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 = 4.04976 4.04976 4.04976 Created orthogonal box = (0 -49.9329 0) to (17.6525 49.9329 5.72723) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.50356 5.25567 5.72723 Created 306 atoms create_atoms CPU = 0.000277042 secs 306 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.50356 5.25567 5.72723 Created 306 atoms create_atoms CPU = 0.000152111 secs 306 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 5 24 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 8.6825 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 606 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 5 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.6825 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) = 4.933 | 4.933 | 4.933 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1986.9203 0 -1986.9203 11212.184 29 0 -2006.0409 0 -2006.0409 1030.4629 Loop time of 0.152501 on 1 procs for 29 steps with 606 atoms 104.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1986.92025638 -2006.0392169 -2006.04087134 Force two-norm initial, final = 28.2767 0.101055 Force max component initial, final = 6.80599 0.0188348 Final line search alpha, max atom move = 1 0.0188348 Iterations, force evaluations = 29 54 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14665 | 0.14665 | 0.14665 | 0.0 | 96.17 Neigh | 0.002887 | 0.002887 | 0.002887 | 0.0 | 1.89 Comm | 0.0018597 | 0.0018597 | 0.0018597 | 0.0 | 1.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0011 | | | 0.72 Nlocal: 606 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5018 ave 5018 max 5018 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: 104756 ave 104756 max 104756 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104756 Ave neighs/atom = 172.865 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 : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.933 | 4.933 | 4.933 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -2006.0409 0 -2006.0409 1030.4629 10096.429 31 0 -2006.048 0 -2006.048 -62.326115 10110.819 Loop time of 0.011198 on 1 procs for 2 steps with 606 atoms 89.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2006.04087134 -2006.04739427 -2006.04799769 Force two-norm initial, final = 11.1935 0.194678 Force max component initial, final = 10.1357 0.122276 Final line search alpha, max atom move = 0.000605585 7.40486e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.010728 | 0.010728 | 0.010728 | 0.0 | 95.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011492 | 0.00011492 | 0.00011492 | 0.0 | 1.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0003555 | | | 3.17 Nlocal: 606 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5010 ave 5010 max 5010 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: 104872 ave 104872 max 104872 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104872 Ave neighs/atom = 173.056 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 = 8.6825 ghost atom cutoff = 8.6825 binsize = 4.34125, bins = 5 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.6825 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) = 5.07 | 5.07 | 5.07 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2006.048 0 -2006.048 -62.326115 Loop time of 9.53674e-07 on 1 procs for 0 steps with 606 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: 606 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5010 ave 5010 max 5010 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: 104792 ave 104792 max 104792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104792 Ave neighs/atom = 172.924 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) = 5.07 | 5.07 | 5.07 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 -2006.048 -2006.048 17.676551 99.865776 5.7275926 -62.326115 -62.326115 19.402454 -224.21715 17.836351 2.6836499 331.29005 Loop time of 1.90735e-06 on 1 procs for 0 steps with 606 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: 606 ave 606 max 606 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5010 ave 5010 max 5010 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 52396 ave 52396 max 52396 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 104792 ave 104792 max 104792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 104792 Ave neighs/atom = 172.924 Neighbor list builds = 0 Dangerous builds = 0 606 -2006.04799768774 eV 2.6836498672958 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00