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 -48.936460 0.0000000) to (59.934678 48.936460 9.9204585) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7471609 6.0332622 6.6136390 Created 1750 atoms using lattice units in orthogonal box = (0.0000000 -48.936460 0.0000000) to (59.934678 48.936460 9.9204585) create_atoms CPU = 0.002 seconds 1750 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7471609 6.0332622 6.6136390 Created 1756 atoms using lattice units in orthogonal box = (0.0000000 -48.936460 0.0000000) to (59.934678 48.936460 9.9204585) create_atoms CPU = 0.002 seconds 1756 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 = 16 26 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 26 atoms, new total = 3480 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 = 16 26 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) = 6.518 | 6.518 | 6.518 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10561.019 0 -10561.019 544117.68 91 0 -11767.07 0 -11767.07 -2195.0634 Loop time of 2.59676 on 1 procs for 91 steps with 3480 atoms 97.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10561.019235847 -11767.0590147841 -11767.069601862 Force two-norm initial, final = 24153.875 0.22977392 Force max component initial, final = 4814.8014 0.018022518 Final line search alpha, max atom move = 1.0000000 0.018022518 Iterations, force evaluations = 91 143 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4429 | 2.4429 | 2.4429 | 0.0 | 94.08 Neigh | 0.11402 | 0.11402 | 0.11402 | 0.0 | 4.39 Comm | 0.015085 | 0.015085 | 0.015085 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02471 | | | 0.95 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9301.00 ave 9301 max 9301 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: 391752.0 ave 391752 max 391752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 391752 Ave neighs/atom = 112.57241 Neighbor list builds = 4 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 = 16 26 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 : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.133 | 6.133 | 6.133 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -11767.07 0 -11767.07 -2195.0634 58193.23 95 0 -11767.246 0 -11767.246 37.48077 58022.995 Loop time of 0.122855 on 1 procs for 4 steps with 3480 atoms 94.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11767.069601862 -11767.2455182278 -11767.2460080745 Force two-norm initial, final = 147.44125 3.5518516 Force max component initial, final = 116.27782 3.3306397 Final line search alpha, max atom move = 0.00014687033 0.00048917215 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.11917 | 0.11917 | 0.11917 | 0.0 | 97.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049332 | 0.00049332 | 0.00049332 | 0.0 | 0.40 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003196 | | | 2.60 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9125.00 ave 9125 max 9125 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: 382264.0 ave 382264 max 382264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 382264 Ave neighs/atom = 109.84598 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 = 16 26 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) = 6.653 | 6.653 | 6.653 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11767.246 0 -11767.246 37.48077 Loop time of 3.789e-06 on 1 procs for 0 steps with 3480 atoms 184.7% 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 | | 3.789e-06 | | |100.00 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9125.00 ave 9125 max 9125 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: 403170.0 ave 403170 max 403170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 403170 Ave neighs/atom = 115.85345 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 = 16 26 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) = 6.653 | 6.653 | 6.653 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 -11767.246 -11767.246 59.889495 97.600415 9.9265383 37.48077 37.48077 91.898908 31.414876 -10.871474 2.6648366 1809.1636 Loop time of 2.429e-06 on 1 procs for 0 steps with 3480 atoms 247.0% 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 | | 2.429e-06 | | |100.00 Nlocal: 3480.00 ave 3480 max 3480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9125.00 ave 9125 max 9125 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 201585.0 ave 201585 max 201585 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 403170.0 ave 403170 max 403170 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 403170 Ave neighs/atom = 115.85345 Neighbor list builds = 0 Dangerous builds = 0 3480 -11767.2460080745 eV 2.66483661687271 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03