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 = 3.52043 3.52043 3.52043 Created orthogonal box = (0 -39.3631 0) to (19.2822 39.3631 8.62325) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.14191 4.72315 5.74883 Created 612 atoms create_atoms CPU = 0.000679016 secs 612 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.14191 4.72315 5.74883 Created 612 atoms create_atoms CPU = 0.000509024 secs 612 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 7 27 3 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 5.9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 48 atoms, new total = 1176 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 7 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 4.574 | 4.574 | 4.574 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6747.2933 0 -6747.2933 -12309.208 38 0 -6768.9196 0 -6768.9196 -27171.306 Loop time of 17.7615 on 1 procs for 38 steps with 1176 atoms 69.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6747.29326528 -6768.91497246 -6768.91960119 Force two-norm initial, final = 8.75393 0.202511 Force max component initial, final = 1.14268 0.0171094 Final line search alpha, max atom move = 1 0.0171094 Iterations, force evaluations = 38 70 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.725 | 17.725 | 17.725 | 0.0 | 99.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0030684 | 0.0030684 | 0.0030684 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03327 | | | 0.19 Nlocal: 1176 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4069 ave 4069 max 4069 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: 90120 ave 90120 max 90120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90120 Ave neighs/atom = 76.6327 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 : 38 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.574 | 4.574 | 4.574 Mbytes Step Temp E_pair E_mol TotEng Press Volume 38 0 -6768.9196 0 -6768.9196 -27171.306 13090.182 44 0 -6769.562 0 -6769.562 -11239.302 12981.509 Loop time of 1.80026 on 1 procs for 6 steps with 1176 atoms 87.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -6768.91960119 -6769.55998439 -6769.56195133 Force two-norm initial, final = 213.368 0.397607 Force max component initial, final = 161.842 0.0291161 Final line search alpha, max atom move = 0.000139734 4.06851e-06 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7987 | 1.7987 | 1.7987 | 0.0 | 99.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028348 | 0.00028348 | 0.00028348 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001254 | | | 0.07 Nlocal: 1176 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4068 ave 4068 max 4068 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: 90720 ave 90720 max 90720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90720 Ave neighs/atom = 77.1429 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 = 5.9 ghost atom cutoff = 5.9 binsize = 2.95, bins = 7 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.9 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) = 4.712 | 4.712 | 4.712 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6769.562 0 -6769.562 -11239.302 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1176 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: 1176 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4068 ave 4068 max 4068 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: 90720 ave 90720 max 90720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90720 Ave neighs/atom = 77.1429 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) = 4.712 | 4.712 | 4.712 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 -6769.562 -6769.562 19.181363 78.726155 8.5965989 -11239.302 -11239.302 3.2566425 -33719.529 -1.6323583 2.3094824 637.27943 Loop time of 2.14577e-06 on 1 procs for 0 steps with 1176 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: 1176 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4068 ave 4068 max 4068 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45360 ave 45360 max 45360 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 90720 ave 90720 max 90720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90720 Ave neighs/atom = 77.1429 Neighbor list builds = 0 Dangerous builds = 0 1176 -2847.83545367787 eV 2.30948240578679 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:20