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 = 4.0500102 4.0500102 4.0500102 Created orthogonal box = (0.0000000 -80.186111 0.0000000) to (49.103764 80.186111 9.9204585) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6786666 5.7275794 6.6136390 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -80.186111 0.0000000) to (49.103764 80.186111 9.9204585) create_atoms CPU = 0.003 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6786666 5.7275794 6.6136390 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -80.186111 0.0000000) to (49.103764 80.186111 9.9204585) create_atoms CPU = 0.003 seconds 2358 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 13 43 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 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 30 atoms, new total = 4680 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_120808805541_005#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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 13 43 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 11.41 | 11.41 | 11.41 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15444.018 0 -15444.018 12086.47 99 0 -15829.627 0 -15829.627 -902.7254 Loop time of 4.62793 on 1 procs for 99 steps with 4680 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15444.0182035916 -15829.6134079422 -15829.6272720334 Force two-norm initial, final = 410.78482 0.29165000 Force max component initial, final = 74.759655 0.036878825 Final line search alpha, max atom move = 1.0000000 0.036878825 Iterations, force evaluations = 99 182 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.433 | 4.433 | 4.433 | 0.0 | 95.79 Neigh | 0.12239 | 0.12239 | 0.12239 | 0.0 | 2.64 Comm | 0.027372 | 0.027372 | 0.027372 | 0.0 | 0.59 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0452 | | | 0.98 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12371.0 ave 12371 max 12371 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: 541704.0 ave 541704 max 541704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 541704 Ave neighs/atom = 115.74872 Neighbor list builds = 3 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 13 43 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 99 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.04 | 11.04 | 11.04 Mbytes Step Temp E_pair E_mol TotEng Press Volume 99 0 -15829.627 0 -15829.627 -902.7254 78122.418 101 0 -15829.673 0 -15829.673 -2.2010062 78030.381 Loop time of 0.131996 on 1 procs for 2 steps with 4680 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 = -15829.6272720334 -15829.6624008863 -15829.6728681915 Force two-norm initial, final = 83.153595 5.0246006 Force max component initial, final = 63.873246 4.0210234 Final line search alpha, max atom move = 4.3487890e-05 0.00017486583 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12762 | 0.12762 | 0.12762 | 0.0 | 96.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00059325 | 0.00059325 | 0.00059325 | 0.0 | 0.45 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003786 | | | 2.87 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12095.0 ave 12095 max 12095 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: 576072.0 ave 576072 max 576072 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 576072 Ave neighs/atom = 123.09231 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 13 43 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 10.55 | 10.55 | 10.55 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15829.673 0 -15829.673 -2.2010062 Loop time of 1.983e-06 on 1 procs for 0 steps with 4680 atoms 201.7% 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 | | 1.983e-06 | | |100.00 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12095.0 ave 12095 max 12095 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: 581244.0 ave 581244 max 581244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 581244 Ave neighs/atom = 124.19744 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 = 7.58441 ghost atom cutoff = 7.58441 binsize = 3.792205, bins = 13 43 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.58441 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) = 10.55 | 10.55 | 10.55 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 -15829.673 -15829.673 49.071622 160.45936 9.9098766 -2.2010062 -2.2010062 -82.508533 16.708318 59.197197 2.5477137 2158.6634 Loop time of 2.654e-06 on 1 procs for 0 steps with 4680 atoms 339.1% 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 | | 2.654e-06 | | |100.00 Nlocal: 4680.00 ave 4680 max 4680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12095.0 ave 12095 max 12095 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 290622.0 ave 290622 max 290622 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 581244.0 ave 581244 max 581244 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 581244 Ave neighs/atom = 124.19744 Neighbor list builds = 0 Dangerous builds = 0 4680 -15829.6728681915 eV 2.54771374464293 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05