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 = 3.615 3.615 3.615 Created orthogonal box = (0 -39.1058 0) to (13.0341 39.1058 3.615) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0131 5.0131 3.615 Created 158 atoms create_atoms CPU = 0.000135899 secs 158 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0131 5.0131 3.615 Created 158 atoms create_atoms CPU = 4.69685e-05 secs 158 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 = 6.42745 ghost atom cutoff = 6.42745 binsize = 3.21373, bins = 5 25 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 6.42745 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 308 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 = 6.42745 ghost atom cutoff = 6.42745 binsize = 3.21373, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.42745 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) = 4.43 | 4.43 | 4.43 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1071.5221 0 -1071.5221 -2765.7715 55 0 -1078.7113 0 -1078.7113 -9229.5023 Loop time of 0.045588 on 1 procs for 55 steps with 308 atoms 109.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1071.52208076 -1078.71034461 -1078.71131947 Force two-norm initial, final = 6.86504 0.067577 Force max component initial, final = 1.79054 0.00893351 Final line search alpha, max atom move = 1 0.00893351 Iterations, force evaluations = 55 97 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.042965 | 0.042965 | 0.042965 | 0.0 | 94.25 Neigh | 0.00062013 | 0.00062013 | 0.00062013 | 0.0 | 1.36 Comm | 0.0013535 | 0.0013535 | 0.0013535 | 0.0 | 2.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006495 | | | 1.42 Nlocal: 308 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2838 ave 2838 max 2838 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: 26328 ave 26328 max 26328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26328 Ave neighs/atom = 85.4805 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 : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.43 | 4.43 | 4.43 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -1078.7113 0 -1078.7113 -9229.5023 3685.1892 60 0 -1078.7646 0 -1078.7646 -1606.7203 3665.5393 Loop time of 0.00596595 on 1 procs for 5 steps with 308 atoms 0.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1078.71131947 -1078.76456953 -1078.76457358 Force two-norm initial, final = 27.3796 0.084129 Force max component initial, final = 20.1588 0.021536 Final line search alpha, max atom move = 0.00495806 0.000106777 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0054281 | 0.0054281 | 0.0054281 | 0.0 | 90.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00012326 | 0.00012326 | 0.00012326 | 0.0 | 2.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004146 | | | 6.95 Nlocal: 308 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2866 ave 2866 max 2866 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: 26352 ave 26352 max 26352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26352 Ave neighs/atom = 85.5584 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 = 6.42745 ghost atom cutoff = 6.42745 binsize = 3.21373, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.42745 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) = 4.568 | 4.568 | 4.568 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1078.7646 0 -1078.7646 -1606.7203 Loop time of 9.53674e-07 on 1 procs for 0 steps with 308 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: 308 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2866 ave 2866 max 2866 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: 26360 ave 26360 max 26360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26360 Ave neighs/atom = 85.5844 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) = 4.568 | 4.568 | 4.568 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 -1078.7646 -1078.7646 13.016525 78.211645 3.6005712 -1606.7203 -1606.7203 6.6072782 -4836.1438 9.3756123 2.2496541 130.99404 Loop time of 9.53674e-07 on 1 procs for 0 steps with 308 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: 308 ave 308 max 308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2866 ave 2866 max 2866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13180 ave 13180 max 13180 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26360 ave 26360 max 26360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26360 Ave neighs/atom = 85.5844 Neighbor list builds = 0 Dangerous builds = 0 308 -1078.76457357537 eV 2.24965412961196 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00