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 = 3.14096 3.14096 3.14096 Created orthogonal box = (0 -41.0766 0) to (19.3622 41.0766 4.44199) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.07625 5.0441 4.44199 Created 230 atoms create_atoms CPU = 0.000298977 secs 230 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.07625 5.0441 4.44199 Created 230 atoms create_atoms CPU = 0.000136137 secs 230 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:979) 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 4 15 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 11.5437 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 455 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 4 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.5437 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) = 4.939 | 4.939 | 4.939 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2784.8126 0 -2784.8126 129867.21 75 0 -3044.2685 0 -3044.2685 12298.754 Loop time of 0.666979 on 1 procs for 75 steps with 455 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2784.81263549 -3044.2657775 -3044.26847484 Force two-norm initial, final = 384.609 0.306771 Force max component initial, final = 140.829 0.0691356 Final line search alpha, max atom move = 0.281183 0.0194398 Iterations, force evaluations = 75 137 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.65103 | 0.65103 | 0.65103 | 0.0 | 97.61 Neigh | 0.0076392 | 0.0076392 | 0.0076392 | 0.0 | 1.15 Comm | 0.006036 | 0.006036 | 0.006036 | 0.0 | 0.90 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002269 | | | 0.34 Nlocal: 455 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7243 ave 7243 max 7243 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: 185948 ave 185948 max 185948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185948 Ave neighs/atom = 408.677 Neighbor list builds = 2 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 : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.939 | 4.939 | 4.939 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -3044.2685 0 -3044.2685 12298.754 7065.7203 81 0 -3044.4419 0 -3044.4419 4846.9551 7084.0063 Loop time of 0.0442631 on 1 procs for 6 steps with 455 atoms 113.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3044.26847484 -3044.43922212 -3044.44189725 Force two-norm initial, final = 56.1147 0.826466 Force max component initial, final = 54.4075 0.245228 Final line search alpha, max atom move = 0.000186275 4.56799e-05 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.042994 | 0.042994 | 0.042994 | 0.0 | 97.13 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033689 | 0.00033689 | 0.00033689 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009317 | | | 2.11 Nlocal: 455 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7243 ave 7243 max 7243 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: 185910 ave 185910 max 185910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185910 Ave neighs/atom = 408.593 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 = 11.5437 ghost atom cutoff = 11.5437 binsize = 5.77186, bins = 4 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.5437 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) = 5.077 | 5.077 | 5.077 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3044.4419 0 -3044.4419 4846.9551 Loop time of 1.19209e-06 on 1 procs for 0 steps with 455 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 | | 1.192e-06 | | |100.00 Nlocal: 455 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7201 ave 7201 max 7201 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: 185614 ave 185614 max 185614 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185614 Ave neighs/atom = 407.943 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) = 5.077 | 5.077 | 5.077 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 -3044.4419 -3044.4419 19.472204 82.153119 4.428328 4846.9551 4846.9551 10.178096 14475.395 55.292204 2.5239139 617.8753 Loop time of 1.90735e-06 on 1 procs for 0 steps with 455 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: 455 ave 455 max 455 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7201 ave 7201 max 7201 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 92807 ave 92807 max 92807 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 185614 ave 185614 max 185614 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 185614 Ave neighs/atom = 407.943 Neighbor list builds = 0 Dangerous builds = 0 455 -3044.44189724681 eV 2.5239138849699 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00