LAMMPS (24 Jan 2020) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:94) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.6063 3.6063 3.6063 Created orthogonal box = (0 -44.1716 0) to (5.10008 44.1716 6.2463) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.10008 5.88907 6.2463 Created 122 atoms create_atoms CPU = 0.000649929 secs 122 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.10008 5.88907 6.2463 Created 122 atoms create_atoms CPU = 0.000476837 secs 122 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 = 11.9775 ghost atom cutoff = 11.9775 binsize = 5.98874, bins = 1 15 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 11.9775 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 240 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 11.9775 ghost atom cutoff = 11.9775 binsize = 5.98874, bins = 1 15 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.9775 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) = 5.034 | 5.034 | 5.034 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1009.0352 0 -1009.0352 -139.73374 1 0 -1009.0359 0 -1009.0359 -140.6608 Loop time of 0.019846 on 1 procs for 1 steps with 240 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1009.03516593 -1009.03516593 -1009.03586168 Force two-norm initial, final = 0.188063 0.061264 Force max component initial, final = 0.0577188 0.0190858 Final line search alpha, max atom move = 1 0.0190858 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.019561 | 0.019561 | 0.019561 | 0.0 | 98.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021553 | 0.00021553 | 0.00021553 | 0.0 | 1.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.938e-05 | | | 0.35 Nlocal: 240 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8555 ave 8555 max 8555 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: 150240 ave 150240 max 150240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 150240 Ave neighs/atom = 626 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:178) Setting up cg style minimization ... Unit style : metal Current step : 1 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.034 | 5.034 | 5.034 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1 0 -1009.0359 0 -1009.0359 -140.6608 2814.3182 2 0 -1009.0359 0 -1009.0359 -71.86265 2814.2062 Loop time of 0.0206871 on 1 procs for 1 steps with 240 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 = -1009.03586168 -1009.03586168 -1009.03586471 Force two-norm initial, final = 0.199264 0.0683434 Force max component initial, final = 0.15915 0.0304203 Final line search alpha, max atom move = 0.00628338 0.000191143 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.020009 | 0.020009 | 0.020009 | 0.0 | 96.72 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00021911 | 0.00021911 | 0.00021911 | 0.0 | 1.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000459 | | | 2.22 Nlocal: 240 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8555 ave 8555 max 8555 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: 150240 ave 150240 max 150240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 150240 Ave neighs/atom = 626 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 = 11.9775 ghost atom cutoff = 11.9775 binsize = 5.98874, bins = 1 15 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.9775 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) = 5.172 | 5.172 | 5.172 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1009.0359 0 -1009.0359 -71.86265 Loop time of 1.90735e-06 on 1 procs for 0 steps with 240 atoms 104.9% 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: 240 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8555 ave 8555 max 8555 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: 150240 ave 150240 max 150240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 150240 Ave neighs/atom = 626 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) = 5.172 | 5.172 | 5.172 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 -1009.0359 -1009.0359 5.0999588 88.343225 6.2462016 -71.86265 -71.86265 1.5851797 -234.49168 17.318546 2.5495855 0.00041332564 Loop time of 1.90735e-06 on 1 procs for 0 steps with 240 atoms 157.3% 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: 240 ave 240 max 240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8555 ave 8555 max 8555 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 75120 ave 75120 max 75120 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 150240 ave 150240 max 150240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 150240 Ave neighs/atom = 626 Neighbor list builds = 0 Dangerous builds = 0 240 -1009.0358647071 eV 2.54958549169685 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00