LAMMPS (24 Jan 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 4.03299 4.03299 4.03299 Created orthogonal box = (0 -44.1832 0) to (9.01804 44.1832 9.87876) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.41082 5.89056 6.58584 Created 242 atoms create_atoms CPU = 0.000588894 secs 242 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.41082 5.89056 6.58584 Created 242 atoms create_atoms CPU = 0.000346184 secs 242 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 2 13 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 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 476 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 2 13 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 5.906 | 5.906 | 5.906 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1363.9998 0 -1363.9998 4774.6052 43 0 -1381.1253 0 -1381.1253 -2645.6396 Loop time of 0.931513 on 1 procs for 43 steps with 476 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1363.9997851 -1381.1240718 -1381.12526135 Force two-norm initial, final = 25.3487 0.0986167 Force max component initial, final = 7.2786 0.0109694 Final line search alpha, max atom move = 1 0.0109694 Iterations, force evaluations = 43 78 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.92388 | 0.92388 | 0.92388 | 0.0 | 99.18 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0058241 | 0.0058241 | 0.0058241 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001813 | | | 0.19 Nlocal: 476 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9113 ave 9113 max 9113 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: 317504 ave 317504 max 317504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 317504 Ave neighs/atom = 667.025 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : metal Current step : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.906 | 5.906 | 5.906 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -1381.1253 0 -1381.1253 -2645.6396 7872.3037 45 0 -1381.1385 0 -1381.1385 -821.2458 7852.4981 Loop time of 0.0546989 on 1 procs for 2 steps with 476 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1381.12526135 -1381.13772355 -1381.13852229 Force two-norm initial, final = 14.7916 0.258699 Force max component initial, final = 10.9731 0.177069 Final line search alpha, max atom move = 0.000379064 6.71204e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.053653 | 0.053653 | 0.053653 | 0.0 | 98.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032735 | 0.00032735 | 0.00032735 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0007186 | | | 1.31 Nlocal: 476 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9113 ave 9113 max 9113 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: 316944 ave 316944 max 316944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 316944 Ave neighs/atom = 665.849 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 2 13 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 6.043 | 6.043 | 6.043 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1381.1385 0 -1381.1385 -821.2458 Loop time of 2.14577e-06 on 1 procs for 0 steps with 476 atoms 139.8% 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 | | 2.146e-06 | | |100.00 Nlocal: 476 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9113 ave 9113 max 9113 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: 317200 ave 317200 max 317200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 317200 Ave neighs/atom = 666.387 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) = 6.043 | 6.043 | 6.043 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 -1381.1385 -1381.1385 9.0070649 88.366417 9.8659135 -821.2458 -821.2458 -36.084136 -2459.069 31.415755 2.5655849 312.17126 Loop time of 1.90735e-06 on 1 procs for 0 steps with 476 atoms 157.3% 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: 476 ave 476 max 476 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9113 ave 9113 max 9113 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 158600 ave 158600 max 158600 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 317200 ave 317200 max 317200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 317200 Ave neighs/atom = 666.387 Neighbor list builds = 0 Dangerous builds = 0 476 -1381.13852228825 eV 2.56558492835686 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01