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 = 3.14741 3.14741 3.14741 Created orthogonal box = (0 -41.7583 0) to (25.5697 41.7583 7.70956) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.64904 4.74491 5.13971 Created 533 atoms create_atoms CPU = 0.000324965 secs 533 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.64904 4.74491 5.13971 Created 533 atoms create_atoms CPU = 0.000187874 secs 533 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 = 8.1961 ghost atom cutoff = 8.1961 binsize = 4.09805, bins = 7 21 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 8.1961 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1050 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 = 8.1961 ghost atom cutoff = 8.1961 binsize = 4.09805, bins = 7 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.1961 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) = 5.036 | 5.036 | 5.036 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7169.7692 0 -7169.7692 12077.56 57 0 -7231.9877 0 -7231.9877 -3052.6471 Loop time of 0.289057 on 1 procs for 57 steps with 1050 atoms 100.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7169.76915815 -7231.98406707 -7231.9877208 Force two-norm initial, final = 49.242 0.158732 Force max component initial, final = 10.9892 0.0156699 Final line search alpha, max atom move = 1 0.0156699 Iterations, force evaluations = 57 87 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27169 | 0.27169 | 0.27169 | 0.0 | 93.99 Neigh | 0.012153 | 0.012153 | 0.012153 | 0.0 | 4.20 Comm | 0.0028276 | 0.0028276 | 0.0028276 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002386 | | | 0.83 Nlocal: 1050 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5154 ave 5154 max 5154 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: 166880 ave 166880 max 166880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 166880 Ave neighs/atom = 158.933 Neighbor list builds = 3 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 : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.036 | 5.036 | 5.036 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -7231.9877 0 -7231.9877 -3052.6471 16463.74 59 0 -7232.0315 0 -7232.0315 1893.5713 16439.514 Loop time of 0.0142829 on 1 procs for 2 steps with 1050 atoms 140.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7231.9877208 -7232.03137637 -7232.03146407 Force two-norm initial, final = 83.6638 0.18822 Force max component initial, final = 61.2451 0.0524489 Final line search alpha, max atom move = 0.000582785 3.05665e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.013784 | 0.013784 | 0.013784 | 0.0 | 96.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012231 | 0.00012231 | 0.00012231 | 0.0 | 0.86 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003765 | | | 2.64 Nlocal: 1050 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5142 ave 5142 max 5142 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: 171068 ave 171068 max 171068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171068 Ave neighs/atom = 162.922 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 = 8.1961 ghost atom cutoff = 8.1961 binsize = 4.09805, bins = 7 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.1961 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) = 5.173 | 5.173 | 5.173 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7232.0315 0 -7232.0315 1893.5713 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1050 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: 1050 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5142 ave 5142 max 5142 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: 171236 ave 171236 max 171236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171236 Ave neighs/atom = 163.082 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) = 5.173 | 5.173 | 5.173 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 -7232.0315 -7232.0315 25.55288 83.516639 7.7032876 1893.5713 1893.5713 -5.1082464 5689.444 -3.6219021 2.4222667 1038.2608 Loop time of 9.53674e-07 on 1 procs for 0 steps with 1050 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: 1050 ave 1050 max 1050 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5142 ave 5142 max 5142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 85618 ave 85618 max 85618 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 171236 ave 171236 max 171236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171236 Ave neighs/atom = 163.082 Neighbor list builds = 0 Dangerous builds = 0 1050 -7198.26149006629 eV 2.42226665911623 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00