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 = 3.6583664 3.6583664 3.6583664 Created orthogonal box = (0.0000000 -44.355335 0.0000000) to (36.215979 44.355335 8.9611309) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1737114 5.1295286 5.9740873 Created 1175 atoms using lattice units in orthogonal box = (0.0000000 -44.355335 0.0000000) to (36.215979 44.355335 8.9611309) create_atoms CPU = 0.002 seconds 1175 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1737114 5.1295286 5.9740873 Created 1183 atoms using lattice units in orthogonal box = (0.0000000 -44.355335 0.0000000) to (36.215979 44.355335 8.9611309) create_atoms CPU = 0.001 seconds 1183 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 25 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 7 atoms, new total = 2351 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_807997826449_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.963 | 5.963 | 5.963 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9027.9254 0 -9027.9254 44552.88 853 0 -9490.1693 0 -9490.1693 -48571.263 Loop time of 29.5417 on 1 procs for 853 steps with 2351 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9027.92539186535 -9490.16146172491 -9490.16933465403 Force two-norm initial, final = 518.21798 0.24267371 Force max component initial, final = 80.602758 0.029599820 Final line search alpha, max atom move = 0.84067910 0.024883950 Iterations, force evaluations = 853 1685 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.759 | 28.759 | 28.759 | 0.0 | 97.35 Neigh | 0.41145 | 0.41145 | 0.41145 | 0.0 | 1.39 Comm | 0.1531 | 0.1531 | 0.1531 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.2183 | | | 0.74 Nlocal: 2351.00 ave 2351 max 2351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7682.00 ave 7682 max 7682 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: 324358.0 ave 324358 max 324358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 324358 Ave neighs/atom = 137.96597 Neighbor list builds = 17 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 853 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.963 | 5.963 | 5.963 Mbytes Step Temp E_pair E_mol TotEng Press Volume 853 0 -9490.1693 0 -9490.1693 -48571.263 28789.818 894 0 -9528.5197 0 -9528.5197 -15.119415 27907.598 Loop time of 0.808058 on 1 procs for 41 steps with 2351 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 = -9490.16933465401 -9528.5165211876 -9528.51967200226 Force two-norm initial, final = 1858.3590 7.0888330 Force max component initial, final = 1461.4766 3.4279240 Final line search alpha, max atom move = 0.00016529038 0.00056660287 Iterations, force evaluations = 41 42 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.71211 | 0.71211 | 0.71211 | 0.0 | 88.13 Neigh | 0.071406 | 0.071406 | 0.071406 | 0.0 | 8.84 Comm | 0.0035344 | 0.0035344 | 0.0035344 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02101 | | | 2.60 Nlocal: 2351.00 ave 2351 max 2351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7671.00 ave 7671 max 7671 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: 331130.0 ave 331130 max 331130 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 331130 Ave neighs/atom = 140.84645 Neighbor list builds = 3 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.101 | 6.101 | 6.101 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9528.5197 0 -9528.5197 -15.119415 Loop time of 2.4e-06 on 1 procs for 0 steps with 2351 atoms 166.7% 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 | | 2.4e-06 | | |100.00 Nlocal: 2351.00 ave 2351 max 2351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7656.00 ave 7656 max 7656 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: 331248.0 ave 331248 max 331248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 331248 Ave neighs/atom = 140.89664 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 24 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.101 | 6.101 | 6.101 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 -9528.5197 -9528.5197 35.475994 85.542015 9.1962 -15.119415 -15.119415 24.943814 131.65762 -201.95968 2.2073992 5406.8927 Loop time of 2.57e-06 on 1 procs for 0 steps with 2351 atoms 311.3% 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 | | 2.57e-06 | | |100.00 Nlocal: 2351.00 ave 2351 max 2351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7656.00 ave 7656 max 7656 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 165624.0 ave 165624 max 165624 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 331248.0 ave 331248 max 331248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 331248 Ave neighs/atom = 140.89664 Neighbor list builds = 0 Dangerous builds = 0 2351 -9528.51967200226 eV 2.20739923676534 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:30