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 = 3.52264 3.52264 3.52264 Created orthogonal box = (0 -37.4497 0) to (37.4462 37.4497 3.52264) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.97073 4.97073 3.52264 Created 453 atoms create_atoms CPU = 0.000283003 secs 453 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.97073 4.97073 3.52264 Created 453 atoms create_atoms CPU = 0.000141859 secs 453 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 = 11.7548 ghost atom cutoff = 11.7548 binsize = 5.87738, bins = 7 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 11.7548 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 901 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 = 11.7548 ghost atom cutoff = 11.7548 binsize = 5.87738, bins = 7 13 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7548 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) = 6.645 | 6.645 | 6.645 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3704.2438 0 -3704.2438 33438.387 229 0 -3815.9279 0 -3815.9279 -4306.475 Loop time of 5.73191 on 1 procs for 229 steps with 901 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3704.24382329 -3815.92473205 -3815.92787303 Force two-norm initial, final = 67.3757 0.232952 Force max component initial, final = 16.8117 0.0252304 Final line search alpha, max atom move = 1 0.0252304 Iterations, force evaluations = 229 399 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.6115 | 5.6115 | 5.6115 | 0.0 | 97.90 Neigh | 0.068672 | 0.068672 | 0.068672 | 0.0 | 1.20 Comm | 0.038754 | 0.038754 | 0.038754 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01297 | | | 0.23 Nlocal: 901 ave 901 max 901 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14523 ave 14523 max 14523 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: 562808 ave 562808 max 562808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 562808 Ave neighs/atom = 624.648 Neighbor list builds = 6 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 : 229 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.646 | 6.646 | 6.646 Mbytes Step Temp E_pair E_mol TotEng Press Volume 229 0 -3815.9279 0 -3815.9279 -4306.475 9879.9558 233 0 -3815.9751 0 -3815.9751 -1592.1623 9865.2807 Loop time of 0.0856459 on 1 procs for 4 steps with 901 atoms 93.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3815.92787303 -3815.9750647 -3815.97508594 Force two-norm initial, final = 44.3244 0.541647 Force max component initial, final = 43.0337 0.349813 Final line search alpha, max atom move = 0.00210294 0.000735635 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.084037 | 0.084037 | 0.084037 | 0.0 | 98.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045085 | 0.00045085 | 0.00045085 | 0.0 | 0.53 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001158 | | | 1.35 Nlocal: 901 ave 901 max 901 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14531 ave 14531 max 14531 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: 556594 ave 556594 max 556594 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556594 Ave neighs/atom = 617.751 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 = 11.7548 ghost atom cutoff = 11.7548 binsize = 5.87738, bins = 7 13 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.7548 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) = 6.784 | 6.784 | 6.784 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3815.9751 0 -3815.9751 -1592.1623 Loop time of 9.53674e-07 on 1 procs for 0 steps with 901 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: 901 ave 901 max 901 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14531 ave 14531 max 14531 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: 556738 ave 556738 max 556738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556738 Ave neighs/atom = 617.911 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) = 6.784 | 6.784 | 6.784 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 -3815.9751 -3815.9751 37.355177 74.899452 3.5259813 -1592.1623 -1592.1623 54.718764 -4888.0711 56.865413 2.3902107 51.90432 Loop time of 1.90735e-06 on 1 procs for 0 steps with 901 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: 901 ave 901 max 901 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14531 ave 14531 max 14531 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 278369 ave 278369 max 278369 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 556738 ave 556738 max 556738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556738 Ave neighs/atom = 617.911 Neighbor list builds = 0 Dangerous builds = 0 901 -3815.97508593966 eV 2.39021068171827 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05