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 = 3.5213918 3.5213918 3.5213918 Created orthogonal box = (0.0000000 -69.723521 0.0000000) to (42.694606 69.723521 8.6256130) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9374715 4.9800000 5.7504087 Created 2356 atoms create_atoms CPU = 0.001 seconds 2356 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9374715 4.9800000 5.7504087 Created 2356 atoms create_atoms CPU = 0.001 seconds 2356 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 ghost atom cutoff = 6 binsize = 3, bins = 15 47 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 56 atoms, new total = 4656 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 ghost atom cutoff = 6 binsize = 3, bins = 15 47 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 6.255 | 6.255 | 6.255 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20591.493 0 -20591.493 -832.23457 26 0 -20647.433 0 -20647.433 -9619.145 Loop time of 2.98606 on 1 procs for 26 steps with 4656 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 = -20591.4933715991 -20647.4151090204 -20647.4334979883 Force two-norm initial, final = 79.617116 0.53044845 Force max component initial, final = 16.262180 0.067247191 Final line search alpha, max atom move = 1.0000000 0.067247191 Iterations, force evaluations = 26 45 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9788 | 2.9788 | 2.9788 | 0.0 | 99.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0030605 | 0.0030605 | 0.0030605 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004177 | | | 0.14 Nlocal: 4656.00 ave 4656 max 4656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10917.0 ave 10917 max 10917 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: 360408.0 ave 360408 max 360408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 360408 Ave neighs/atom = 77.407216 Neighbor list builds = 0 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 : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.255 | 6.255 | 6.255 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -20647.433 0 -20647.433 -9619.145 51353.765 29 0 -20647.955 0 -20647.955 -2454.1491 51153.29 Loop time of 0.397938 on 1 procs for 3 steps with 4656 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 = -20647.4334979883 -20647.9543175016 -20647.9551694593 Force two-norm initial, final = 376.36753 0.66886024 Force max component initial, final = 266.75685 0.095892338 Final line search alpha, max atom move = 0.00013036866 1.2501355e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39595 | 0.39595 | 0.39595 | 0.0 | 99.50 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.000364 | 0.000364 | 0.000364 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001622 | | | 0.41 Nlocal: 4656.00 ave 4656 max 4656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10953.0 ave 10953 max 10953 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: 361896.0 ave 361896 max 361896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 361896 Ave neighs/atom = 77.726804 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 ghost atom cutoff = 6 binsize = 3, bins = 15 47 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 6.393 | 6.393 | 6.393 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -20647.955 0 -20647.955 -2454.1491 Loop time of 2.00002e-06 on 1 procs for 0 steps with 4656 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: 4656.00 ave 4656 max 4656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10953.0 ave 10953 max 10953 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: 361968.0 ave 361968 max 361968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 361968 Ave neighs/atom = 77.742268 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) = 6.393 | 6.393 | 6.393 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 -20647.955 -20647.955 42.604595 139.44704 8.6100927 -2454.1491 -2454.1491 0.66443758 -7362.5781 -0.53375493 2.2016861 1744.8866 Loop time of 2.39999e-06 on 1 procs for 0 steps with 4656 atoms 125.0% 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 | | 2.4e-06 | | |100.00 Nlocal: 4656.00 ave 4656 max 4656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10953.0 ave 10953 max 10953 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 180984.0 ave 180984 max 180984 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 361968.0 ave 361968 max 361968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 361968 Ave neighs/atom = 77.742268 Neighbor list builds = 0 Dangerous builds = 0 4656 -20647.9551694593 eV 2.20168610170789 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03