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 = 3.68004 3.68004 3.68004 Created orthogonal box = (0 -56.0565 0) to (28.0264 56.0565 3.68004) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.83214 4.83214 3.68004 Created 466 atoms create_atoms CPU = 0.00029397 secs 466 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.83214 4.83214 3.68004 Created 466 atoms create_atoms CPU = 0.000144958 secs 466 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.86322, bins = 10 40 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 5.72645 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 924 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.86322, bins = 10 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.569 | 4.569 | 4.569 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3892.3456 0 -3892.3456 8269.1102 62 0 -3919.6864 0 -3919.6864 -5200.8358 Loop time of 0.123596 on 1 procs for 62 steps with 924 atoms 105.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3892.34563616 -3919.68370773 -3919.68641773 Force two-norm initial, final = 33.0444 0.201276 Force max component initial, final = 7.33628 0.046161 Final line search alpha, max atom move = 1 0.046161 Iterations, force evaluations = 62 113 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.1176 | 0.1176 | 0.1176 | 0.0 | 95.15 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0036631 | 0.0036631 | 0.0036631 | 0.0 | 2.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002335 | | | 1.89 Nlocal: 924 ave 924 max 924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5482 ave 5482 max 5482 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: 49976 ave 49976 max 49976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 49976 Ave neighs/atom = 54.0866 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 : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.569 | 4.569 | 4.569 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -3919.6864 0 -3919.6864 -5200.8358 11563.14 66 0 -3919.7314 0 -3919.7314 -3628.9185 11550.128 Loop time of 0.00550103 on 1 procs for 4 steps with 924 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 = -3919.68641773 -3919.73029769 -3919.73140715 Force two-norm initial, final = 29.9929 1.99293 Force max component initial, final = 29.9735 1.96272 Final line search alpha, max atom move = 0.000156532 0.000307227 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.004905 | 0.004905 | 0.004905 | 0.0 | 89.16 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00014687 | 0.00014687 | 0.00014687 | 0.0 | 2.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0004492 | | | 8.17 Nlocal: 924 ave 924 max 924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5519 ave 5519 max 5519 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: 51000 ave 51000 max 51000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51000 Ave neighs/atom = 55.1948 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 = 5.72645 ghost atom cutoff = 5.72645 binsize = 2.86322, bins = 10 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.72645 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) = 4.707 | 4.707 | 4.707 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3919.7314 0 -3919.7314 -3628.9185 Loop time of 9.53674e-07 on 1 procs for 0 steps with 924 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: 924 ave 924 max 924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5519 ave 5519 max 5519 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: 51028 ave 51028 max 51028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51028 Ave neighs/atom = 55.2251 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) = 4.707 | 4.707 | 4.707 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 -3919.7314 -3919.7314 27.946546 112.1129 3.686405 -3628.9185 -3628.9185 33.08319 -11192.568 272.72886 2.3269503 391.821 Loop time of 1.90735e-06 on 1 procs for 0 steps with 924 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: 924 ave 924 max 924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5519 ave 5519 max 5519 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25514 ave 25514 max 25514 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 51028 ave 51028 max 51028 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51028 Ave neighs/atom = 55.2251 Neighbor list builds = 0 Dangerous builds = 0 924 -3919.73140714544 eV 2.32695032446757 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00