list builds = 0 Dangerous builds = 0 460 -1333.08645908624 eV 2.55385004807998 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01