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 = 3.52221 3.52221 3.52221 Created orthogonal box = (0 -43.5709 0) to (20.5378 43.5709 4.98116) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.04054 5.97983 4.98116 Created 412 atoms create_atoms CPU = 0.000428915 secs 412 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.04054 5.97983 4.98116 Created 412 atoms create_atoms CPU = 0.000289917 secs 412 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 7 27 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 6.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 808 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 7 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 4.955 | 4.955 | 4.955 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4644.2635 0 -4644.2635 1059.843 71 0 -4657.7376 0 -4657.7376 -7259.1868 Loop time of 25.8437 on 1 procs for 71 steps with 808 atoms 91.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4644.26354354 -4657.73432895 -4657.73760914 Force two-norm initial, final = 14.7772 0.166485 Force max component initial, final = 4.23935 0.0154359 Final line search alpha, max atom move = 1 0.0154359 Iterations, force evaluations = 71 129 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 25.815 | 25.815 | 25.815 | 0.0 | 99.89 Neigh | 0.022545 | 0.022545 | 0.022545 | 0.0 | 0.09 Comm | 0.0040672 | 0.0040672 | 0.0040672 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002556 | | | 0.01 Nlocal: 808 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4533 ave 4533 max 4533 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: 93936 ave 93936 max 93936 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 93936 Ave neighs/atom = 116.257 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 : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.956 | 4.956 | 4.956 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -4657.7376 0 -4657.7376 -7259.1868 8914.7938 73 0 -4657.7762 0 -4657.7762 -2667.6146 8892.9146 Loop time of 0.99313 on 1 procs for 2 steps with 808 atoms 84.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4657.73760914 -4657.77475515 -4657.77617181 Force two-norm initial, final = 44.2898 0.556166 Force max component initial, final = 31.4956 0.383588 Final line search alpha, max atom move = 0.000152931 5.86626e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.99268 | 0.99268 | 0.99268 | 0.0 | 99.95 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00010586 | 0.00010586 | 0.00010586 | 0.0 | 0.01 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000345 | | | 0.03 Nlocal: 808 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4547 ave 4547 max 4547 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: 96312 ave 96312 max 96312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 96312 Ave neighs/atom = 119.198 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 = 6.6 ghost atom cutoff = 6.6 binsize = 3.3, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.6 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) = 5.093 | 5.093 | 5.093 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4657.7762 0 -4657.7762 -2667.6146 Loop time of 9.53674e-07 on 1 procs for 0 steps with 808 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: 808 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4547 ave 4547 max 4547 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: 98464 ave 98464 max 98464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98464 Ave neighs/atom = 121.861 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) = 5.093 | 5.093 | 5.093 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 -4657.7762 -4657.7762 20.513188 87.141727 4.9749051 -2667.6146 -2667.6146 69.025551 -8006.4001 -65.469176 2.3932084 444.48335 Loop time of 1.19209e-06 on 1 procs for 0 steps with 808 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: 808 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4547 ave 4547 max 4547 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 49232 ave 49232 max 49232 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 98464 ave 98464 max 98464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 98464 Ave neighs/atom = 121.861 Neighbor list builds = 0 Dangerous builds = 0 808 -2288.99241386415 eV 2.3932084221074 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:27