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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -43.807450 0.0000000) to (14.602483 43.807450 4.0500001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6163397 5.6163397 4.0500001 Created 156 atoms using lattice units in orthogonal box = (0.0000000 -43.807450 0.0000000) to (14.602483 43.807450 4.0500001) create_atoms CPU = 0.002 seconds 156 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6163397 5.6163397 4.0500001 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -43.807450 0.0000000) to (14.602483 43.807450 4.0500001) create_atoms CPU = 0.001 seconds 158 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 4 21 1 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 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 312 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_678952612413_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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 4 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 4.460 | 4.460 | 4.460 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1035.7587 0 -1035.7587 3877.5616 17 0 -1044.9991 0 -1044.9991 4164.0184 Loop time of 0.196984 on 1 procs for 17 steps with 312 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1035.75872656267 -1044.99845716666 -1044.9991338125 Force two-norm initial, final = 10.303560 0.066267311 Force max component initial, final = 2.6508788 0.022309411 Final line search alpha, max atom move = 1.0000000 0.022309411 Iterations, force evaluations = 17 29 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19247 | 0.19247 | 0.19247 | 0.0 | 97.71 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0024382 | 0.0024382 | 0.0024382 | 0.0 | 1.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002074 | | | 1.05 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3788.00 ave 3788 max 3788 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: 44120.0 ave 44120 max 44120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44120 Ave neighs/atom = 141.41026 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 4 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 17 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.459 | 4.459 | 4.459 Mbytes Step Temp E_pair E_mol TotEng Press Volume 17 0 -1044.9991 0 -1044.9991 4164.0184 5181.5503 28 0 -1045.1497 0 -1045.1497 5.7655333 5208.5464 Loop time of 0.0874649 on 1 procs for 11 steps with 312 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 = -1044.9991338125 -1045.14922598677 -1045.14969780631 Force two-norm initial, final = 31.889754 0.25072693 Force max component initial, final = 31.154131 0.12254756 Final line search alpha, max atom move = 0.00095893691 0.00011751538 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.083184 | 0.083184 | 0.083184 | 0.0 | 95.11 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010006 | 0.0010006 | 0.0010006 | 0.0 | 1.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00328 | | | 3.75 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3743.00 ave 3743 max 3743 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: 44188.0 ave 44188 max 44188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44188 Ave neighs/atom = 141.62821 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 4 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 4.597 | 4.597 | 4.597 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1045.1497 0 -1045.1497 5.7655333 Loop time of 6.645e-06 on 1 procs for 0 steps with 312 atoms 195.6% 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 | | 6.645e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3743.00 ave 3743 max 3743 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: 43968.0 ave 43968 max 43968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43968 Ave neighs/atom = 140.92308 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 = 8.499539 ghost atom cutoff = 8.499539 binsize = 4.2497695, bins = 4 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.499539 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) = 4.597 | 4.597 | 4.597 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 -1045.1497 -1045.1497 14.562253 88.540446 4.0396736 5.7655333 5.7655333 37.592424 -9.0459527 -11.249871 2.5988757 207.77684 Loop time of 6.495e-06 on 1 procs for 0 steps with 312 atoms 200.2% 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 | | 6.495e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3743.00 ave 3743 max 3743 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 21984.0 ave 21984 max 21984 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 43968.0 ave 43968 max 43968 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 43968 Ave neighs/atom = 140.92308 Neighbor list builds = 0 Dangerous builds = 0 312 -1045.14969780631 eV 2.59887571434422 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00