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 = 2.85531 2.85531 2.85531 Created orthogonal box = (0 -37.8829 0) to (13.3926 37.8829 4.03802) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.87004 4.30455 4.03802 Created 178 atoms create_atoms CPU = 0.000247002 secs 178 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.87004 4.30455 4.03802 Created 178 atoms create_atoms CPU = 0.000119925 secs 178 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 4 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 348 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 4 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.453 | 4.453 | 4.453 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1383.2081 0 -1383.2081 1128.0347 16 0 -1388.9451 0 -1388.9451 -9081.2159 Loop time of 0.034734 on 1 procs for 16 steps with 348 atoms 86.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1383.20814846 -1388.94390107 -1388.94510277 Force two-norm initial, final = 10.83 0.100451 Force max component initial, final = 2.99981 0.01464 Final line search alpha, max atom move = 1 0.01464 Iterations, force evaluations = 16 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.033847 | 0.033847 | 0.033847 | 0.0 | 97.45 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005641 | 0.0005641 | 0.0005641 | 0.0 | 1.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003233 | | | 0.93 Nlocal: 348 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3436 ave 3436 max 3436 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: 46848 ave 46848 max 46848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46848 Ave neighs/atom = 134.621 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 : 16 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.453 | 4.453 | 4.453 Mbytes Step Temp E_pair E_mol TotEng Press Volume 16 0 -1388.9451 0 -1388.9451 -9081.2159 4097.3821 20 0 -1388.9936 0 -1388.9936 -1791.0517 4080.0637 Loop time of 0.00978589 on 1 procs for 4 steps with 348 atoms 102.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1388.94510277 -1388.99339217 -1388.9935826 Force two-norm initial, final = 30.7724 0.119822 Force max component initial, final = 25.4089 0.0226501 Final line search alpha, max atom move = 0.000743629 1.68432e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0091434 | 0.0091434 | 0.0091434 | 0.0 | 93.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00014305 | 0.00014305 | 0.00014305 | 0.0 | 1.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004995 | | | 5.10 Nlocal: 348 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3506 ave 3506 max 3506 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: 47160 ave 47160 max 47160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47160 Ave neighs/atom = 135.517 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 4 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 4.592 | 4.592 | 4.592 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1388.9936 0 -1388.9936 -1791.0517 Loop time of 1.90735e-06 on 1 procs for 0 steps with 348 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: 348 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3596 ave 3596 max 3596 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: 47256 ave 47256 max 47256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47256 Ave neighs/atom = 135.793 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) = 4.592 | 4.592 | 4.592 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 -1388.9936 -1388.9936 13.374776 75.76572 4.0263144 -1791.0517 -1791.0517 -4.8472081 -5369.9353 1.6274214 2.2720048 283.03158 Loop time of 1.19209e-06 on 1 procs for 0 steps with 348 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: 348 ave 348 max 348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3596 ave 3596 max 3596 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23628 ave 23628 max 23628 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 47256 ave 47256 max 47256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 47256 Ave neighs/atom = 135.793 Neighbor list builds = 0 Dangerous builds = 0 348 -1388.99358260066 eV 2.27200475307191 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00