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 = 3.58787 3.58787 3.58787 Created orthogonal box = (0 -56.5054 0) to (34.6002 56.5054 8.78845) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.58067 5.46792 5.85897 Created 1494 atoms create_atoms CPU = 0.000686884 secs 1494 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.58067 5.46792 5.85897 Created 1494 atoms create_atoms CPU = 0.000547171 secs 1494 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 = 8.23106 ghost atom cutoff = 8.23106 binsize = 4.11553, bins = 9 28 3 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 8.23106 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 36 atoms, new total = 2952 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 = 8.23106 ghost atom cutoff = 8.23106 binsize = 4.11553, bins = 9 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.23106 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) = 7.039 | 7.039 | 7.039 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10326.366 0 -10326.366 2982.073 22 0 -10367.559 0 -10367.559 -6197.0863 Loop time of 1.3838 on 1 procs for 22 steps with 2952 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10326.3656112 -10367.5486834 -10367.5588224 Force two-norm initial, final = 55.3432 0.268429 Force max component initial, final = 10.9921 0.0216092 Final line search alpha, max atom move = 1 0.0216092 Iterations, force evaluations = 22 39 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3783 | 1.3783 | 1.3783 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0028868 | 0.0028868 | 0.0028868 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002571 | | | 0.19 Nlocal: 2952 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11610 ave 11610 max 11610 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: 586152 ave 586152 max 586152 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 586152 Ave neighs/atom = 198.561 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 : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.039 | 7.039 | 7.039 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -10367.559 0 -10367.559 -6197.0863 34364.592 25 0 -10367.746 0 -10367.746 -1774.7112 34256.603 Loop time of 0.210729 on 1 procs for 3 steps with 2952 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10367.5588224 -10367.7421372 -10367.7455801 Force two-norm initial, final = 155.282 0.605382 Force max component initial, final = 130.433 0.387846 Final line search alpha, max atom move = 9.70801e-05 3.76522e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20904 | 0.20904 | 0.20904 | 0.0 | 99.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033879 | 0.00033879 | 0.00033879 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001347 | | | 0.64 Nlocal: 2952 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11610 ave 11610 max 11610 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: 587808 ave 587808 max 587808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 587808 Ave neighs/atom = 199.122 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 = 8.23106 ghost atom cutoff = 8.23106 binsize = 4.11553, bins = 9 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.23106 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) = 7.177 | 7.177 | 7.177 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10367.746 0 -10367.746 -1774.7112 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2952 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: 2952 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11610 ave 11610 max 11610 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: 587952 ave 587952 max 587952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 587952 Ave neighs/atom = 199.171 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) = 7.177 | 7.177 | 7.177 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 -10367.746 -10367.746 34.572599 113.01089 8.7678268 -1774.7112 -1774.7112 18.125062 -5359.4376 17.178871 2.3056719 951.25882 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2952 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: 2952 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11610 ave 11610 max 11610 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 293976 ave 293976 max 293976 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 587952 ave 587952 max 587952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 587952 Ave neighs/atom = 199.171 Neighbor list builds = 0 Dangerous builds = 0 2952 -10367.7455801409 eV 2.30567188162806 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01