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 = 4.02485 4.02485 4.02485 Created orthogonal box = (0 -53.3996 0) to (32.698 53.3996 9.85882) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.94509 6.06768 6.57254 Created 1065 atoms create_atoms CPU = 0.000482082 secs 1065 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.94509 6.06768 6.57254 Created 1065 atoms create_atoms CPU = 0.000348091 secs 1065 atoms in group lower Displacing atoms ... 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 8 26 3 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 8.365 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 41 atoms, new total = 2089 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 8 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 5.626 | 5.626 | 5.626 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5478.2631 0 -5478.2631 519.17545 41 0 -5519.8074 0 -5519.8074 -6742.8046 Loop time of 0.440804 on 1 procs for 41 steps with 2089 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5478.2631286 -5519.80199292 -5519.8073956 Force two-norm initial, final = 27.9459 0.187854 Force max component initial, final = 3.24563 0.0511681 Final line search alpha, max atom move = 1 0.0511681 Iterations, force evaluations = 41 71 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.43388 | 0.43388 | 0.43388 | 0.0 | 98.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0034001 | 0.0034001 | 0.0034001 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003527 | | | 0.80 Nlocal: 2089 ave 2089 max 2089 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7870 ave 7870 max 7870 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: 290484 ave 290484 max 290484 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 290484 Ave neighs/atom = 139.054 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 : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.626 | 5.626 | 5.626 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -5519.8074 0 -5519.8074 -6742.8046 34428.195 45 0 -5520.1637 0 -5520.1637 -1961.7204 34217.679 Loop time of 0.0454719 on 1 procs for 4 steps with 2089 atoms 110.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5519.8073956 -5520.16238404 -5520.16368609 Force two-norm initial, final = 163.775 1.99704 Force max component initial, final = 118.771 1.74216 Final line search alpha, max atom move = 0.000116166 0.000202379 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.04402 | 0.04402 | 0.04402 | 0.0 | 96.81 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027561 | 0.00027561 | 0.00027561 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001176 | | | 2.59 Nlocal: 2089 ave 2089 max 2089 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7712 ave 7712 max 7712 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: 292516 ave 292516 max 292516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292516 Ave neighs/atom = 140.027 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 = 8.365 ghost atom cutoff = 8.365 binsize = 4.1825, bins = 8 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.365 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) = 5.763 | 5.763 | 5.763 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5520.1637 0 -5520.1637 -1961.7204 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2089 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: 2089 ave 2089 max 2089 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7739 ave 7739 max 7739 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: 292562 ave 292562 max 292562 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292562 Ave neighs/atom = 140.049 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) = 5.763 | 5.763 | 5.763 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 -5520.1637 -5520.1637 32.603585 106.79927 9.8269088 -1961.7204 -1961.7204 81.337586 -5922.1551 -44.343515 2.5120473 871.07966 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2089 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: 2089 ave 2089 max 2089 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7739 ave 7739 max 7739 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 146281 ave 146281 max 146281 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 292562 ave 292562 max 292562 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 292562 Ave neighs/atom = 140.049 Neighbor list builds = 0 Dangerous builds = 0 2089 -5455.95981046374 eV 2.51204731844553 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00