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 = 3.63857 3.63857 3.63857 Created orthogonal box = (0 -36.7514 0) to (25.9846 36.7514 5.14571) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.58551 5.76435 5.14571 Created 410 atoms create_atoms CPU = 0.000290155 secs 410 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.58551 5.76435 5.14571 Created 410 atoms create_atoms CPU = 0.000179052 secs 410 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 16 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 808 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 16 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.396 | 5.396 | 5.396 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2716.0216 0 -2716.0216 6090.502 32 0 -2737.2187 0 -2737.2187 -6787.6736 Loop time of 0.327177 on 1 procs for 32 steps with 808 atoms 100.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2716.02157217 -2737.21653078 -2737.21865037 Force two-norm initial, final = 38.0595 0.129622 Force max component initial, final = 8.68127 0.013558 Final line search alpha, max atom move = 1 0.013558 Iterations, force evaluations = 32 54 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.31894 | 0.31894 | 0.31894 | 0.0 | 97.48 Neigh | 0.0043862 | 0.0043862 | 0.0043862 | 0.0 | 1.34 Comm | 0.0025327 | 0.0025327 | 0.0025327 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001313 | | | 0.40 Nlocal: 808 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7619 ave 7619 max 7619 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: 255460 ave 255460 max 255460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255460 Ave neighs/atom = 316.163 Neighbor list builds = 1 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 : 32 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.396 | 5.396 | 5.396 Mbytes Step Temp E_pair E_mol TotEng Press Volume 32 0 -2737.2187 0 -2737.2187 -6787.6736 9827.9926 38 0 -2737.3464 0 -2737.3464 -218.111 9782.8755 Loop time of 0.0375781 on 1 procs for 6 steps with 808 atoms 106.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2737.21865037 -2737.34612983 -2737.34643927 Force two-norm initial, final = 60.9955 1.38901 Force max component initial, final = 52.3628 1.29254 Final line search alpha, max atom move = 0.000333853 0.000431517 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.036498 | 0.036498 | 0.036498 | 0.0 | 97.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027776 | 0.00027776 | 0.00027776 | 0.0 | 0.74 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000802 | | | 2.13 Nlocal: 808 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7589 ave 7589 max 7589 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: 255364 ave 255364 max 255364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255364 Ave neighs/atom = 316.045 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 6 16 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.534 | 5.534 | 5.534 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2737.3464 0 -2737.3464 -218.111 Loop time of 9.53674e-07 on 1 procs for 0 steps with 808 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: 808 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7619 ave 7619 max 7619 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: 255508 ave 255508 max 255508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255508 Ave neighs/atom = 316.223 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) = 5.534 | 5.534 | 5.534 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 -2737.3464 -2737.3464 25.8513 73.502757 5.1484975 -218.111 -218.111 -75.931853 -790.19892 211.79778 2.2495292 457.83803 Loop time of 1.90735e-06 on 1 procs for 0 steps with 808 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: 808 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7619 ave 7619 max 7619 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 127754 ave 127754 max 127754 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 255508 ave 255508 max 255508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 255508 Ave neighs/atom = 316.223 Neighbor list builds = 0 Dangerous builds = 0 808 -2737.34643926806 eV 2.24952923134486 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00