LAMMPS (19 Mar 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 = 3.51847 3.51847 3.51847 Created orthogonal box = (0 -52.0722 0) to (42.5139 52.0722 8.61847) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.24144 4.99289 5.74565 Created 1758 atoms create_atoms CPU = 0.000867128 secs 1758 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.24144 4.99289 5.74565 Created 1757 atoms create_atoms CPU = 0.000756025 secs 1757 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 ghost atom cutoff = 8 binsize = 4, bins = 11 27 3 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 43 atoms, new total = 3472 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 8 ghost atom cutoff = 8 binsize = 4, bins = 11 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 7.898 | 7.898 | 7.898 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14944.911 0 -14944.911 -3883.6819 55 0 -15030.077 0 -15030.077 -11973.003 Loop time of 1.05862 on 1 procs for 55 steps with 3472 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -14944.9113892 -15030.0624672 -15030.0773657 Force two-norm initial, final = 84.105 0.418113 Force max component initial, final = 13.457 0.0347359 Final line search alpha, max atom move = 1 0.0347359 Iterations, force evaluations = 55 101 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0342 | 1.0342 | 1.0342 | 0.0 | 97.70 Neigh | 0.013381 | 0.013381 | 0.013381 | 0.0 | 1.26 Comm | 0.0059354 | 0.0059354 | 0.0059354 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005071 | | | 0.48 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12556 ave 12556 max 12556 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: 689240 ave 689240 max 689240 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 689240 Ave neighs/atom = 198.514 Neighbor list builds = 1 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:190) Setting up cg style minimization ... Unit style : metal Current step : 55 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.898 | 7.898 | 7.898 Mbytes Step Temp E_pair E_mol TotEng Press Volume 55 0 -15030.077 0 -15030.077 -11973.003 38158.978 59 0 -15030.7 0 -15030.7 -2386.1158 37976.9 Loop time of 0.070287 on 1 procs for 4 steps with 3472 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15030.0773657 -15030.6990191 -15030.6996724 Force two-norm initial, final = 370.075 0.638048 Force max component initial, final = 264.701 0.0731719 Final line search alpha, max atom move = 0.000178672 1.30737e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.068513 | 0.068513 | 0.068513 | 0.0 | 97.48 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00038719 | 0.00038719 | 0.00038719 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001387 | | | 1.97 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12252 ave 12252 max 12252 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: 689322 ave 689322 max 689322 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 689322 Ave neighs/atom = 198.537 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 ghost atom cutoff = 8 binsize = 4, bins = 11 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 8.035 | 8.035 | 8.035 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15030.7 0 -15030.7 -2386.1158 Loop time of 9.53674e-07 on 1 procs for 0 steps with 3472 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 | | 9.537e-07 | | |100.00 Nlocal: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12435 ave 12435 max 12435 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: 689592 ave 689592 max 689592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 689592 Ave neighs/atom = 198.615 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) = 8.035 | 8.035 | 8.035 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 -15030.7 -15030.7 42.402468 104.14438 8.5998832 -2386.1158 -2386.1158 3.0788986 -7161.2707 -0.15565964 2.1970872 1519.0472 Loop time of 1.19209e-06 on 1 procs for 0 steps with 3472 atoms 167.8% 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: 3472 ave 3472 max 3472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12435 ave 12435 max 12435 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 344796 ave 344796 max 344796 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 689592 ave 689592 max 689592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 689592 Ave neighs/atom = 198.615 Neighbor list builds = 0 Dangerous builds = 0 3472 -15030.699672411 eV 2.19708720775972 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01