LAMMPS (19 Mar 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 = 3.61358 3.61358 3.61358 Created orthogonal box = (0 -42.7601 0) to (52.3658 42.7601 8.85143) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.98466 5.49726 5.90095 Created 1682 atoms create_atoms CPU = 0.00087285 secs 1682 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.98466 5.49726 5.90095 Created 1681 atoms create_atoms CPU = 0.000769138 secs 1681 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.75339, bins = 14 23 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 7.50679 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 51 atoms, new total = 3312 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.75339, bins = 14 23 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 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) = 6.612 | 6.612 | 6.612 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11595.558 0 -11595.558 2322.53 54 0 -11682.55 0 -11682.55 -14415.155 Loop time of 2.00942 on 1 procs for 54 steps with 3312 atoms 47.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11595.5575001 -11682.540031 -11682.5498605 Force two-norm initial, final = 55.0664 0.284346 Force max component initial, final = 5.75738 0.0518861 Final line search alpha, max atom move = 1 0.0518861 Iterations, force evaluations = 54 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9455 | 1.9455 | 1.9455 | 0.0 | 96.82 Neigh | 0.02512 | 0.02512 | 0.02512 | 0.0 | 1.25 Comm | 0.032396 | 0.032396 | 0.032396 | 0.0 | 1.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006404 | | | 0.32 Nlocal: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10286 ave 10286 max 10286 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: 465914 ave 465914 max 465914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 465914 Ave neighs/atom = 140.675 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) Setting up cg style minimization ... Unit style : metal Current step : 54 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.612 | 6.612 | 6.612 Mbytes Step Temp E_pair E_mol TotEng Press Volume 54 0 -11682.55 0 -11682.55 -14415.155 39639.597 59 0 -11683.862 0 -11683.862 -3128.7832 39313.019 Loop time of 0.149075 on 1 procs for 5 steps with 3312 atoms 47.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11682.5498605 -11683.8541518 -11683.8616243 Force two-norm initial, final = 448.643 5.52662 Force max component initial, final = 324.952 4.77622 Final line search alpha, max atom move = 3.45652e-05 0.000165091 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13384 | 0.13384 | 0.13384 | 0.0 | 89.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042295 | 0.00042295 | 0.00042295 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01481 | | | 9.94 Nlocal: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10041 ave 10041 max 10041 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: 465120 ave 465120 max 465120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 465120 Ave neighs/atom = 140.435 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.75339, bins = 14 23 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 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) = 6.747 | 6.747 | 6.747 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11683.862 0 -11683.862 -3128.7832 Loop time of 1.90735e-06 on 1 procs for 0 steps with 3312 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: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10051 ave 10051 max 10051 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: 466138 ave 466138 max 466138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 466138 Ave neighs/atom = 140.742 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) = 6.747 | 6.747 | 6.747 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 -11683.862 -11683.862 52.16334 85.520152 8.8125692 -3128.7832 -3128.7832 193.89918 -9468.4835 -111.76529 2.3944605 1716.1778 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3312 atoms 314.6% 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: 3312 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10051 ave 10051 max 10051 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 233069 ave 233069 max 233069 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 466138 ave 466138 max 466138 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 466138 Ave neighs/atom = 140.742 Neighbor list builds = 0 Dangerous builds = 0 3312 -11683.8781842802 eV 2.39446047627375 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02