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 = 3.52 3.52 3.52 Created orthogonal box = (0 -54.9877 0) to (27.4921 54.9877 3.52) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.95759 4.95759 3.52 Created 490 atoms create_atoms CPU = 0.000303984 secs 490 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.95759 4.95759 3.52 Created 490 atoms create_atoms CPU = 0.000177145 secs 490 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 974 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.004 | 5.004 | 5.004 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4254.4015 0 -4254.4015 29161.787 79 0 -4324.3079 0 -4324.3079 1163.3528 Loop time of 0.362045 on 1 procs for 79 steps with 974 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4254.40146608 -4324.30409014 -4324.30790532 Force two-norm initial, final = 67.0452 0.260929 Force max component initial, final = 18.5936 0.0664761 Final line search alpha, max atom move = 1 0.0664761 Iterations, force evaluations = 79 140 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.34882 | 0.34882 | 0.34882 | 0.0 | 96.35 Neigh | 0.0034041 | 0.0034041 | 0.0034041 | 0.0 | 0.94 Comm | 0.0060813 | 0.0060813 | 0.0060813 | 0.0 | 1.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003741 | | | 1.03 Nlocal: 974 ave 974 max 974 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: 129300 ave 129300 max 129300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129300 Ave neighs/atom = 132.752 Neighbor list builds = 1 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 : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.004 | 5.004 | 5.004 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -4324.3079 0 -4324.3079 1163.3528 10642.548 82 0 -4324.3331 0 -4324.3331 23.214588 10649.243 Loop time of 0.0166912 on 1 procs for 3 steps with 974 atoms 119.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4324.30790532 -4324.33260316 -4324.3330662 Force two-norm initial, final = 19.8499 0.265598 Force max component initial, final = 17.3888 0.0571463 Final line search alpha, max atom move = 0.000194425 1.11106e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.015683 | 0.015683 | 0.015683 | 0.0 | 93.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00023031 | 0.00023031 | 0.00023031 | 0.0 | 1.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000778 | | | 4.66 Nlocal: 974 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7196 ave 7196 max 7196 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: 129672 ave 129672 max 129672 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129672 Ave neighs/atom = 133.133 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 9 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.141 | 5.141 | 5.141 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4324.3331 0 -4324.3331 23.214588 Loop time of 1.90735e-06 on 1 procs for 0 steps with 974 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: 974 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7196 ave 7196 max 7196 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: 129648 ave 129648 max 129648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129648 Ave neighs/atom = 133.109 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) = 5.141 | 5.141 | 5.141 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 -4324.3331 -4324.3331 27.452143 109.97535 3.5273384 23.214588 23.214588 -2.9578072 75.578107 -2.9765366 2.2501772 148.28207 Loop time of 1.90735e-06 on 1 procs for 0 steps with 974 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: 974 ave 974 max 974 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7196 ave 7196 max 7196 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 64824 ave 64824 max 64824 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 129648 ave 129648 max 129648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129648 Ave neighs/atom = 133.109 Neighbor list builds = 0 Dangerous builds = 0 974 -4324.33306619925 eV 2.25017717598529 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00