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 = 3.61473 3.61473 3.61473 Created orthogonal box = (0 -44.7154 0) to (14.9039 44.7154 3.61473) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3835 4.3835 3.61473 Created 206 atoms create_atoms CPU = 0.000212908 secs 206 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3835 4.3835 3.61473 Created 206 atoms create_atoms CPU = 7.79629e-05 secs 206 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 6 33 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 5.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 400 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 6 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.444 | 4.444 | 4.444 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1404.3456 0 -1404.3456 -5714.6588 29 0 -1407.2885 0 -1407.2885 -14946.586 Loop time of 0.0460131 on 1 procs for 29 steps with 400 atoms 108.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1404.34557062 -1407.28725635 -1407.28853539 Force two-norm initial, final = 2.13032 0.0777287 Force max component initial, final = 0.592339 0.00890954 Final line search alpha, max atom move = 1 0.00890954 Iterations, force evaluations = 29 55 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.044431 | 0.044431 | 0.044431 | 0.0 | 96.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00095749 | 0.00095749 | 0.00095749 | 0.0 | 2.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006247 | | | 1.36 Nlocal: 400 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2692 ave 2692 max 2692 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: 21248 ave 21248 max 21248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21248 Ave neighs/atom = 53.12 Neighbor list builds = 0 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 : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.444 | 4.444 | 4.444 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -1407.2885 0 -1407.2885 -14946.586 4817.9559 34 0 -1407.4448 0 -1407.4448 -3820.0594 4777.7136 Loop time of 0.00615096 on 1 procs for 5 steps with 400 atoms 162.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1407.28853539 -1407.44358948 -1407.44479128 Force two-norm initial, final = 52.4404 0.438977 Force max component initial, final = 38.4374 0.326179 Final line search alpha, max atom move = 0.000271185 8.84548e-05 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.0056629 | 0.0056629 | 0.0056629 | 0.0 | 92.07 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011086 | 0.00011086 | 0.00011086 | 0.0 | 1.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003772 | | | 6.13 Nlocal: 400 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2696 ave 2696 max 2696 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: 21456 ave 21456 max 21456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21456 Ave neighs/atom = 53.64 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 = 5.5 ghost atom cutoff = 5.5 binsize = 2.75, bins = 6 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.5 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) = 4.582 | 4.582 | 4.582 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 1395.7683 0 1395.7683 -3820.0594 Loop time of 1.19209e-06 on 1 procs for 0 steps with 400 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: 400 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2704 ave 2704 max 2704 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: 21468 ave 21468 max 21468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21468 Ave neighs/atom = 53.67 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) = 4.582 | 4.582 | 4.582 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 1395.7683 -1407.4448 14.838139 89.430708 3.6004269 -3820.0594 -3820.0594 -84.91071 -11484.217 108.94925 2.3044169 56.728475 Loop time of 9.53674e-07 on 1 procs for 0 steps with 400 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: 400 ave 400 max 400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2704 ave 2704 max 2704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 10734 ave 10734 max 10734 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 21468 ave 21468 max 21468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 21468 Ave neighs/atom = 53.67 Neighbor list builds = 0 Dangerous builds = 0 400 1395.76827188839 eV 2.30441691067719 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00