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 = 3.65334 3.65334 3.65334 Created orthogonal box = (0 -43.8438 0) to (15.4998 43.8438 5.16661) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.16661 6.08891 5.16661 Created 292 atoms create_atoms CPU = 0.000595808 secs 292 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.16661 6.08891 5.16661 Created 292 atoms create_atoms CPU = 0.000448942 secs 292 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 4 21 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 8.76342 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 568 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 4 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 4.942 | 4.942 | 4.942 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1828.6946 0 -1828.6946 707.39262 28 0 -1845.9516 0 -1845.9516 -13913.613 Loop time of 0.406813 on 1 procs for 28 steps with 568 atoms 46.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1828.69458939 -1845.94992357 -1845.95160765 Force two-norm initial, final = 18.1189 0.147047 Force max component initial, final = 4.18324 0.0194219 Final line search alpha, max atom move = 1 0.0194219 Iterations, force evaluations = 28 50 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40321 | 0.40321 | 0.40321 | 0.0 | 99.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0024071 | 0.0024071 | 0.0024071 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001194 | | | 0.29 Nlocal: 568 ave 568 max 568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5532 ave 5532 max 5532 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: 125744 ave 125744 max 125744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 125744 Ave neighs/atom = 221.38 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 : 28 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.942 | 4.942 | 4.942 Mbytes Step Temp E_pair E_mol TotEng Press Volume 28 0 -1845.9516 0 -1845.9516 -13913.613 7022.1548 39 0 -1846.3484 0 -1846.3484 -3853.9126 6964.3052 Loop time of 0.112875 on 1 procs for 11 steps with 568 atoms 45.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1845.95160765 -1846.34655082 -1846.34835197 Force two-norm initial, final = 80.983 1.1401 Force max component initial, final = 78.7703 0.894609 Final line search alpha, max atom move = 0.000331224 0.000296316 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11034 | 0.11034 | 0.11034 | 0.0 | 97.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00061655 | 0.00061655 | 0.00061655 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001915 | | | 1.70 Nlocal: 568 ave 568 max 568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5532 ave 5532 max 5532 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: 126304 ave 126304 max 126304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126304 Ave neighs/atom = 222.366 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 = 8.76342 ghost atom cutoff = 8.76342 binsize = 4.38171, bins = 4 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.76342 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) = 5.081 | 5.081 | 5.081 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1846.3484 0 -1846.3484 -3853.9126 Loop time of 1.19209e-06 on 1 procs for 0 steps with 568 atoms 167.8% 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 | | 1.192e-06 | | |100.00 Nlocal: 568 ave 568 max 568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5675 ave 5675 max 5675 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: 126608 ave 126608 max 126608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126608 Ave neighs/atom = 222.901 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) = 5.081 | 5.081 | 5.081 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 -1846.3484 -1846.3484 15.334038 87.687564 5.1794454 -3853.9126 -3853.9126 -129.7849 -11225.632 -206.32104 2.3662298 377.47985 Loop time of 1.90735e-06 on 1 procs for 0 steps with 568 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: 568 ave 568 max 568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5675 ave 5675 max 5675 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 63304 ave 63304 max 63304 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 126608 ave 126608 max 126608 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 126608 Ave neighs/atom = 222.901 Neighbor list builds = 0 Dangerous builds = 0 568 -1846.34835197418 eV 2.36622977232855 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00