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 -52.6522 0) to (26.3247 52.6522 2.85531) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.02613 4.02613 2.85531 Created 341 atoms create_atoms CPU = 0.000242949 secs 341 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.02613 4.02613 2.85531 Created 341 atoms create_atoms CPU = 0.00012207 secs 341 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 = 8 29 1 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 4 atoms, new total = 678 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 = 8 29 1 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) = 4.551 | 4.551 | 4.551 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2656.1616 0 -2656.1616 27591.43 29 0 -2713.7025 0 -2713.7025 -2717.3292 Loop time of 0.126933 on 1 procs for 29 steps with 678 atoms 102.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2656.16156748 -2713.70068701 -2713.70254573 Force two-norm initial, final = 167.225 0.13039 Force max component initial, final = 62.5005 0.0352346 Final line search alpha, max atom move = 1 0.0352346 Iterations, force evaluations = 29 48 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1238 | 0.1238 | 0.1238 | 0.0 | 97.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0021112 | 0.0021112 | 0.0021112 | 0.0 | 1.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001027 | | | 0.81 Nlocal: 678 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6510 ave 6510 max 6510 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: 92118 ave 92118 max 92118 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92118 Ave neighs/atom = 135.867 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 : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.551 | 4.551 | 4.551 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -2713.7025 0 -2713.7025 -2717.3292 7915.23 31 0 -2713.7121 0 -2713.7121 -530.48726 7905.2322 Loop time of 0.00911498 on 1 procs for 2 steps with 678 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 = -2713.70254573 -2713.71053268 -2713.71206775 Force two-norm initial, final = 17.2829 0.136979 Force max component initial, final = 14.9329 0.0371329 Final line search alpha, max atom move = 0.000300033 1.11411e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0085659 | 0.0085659 | 0.0085659 | 0.0 | 93.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015593 | 0.00015593 | 0.00015593 | 0.0 | 1.71 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003932 | | | 4.31 Nlocal: 678 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6507 ave 6507 max 6507 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: 92972 ave 92972 max 92972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92972 Ave neighs/atom = 137.127 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 = 8 29 1 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) = 4.689 | 4.689 | 4.689 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2713.7121 0 -2713.7121 -530.48726 Loop time of 1.19209e-06 on 1 procs for 0 steps with 678 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: 678 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6510 ave 6510 max 6510 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: 93010 ave 93010 max 93010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93010 Ave neighs/atom = 137.183 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 -2713.7121 -2713.7121 26.325414 105.30444 2.851627 -530.48726 -530.48726 -4.6763262 -1584.7495 -2.0359775 2.2604448 111.473 Loop time of 9.53674e-07 on 1 procs for 0 steps with 678 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: 678 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6510 ave 6510 max 6510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 46505 ave 46505 max 46505 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 93010 ave 93010 max 93010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93010 Ave neighs/atom = 137.183 Neighbor list builds = 0 Dangerous builds = 0 678 -2713.71206774904 eV 2.26044477625437 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00