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 = 3.49194 3.49194 3.49194 Created orthogonal box = (0 -45.7998 0) to (32.3829 45.7998 4.93835) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.02473 5.85767 4.93835 Created 692 atoms create_atoms CPU = 0.000586987 secs 692 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.02473 5.85767 4.93835 Created 692 atoms create_atoms CPU = 0.000449896 secs 692 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 = 6.85342 ghost atom cutoff = 6.85342 binsize = 3.42671, bins = 10 27 2 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 6.85342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1368 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 = 6.85342 ghost atom cutoff = 6.85342 binsize = 3.42671, bins = 10 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85342 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) = 5.085 | 5.085 | 5.085 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5971.3725 0 -5971.3725 24014.096 64 0 -6056.1442 0 -6056.1442 -3270.5828 Loop time of 0.984239 on 1 procs for 64 steps with 1368 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5971.37249405 -6056.13818359 -6056.14415938 Force two-norm initial, final = 111.009 0.318785 Force max component initial, final = 21.1084 0.0506778 Final line search alpha, max atom move = 1 0.0506778 Iterations, force evaluations = 64 107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.96588 | 0.96588 | 0.96588 | 0.0 | 98.13 Neigh | 0.0091801 | 0.0091801 | 0.0091801 | 0.0 | 0.93 Comm | 0.0054078 | 0.0054078 | 0.0054078 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003774 | | | 0.38 Nlocal: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7536 ave 7536 max 7536 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: 182062 ave 182062 max 182062 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182062 Ave neighs/atom = 133.086 Neighbor list builds = 2 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 : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.085 | 5.085 | 5.085 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -6056.1442 0 -6056.1442 -3270.5828 14648.439 66 0 -6056.1539 0 -6056.1539 -3150.92 14647.42 Loop time of 0.0528898 on 1 procs for 2 steps with 1368 atoms 94.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6056.14415938 -6056.15390925 -6056.15391708 Force two-norm initial, final = 21.8295 0.353138 Force max component initial, final = 15.9296 0.12564 Final line search alpha, max atom move = 0.00216203 0.000271637 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.051935 | 0.051935 | 0.051935 | 0.0 | 98.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022411 | 0.00022411 | 0.00022411 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000731 | | | 1.38 Nlocal: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7528 ave 7528 max 7528 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: 182000 ave 182000 max 182000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 182000 Ave neighs/atom = 133.041 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 = 6.85342 ghost atom cutoff = 6.85342 binsize = 3.42671, bins = 10 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.85342 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) = 5.223 | 5.223 | 5.223 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6056.1539 0 -6056.1539 -3150.92 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1368 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: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7528 ave 7528 max 7528 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: 181996 ave 181996 max 181996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181996 Ave neighs/atom = 133.038 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) = 5.223 | 5.223 | 5.223 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 -6056.1539 -6056.1539 32.402472 91.599674 4.9350216 -3150.92 -3150.92 13.75113 -9476.348 9.836885 2.3116857 930.35024 Loop time of 1.19209e-06 on 1 procs for 0 steps with 1368 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: 1368 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7528 ave 7528 max 7528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90998 ave 90998 max 90998 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 181996 ave 181996 max 181996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 181996 Ave neighs/atom = 133.038 Neighbor list builds = 0 Dangerous builds = 0 1368 -6056.15391708245 eV 2.31168573235938 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01