LAMMPS (24 Dec 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 = 3.6041287 3.6041287 3.6041287 Created orthogonal box = (0.0000000 -53.339838 0.0000000) to (43.548852 53.339838 8.8282762) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3690366 5.1144334 5.8855175 Created 1755 atoms create_atoms CPU = 0.001 seconds 1755 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3690366 5.1144334 5.8855175 Created 1755 atoms create_atoms CPU = 0.001 seconds 1755 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 33 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 51 atoms, new total = 3459 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 33 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 6.101 | 6.101 | 6.101 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14246.653 0 -14246.653 6888.5742 531 0 -14534.819 0 -14534.819 -16304.878 Loop time of 43.5229 on 1 procs for 531 steps with 3459 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 = -14246.6528871819 -14534.8045808863 -14534.8186225816 Force two-norm initial, final = 125.05244 0.51251306 Force max component initial, final = 16.663709 0.17180809 Final line search alpha, max atom move = 0.37434760 0.064315946 Iterations, force evaluations = 531 1035 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 43.32 | 43.32 | 43.32 | 0.0 | 99.53 Neigh | 0.092217 | 0.092217 | 0.092217 | 0.0 | 0.21 Comm | 0.049756 | 0.049756 | 0.049756 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06099 | | | 0.14 Nlocal: 3459.00 ave 3459 max 3459 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9012.00 ave 9012 max 9012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 334792.0 ave 334792 max 334792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 334792 Ave neighs/atom = 96.788667 Neighbor list builds = 10 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:188) Setting up cg style minimization ... Unit style : metal Current step : 531 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.104 | 6.104 | 6.104 Mbytes Step Temp E_pair E_mol TotEng Press Volume 531 0 -14534.819 0 -14534.819 -16304.878 41014.206 536 0 -14536.41 0 -14536.41 -3115.9622 40688.095 Loop time of 0.280042 on 1 procs for 5 steps with 3459 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 = -14534.8186225815 -14536.4006794053 -14536.4104181811 Force two-norm initial, final = 560.39945 9.1831044 Force max component initial, final = 417.66453 8.3436490 Final line search alpha, max atom move = 2.5487554e-05 0.00021265921 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27834 | 0.27834 | 0.27834 | 0.0 | 99.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0003157 | 0.0003157 | 0.0003157 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00139 | | | 0.50 Nlocal: 3459.00 ave 3459 max 3459 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9008.00 ave 9008 max 9008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 335126.0 ave 335126 max 335126 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 335126 Ave neighs/atom = 96.885227 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 14 33 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 6.242 | 6.242 | 6.242 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14536.41 0 -14536.41 -3115.9622 Loop time of 2.00002e-06 on 1 procs for 0 steps with 3459 atoms 150.0% 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 | | 2e-06 | | |100.00 Nlocal: 3459.00 ave 3459 max 3459 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9047.00 ave 9047 max 9047 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 337586.0 ave 337586 max 337586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 337586 Ave neighs/atom = 97.596415 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) = 6.242 | 6.242 | 6.242 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 -14536.41 -14536.41 43.356515 106.67968 8.7969334 -3115.9622 -3115.9622 -145.80414 -9529.4641 327.38172 2.2631649 10889.952 Loop time of 2.20002e-06 on 1 procs for 0 steps with 3459 atoms 181.8% 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 | | 2.2e-06 | | |100.00 Nlocal: 3459.00 ave 3459 max 3459 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9047.00 ave 9047 max 9047 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 168793.0 ave 168793 max 168793 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 337586.0 ave 337586 max 337586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 337586 Ave neighs/atom = 97.596415 Neighbor list builds = 0 Dangerous builds = 0 3459 -14536.4104181811 eV 2.26316487484481 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:44