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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -71.459230 0.0000000) to (41.254670 71.459230 7.0067573) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3468723 6.4126448 7.0067573 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -71.459230 0.0000000) to (41.254670 71.459230 7.0067573) create_atoms CPU = 0.008 seconds 1251 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3468723 6.4126448 7.0067573 Created 1251 atoms using lattice units in orthogonal box = (0.0000000 -71.459230 0.0000000) to (41.254670 71.459230 7.0067573) create_atoms CPU = 0.008 seconds 1251 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 46 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 2488 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 46 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.300 | 5.300 | 5.300 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8310.6022 0 -8310.6022 2530.165 35 0 -8338.3841 0 -8338.3841 799.35608 Loop time of 11.7515 on 1 procs for 35 steps with 2488 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 = -8310.6022120458 -8338.37600452309 -8338.38409123277 Force two-norm initial, final = 29.847124 0.29701431 Force max component initial, final = 3.4757813 0.054176460 Final line search alpha, max atom move = 1.0000000 0.054176460 Iterations, force evaluations = 35 67 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 11.722 | 11.722 | 11.722 | 0.0 | 99.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.012409 | 0.012409 | 0.012409 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01668 | | | 0.14 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8048.00 ave 8048 max 8048 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: 134624.0 ave 134624 max 134624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134624 Ave neighs/atom = 54.109325 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 46 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 35 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.300 | 5.300 | 5.300 Mbytes Step Temp E_pair E_mol TotEng Press Volume 35 0 -8338.3841 0 -8338.3841 799.35608 41312.219 36 0 -8338.3869 0 -8338.3869 750.5343 41314.903 Loop time of 0.509521 on 1 procs for 1 steps with 2488 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8338.3840912327 -8338.3840912327 -8338.38694913664 Force two-norm initial, final = 9.2997109 1.1250688 Force max component initial, final = 7.0459379 0.80366408 Final line search alpha, max atom move = 0.00014192575 0.00011406062 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.50714 | 0.50714 | 0.50714 | 0.0 | 99.53 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00054257 | 0.00054257 | 0.00054257 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001843 | | | 0.36 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8039.00 ave 8039 max 8039 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: 134960.0 ave 134960 max 134960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134960 Ave neighs/atom = 54.244373 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 46 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.438 | 5.438 | 5.438 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8338.3869 0 -8338.3869 750.5343 Loop time of 6.645e-06 on 1 procs for 0 steps with 2488 atoms 180.6% 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: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8039.00 ave 8039 max 8039 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: 134944.0 ave 134944 max 134944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134944 Ave neighs/atom = 54.237942 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 14 46 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.438 | 5.438 | 5.438 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 -8338.3869 -8338.3869 41.273926 142.91846 7.0039434 750.5343 750.5343 -28.189036 2310.9452 -31.153276 2.5414635 1086.4462 Loop time of 7.297e-06 on 1 procs for 0 steps with 2488 atoms 274.1% 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 | | 7.297e-06 | | |100.00 Nlocal: 2488.00 ave 2488 max 2488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8039.00 ave 8039 max 8039 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 67472.0 ave 67472 max 67472 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 134944.0 ave 134944 max 134944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 134944 Ave neighs/atom = 54.237942 Neighbor list builds = 0 Dangerous builds = 0 2488 -8338.38694913664 eV 2.5414634669637 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:13