LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 4.0709491 4.0709491 4.0709491 Created orthogonal box = (0.0000000 -55.966297 0.0000000) to (15.232097 55.966297 9.9717481) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5280415 6.2184775 6.6478321 Created 504 atoms using lattice units in orthogonal box = (0.0000000 -55.966297 0.0000000) to (15.232097 55.966297 9.9717481) create_atoms CPU = 0.001 seconds 504 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5280415 6.2184775 6.6478321 Created 508 atoms using lattice units in orthogonal box = (0.0000000 -55.966297 0.0000000) to (15.232097 55.966297 9.9717481) create_atoms CPU = 0.001 seconds 508 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 37 4 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1008 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_304347095149_000#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 37 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.515 | 4.515 | 4.515 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3352.4212 0 -3352.4212 7919.2838 40 0 -3384.8485 0 -3384.8485 2909.9325 Loop time of 2.44664 on 1 procs for 40 steps with 1008 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 = -3352.42119313303 -3384.84582386781 -3384.84846683744 Force two-norm initial, final = 46.458383 0.10927207 Force max component initial, final = 9.5472643 0.0095658045 Final line search alpha, max atom move = 1.0000000 0.0095658045 Iterations, force evaluations = 40 76 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4384 | 2.4384 | 2.4384 | 0.0 | 99.66 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0033771 | 0.0033771 | 0.0033771 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004848 | | | 0.20 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3472.00 ave 3472 max 3472 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: 54568.0 ave 54568 max 54568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54568 Ave neighs/atom = 54.134921 Neighbor list builds = 0 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 37 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.515 | 4.515 | 4.515 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -3384.8485 0 -3384.8485 2909.9325 17001.513 45 0 -3384.9918 0 -3384.9918 1.9116179 17054.43 Loop time of 0.214389 on 1 procs for 5 steps with 1008 atoms 99.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3384.84846683745 -3384.99020512913 -3384.99179658639 Force two-norm initial, final = 68.973815 0.62468719 Force max component initial, final = 65.711649 0.49879407 Final line search alpha, max atom move = 0.00023791028 0.00011866823 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21269 | 0.21269 | 0.21269 | 0.0 | 99.21 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00023154 | 0.00023154 | 0.00023154 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001468 | | | 0.68 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3559.00 ave 3559 max 3559 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: 54208.0 ave 54208 max 54208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54208 Ave neighs/atom = 53.777778 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 37 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.653 | 4.653 | 4.653 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3384.9918 0 -3384.9918 1.9116179 Loop time of 2.008e-06 on 1 procs for 0 steps with 1008 atoms 149.4% 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 | | 2.008e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3559.00 ave 3559 max 3559 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: 54208.0 ave 54208 max 54208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54208 Ave neighs/atom = 53.777778 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 37 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.653 | 4.653 | 4.653 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 -3384.9918 -3384.9918 15.233454 112.42635 9.9579676 1.9116179 1.9116179 46.863328 -16.59472 -24.533755 2.5295905 490.27988 Loop time of 2.152e-06 on 1 procs for 0 steps with 1008 atoms 185.9% 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 | | 2.152e-06 | | |100.00 Nlocal: 1008.00 ave 1008 max 1008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3559.00 ave 3559 max 3559 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 27104.0 ave 27104 max 27104 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 54208.0 ave 54208 max 54208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 54208 Ave neighs/atom = 53.777778 Neighbor list builds = 0 Dangerous builds = 0 1008 -3384.99179658639 eV 2.52959052495943 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02