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 = 3.61115 3.61115 3.61115 Created orthogonal box = (0 -62.5506 0) to (25.5347 62.5506 8.84548) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.12833 5.42074 5.89699 Created 1204 atoms create_atoms CPU = 0.000628233 secs 1204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.12833 5.42074 5.89699 Created 1204 atoms create_atoms CPU = 0.000498056 secs 1204 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 47 4 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, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 24 atoms, new total = 2384 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 47 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.869 | 5.869 | 5.869 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10059.365 0 -10059.365 853.84336 39 0 -10107.741 0 -10107.741 -8252.4185 Loop time of 3.92647 on 1 procs for 39 steps with 2384 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10059.3645703 -10107.7340791 -10107.7406914 Force two-norm initial, final = 35.6019 0.257018 Force max component initial, final = 5.20844 0.0472844 Final line search alpha, max atom move = 0.82437 0.0389799 Iterations, force evaluations = 39 67 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.9197 | 3.9197 | 3.9197 | 0.0 | 99.83 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0029402 | 0.0029402 | 0.0029402 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003834 | | | 0.10 Nlocal: 2384 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5786 ave 5786 max 5786 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: 127792 ave 127792 max 127792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 127792 Ave neighs/atom = 53.604 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 : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.869 | 5.869 | 5.869 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -10107.741 0 -10107.741 -8252.4185 28256.207 42 0 -10107.968 0 -10107.968 -2243.0389 28152.198 Loop time of 0.342504 on 1 procs for 3 steps with 2384 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10107.7406914 -10107.9677883 -10107.9679031 Force two-norm initial, final = 174.007 0.329363 Force max component initial, final = 124.412 0.0561924 Final line search alpha, max atom move = 0.000511977 2.87692e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34117 | 0.34117 | 0.34117 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0002346 | 0.0002346 | 0.0002346 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001095 | | | 0.32 Nlocal: 2384 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5800 ave 5800 max 5800 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: 128662 ave 128662 max 128662 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128662 Ave neighs/atom = 53.969 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 = 5.35 ghost atom cutoff = 5.35 binsize = 2.675, bins = 10 47 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 5.35 pair build: full/bin/ghost stencil: full/ghost/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) = 6.007 | 6.007 | 6.007 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10107.968 0 -10107.968 -2243.0389 Loop time of 1.19209e-06 on 1 procs for 0 steps with 2384 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: 2384 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5813 ave 5813 max 5813 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: 128664 ave 128664 max 128664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128664 Ave neighs/atom = 53.9698 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) = 6.007 | 6.007 | 6.007 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 -10107.968 -10107.968 25.48917 125.10122 8.8286659 -2243.0389 -2243.0389 -3.1922757 -6725.585 -0.33936124 2.3582394 729.42556 Loop time of 9.53674e-07 on 1 procs for 0 steps with 2384 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: 2384 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5813 ave 5813 max 5813 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 64332 ave 64332 max 64332 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 128664 ave 128664 max 128664 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128664 Ave neighs/atom = 53.9698 Neighbor list builds = 0 Dangerous builds = 0 2384 -10107.9679031459 eV 2.35823940078011 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04