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 = 3.52422 3.52422 3.52422 Created orthogonal box = (0 -49.8435 0) to (24.92 49.8435 3.52422) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9872 3.9872 3.52422 Created 402 atoms create_atoms CPU = 0.000236034 secs 402 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9872 3.9872 3.52422 Created 402 atoms create_atoms CPU = 0.000101089 secs 402 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 = 6.31717 ghost atom cutoff = 6.31717 binsize = 3.15858, bins = 8 32 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 6.31717 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 792 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 = 6.31717 ghost atom cutoff = 6.31717 binsize = 3.15858, bins = 8 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.31717 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) = 4.552 | 4.552 | 4.552 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3508.5557 0 -3508.5557 -739.89903 54 0 -3519.5327 0 -3519.5327 -6051.4859 Loop time of 0.158818 on 1 procs for 54 steps with 792 atoms 100.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3508.55573003 -3519.52979099 -3519.53268686 Force two-norm initial, final = 14.0709 0.168446 Force max component initial, final = 3.98912 0.0287156 Final line search alpha, max atom move = 1 0.0287156 Iterations, force evaluations = 54 97 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15138 | 0.15138 | 0.15138 | 0.0 | 95.32 Neigh | 0.002439 | 0.002439 | 0.002439 | 0.0 | 1.54 Comm | 0.0031366 | 0.0031366 | 0.0031366 | 0.0 | 1.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001864 | | | 1.17 Nlocal: 792 ave 792 max 792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5274 ave 5274 max 5274 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: 67904 ave 67904 max 67904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67904 Ave neighs/atom = 85.7374 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 : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.552 | 4.552 | 4.552 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -3519.5327 0 -3519.5327 -6051.4859 8754.8742 57 0 -3519.5924 0 -3519.5924 -107.30664 8727.4694 Loop time of 0.0107081 on 1 procs for 3 steps with 792 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 = -3519.53268686 -3519.59123173 -3519.59239725 Force two-norm initial, final = 51.2893 0.169873 Force max component initial, final = 40.0572 0.0159956 Final line search alpha, max atom move = 0.000336384 5.38067e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0099411 | 0.0099411 | 0.0099411 | 0.0 | 92.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00017905 | 0.00017905 | 0.00017905 | 0.0 | 1.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005879 | | | 5.49 Nlocal: 792 ave 792 max 792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5253 ave 5253 max 5253 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: 67864 ave 67864 max 67864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67864 Ave neighs/atom = 85.6869 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 = 6.31717 ghost atom cutoff = 6.31717 binsize = 3.15858, bins = 8 32 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.31717 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) = 4.689 | 4.689 | 4.689 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3519.5924 0 -3519.5924 -107.30664 Loop time of 9.53674e-07 on 1 procs for 0 steps with 792 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: 792 ave 792 max 792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5253 ave 5253 max 5253 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: 67864 ave 67864 max 67864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67864 Ave neighs/atom = 85.6869 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) = 4.689 | 4.689 | 4.689 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 -3519.5924 -3519.5924 24.898045 99.687056 3.516287 -107.30664 -107.30664 -1.5944772 -322.26477 1.9393368 2.2121058 288.59057 Loop time of 9.53674e-07 on 1 procs for 0 steps with 792 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: 792 ave 792 max 792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5253 ave 5253 max 5253 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33932 ave 33932 max 33932 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 67864 ave 67864 max 67864 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67864 Ave neighs/atom = 85.6869 Neighbor list builds = 0 Dangerous builds = 0 792 -3519.59239725319 eV 2.21210576325789 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00