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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -53.112931 0.0000000) to (18.778257 53.112931 4.0498230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8037401 4.9407377 4.0498230 Created 344 atoms using lattice units in orthogonal box = (0.0000000 -53.112931 0.0000000) to (18.778257 53.112931 4.0498230) create_atoms CPU = 0.001 seconds 344 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8037401 4.9407377 4.0498230 Created 346 atoms using lattice units in orthogonal box = (0.0000000 -53.112931 0.0000000) to (18.778257 53.112931 4.0498230) create_atoms CPU = 0.001 seconds 346 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 = 7 36 2 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 2 atoms, new total = 688 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_179158257180_001#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 ghost atom cutoff = 6 binsize = 3, bins = 7 36 2 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) = 4.527 | 4.527 | 4.527 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2441.0759 0 -2441.0759 99322.031 116 0 -2941.1637 0 -2941.1637 5784.2264 Loop time of 3.70934 on 1 procs for 116 steps with 688 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2441.07593623479 -2941.16123052935 -2941.16367127723 Force two-norm initial, final = 994.38910 0.14865494 Force max component initial, final = 274.02862 0.024253819 Final line search alpha, max atom move = 1.0000000 0.024253819 Iterations, force evaluations = 116 210 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.683 | 3.683 | 3.683 | 0.0 | 99.29 Neigh | 0.01077 | 0.01077 | 0.01077 | 0.0 | 0.29 Comm | 0.0084211 | 0.0084211 | 0.0084211 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007127 | | | 0.19 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4336.00 ave 4336 max 4336 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: 44236.0 ave 44236 max 44236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44236 Ave neighs/atom = 64.296512 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 7 36 2 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 : 116 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.527 | 4.527 | 4.527 Mbytes Step Temp E_pair E_mol TotEng Press Volume 116 0 -2941.1637 0 -2941.1637 5784.2264 8078.3298 121 0 -2941.2826 0 -2941.2826 -25.78326 8105.3817 Loop time of 0.136963 on 1 procs for 5 steps with 688 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 = -2941.16367127723 -2941.28260906263 -2941.28264662987 Force two-norm initial, final = 65.200802 0.29042736 Force max component initial, final = 62.445116 0.13638664 Final line search alpha, max atom move = 0.0013344453 0.00018200051 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13554 | 0.13554 | 0.13554 | 0.0 | 98.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00026349 | 0.00026349 | 0.00026349 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001156 | | | 0.84 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4336.00 ave 4336 max 4336 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: 44272.0 ave 44272 max 44272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44272 Ave neighs/atom = 64.348837 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 = 7 36 2 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.665 | 4.665 | 4.665 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2941.2826 0 -2941.2826 -25.78326 Loop time of 1.635e-06 on 1 procs for 0 steps with 688 atoms 183.5% 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 | | 1.635e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4336.00 ave 4336 max 4336 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: 44256.0 ave 44256 max 44256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44256 Ave neighs/atom = 64.325581 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 = 7 36 2 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 bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 4.665 | 4.665 | 4.665 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 -2941.2826 -2941.2826 18.783137 106.63727 4.0466566 -25.78326 -25.78326 -25.606007 -27.063717 -24.680056 2.3004387 323.65957 Loop time of 1.857e-06 on 1 procs for 0 steps with 688 atoms 215.4% 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 | | 1.857e-06 | | |100.00 Nlocal: 688.000 ave 688 max 688 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4336.00 ave 4336 max 4336 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 22128.0 ave 22128 max 22128 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 44256.0 ave 44256 max 44256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44256 Ave neighs/atom = 64.325581 Neighbor list builds = 0 Dangerous builds = 0 688 -2941.28264662987 eV 2.30043873668366 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04