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 = 3.60735 3.60735 3.60735 Created orthogonal box = (0 -47.8605 0) to (16.92 47.8605 5.10157) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.15272 5.43829 5.10157 Created 359 atoms create_atoms CPU = 0.00088191 secs 359 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.15272 5.43829 5.10157 Created 359 atoms create_atoms CPU = 0.000718832 secs 359 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 16 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 12.1544 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 704 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 16 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 6.266 | 6.266 | 6.266 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2472.9343 0 -2472.9343 5434.68 45 0 -2482.4271 0 -2482.4271 2457.9997 Loop time of 1.54424 on 1 procs for 45 steps with 704 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2472.93431082 -2482.42505555 -2482.42707722 Force two-norm initial, final = 20.1386 0.130461 Force max component initial, final = 3.55503 0.0129968 Final line search alpha, max atom move = 1 0.0129968 Iterations, force evaluations = 45 89 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5321 | 1.5321 | 1.5321 | 0.0 | 99.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0092731 | 0.0092731 | 0.0092731 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002843 | | | 0.18 Nlocal: 704 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12256 ave 12256 max 12256 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: 442440 ave 442440 max 442440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 442440 Ave neighs/atom = 628.466 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 : 45 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.266 | 6.266 | 6.266 Mbytes Step Temp E_pair E_mol TotEng Press Volume 45 0 -2482.4271 0 -2482.4271 2457.9997 8262.4953 47 0 -2482.4297 0 -2482.4297 2906.1208 8259.8407 Loop time of 0.092396 on 1 procs for 2 steps with 704 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 = -2482.42707722 -2482.42966268 -2482.42968522 Force two-norm initial, final = 8.11354 0.13335 Force max component initial, final = 7.6398 0.0201088 Final line search alpha, max atom move = 0.0012202 2.45367e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.090572 | 0.090572 | 0.090572 | 0.0 | 98.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000525 | 0.000525 | 0.000525 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001299 | | | 1.41 Nlocal: 704 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12292 ave 12292 max 12292 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: 440352 ave 440352 max 440352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 440352 Ave neighs/atom = 625.5 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 = 12.1544 ghost atom cutoff = 12.1544 binsize = 6.0772, bins = 3 16 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 12.1544 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) = 6.404 | 6.404 | 6.404 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2482.4297 0 -2482.4297 2906.1208 Loop time of 1.19209e-06 on 1 procs for 0 steps with 704 atoms 251.7% 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: 704 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12292 ave 12292 max 12292 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: 440352 ave 440352 max 440352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 440352 Ave neighs/atom = 625.5 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) = 6.404 | 6.404 | 6.404 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 -2482.4297 -2482.4297 16.924471 95.721098 5.0985759 2906.1208 2906.1208 -3.9015685 8725.2392 -2.9753742 2.3792795 213.48625 Loop time of 1.90735e-06 on 1 procs for 0 steps with 704 atoms 104.9% 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: 704 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12292 ave 12292 max 12292 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 220176 ave 220176 max 220176 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 440352 ave 440352 max 440352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 440352 Ave neighs/atom = 625.5 Neighbor list builds = 0 Dangerous builds = 0 704 -2482.42968521505 eV 2.37927949497988 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01