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 = 3.5878697 3.5878697 3.5878697 Created orthogonal box = (0.0000000 -42.452247 0.0000000) to (51.993172 42.452247 8.7884501) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9420768 5.4581460 5.8589667 Created 1663 atoms using lattice units in orthogonal box = (0.0000000 -42.452247 0.0000000) to (51.993172 42.452247 8.7884501) create_atoms CPU = 0.003 seconds 1663 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9420768 5.4581460 5.8589667 Created 1687 atoms using lattice units in orthogonal box = (0.0000000 -42.452247 0.0000000) to (51.993172 42.452247 8.7884501) create_atoms CPU = 0.003 seconds 1687 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 = 8.2999891 ghost atom cutoff = 8.2999891 binsize = 4.1499946, bins = 13 21 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 8.299989119441689 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 31 atoms, new total = 3319 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_987541074959_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 = 8.2999891 ghost atom cutoff = 8.2999891 binsize = 4.1499946, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.299989119441689 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) = 7.451 | 7.451 | 7.451 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11529.821 0 -11529.821 8692.3449 189 0 -11641.496 0 -11641.496 -9876.0264 Loop time of 25.29 on 1 procs for 189 steps with 3319 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11529.8209794636 -11641.4857412179 -11641.4960064525 Force two-norm initial, final = 92.321597 0.35477705 Force max component initial, final = 10.122325 0.098334051 Final line search alpha, max atom move = 0.75569571 0.074310620 Iterations, force evaluations = 189 350 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 24.839 | 24.839 | 24.839 | 0.0 | 98.22 Neigh | 0.33409 | 0.33409 | 0.33409 | 0.0 | 1.32 Comm | 0.04931 | 0.04931 | 0.04931 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06777 | | | 0.27 Nlocal: 3319.00 ave 3319 max 3319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11553.0 ave 11553 max 11553 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: 661948.0 ave 661948 max 661948 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 661948 Ave neighs/atom = 199.44200 Neighbor list builds = 8 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 = 8.2999891 ghost atom cutoff = 8.2999891 binsize = 4.1499946, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.299989119441689 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 189 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.449 | 7.449 | 7.449 Mbytes Step Temp E_pair E_mol TotEng Press Volume 189 0 -11641.496 0 -11641.496 -9876.0264 38796.208 194 0 -11642.424 0 -11642.424 -2.9103031 38520.78 Loop time of 0.56026 on 1 procs for 5 steps with 3319 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11641.4960064525 -11642.4208961529 -11642.424107891 Force two-norm initial, final = 419.05276 1.0786304 Force max component initial, final = 284.47797 0.73389675 Final line search alpha, max atom move = 4.2729962e-05 3.1359380e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.55463 | 0.55463 | 0.55463 | 0.0 | 98.99 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00080014 | 0.00080014 | 0.00080014 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004833 | | | 0.86 Nlocal: 3319.00 ave 3319 max 3319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11553.0 ave 11553 max 11553 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: 661978.0 ave 661978 max 661978 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 661978 Ave neighs/atom = 199.45104 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 = 8.2999891 ghost atom cutoff = 8.2999891 binsize = 4.1499946, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.299989119441689 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) = 7.587 | 7.587 | 7.587 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11642.424 0 -11642.424 -2.9103031 Loop time of 2.495e-06 on 1 procs for 0 steps with 3319 atoms 200.4% 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 | | 2.495e-06 | | |100.00 Nlocal: 3319.00 ave 3319 max 3319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11560.0 ave 11560 max 11560 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: 663204.0 ave 663204 max 663204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 663204 Ave neighs/atom = 199.82043 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 = 8.2999891 ghost atom cutoff = 8.2999891 binsize = 4.1499946, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.299989119441689 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) = 7.587 | 7.587 | 7.587 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 -11642.424 -11642.424 51.874474 84.562774 8.7813673 -2.9103031 -2.9103031 30.454933 -17.001141 -22.184701 2.292336 2009.5156 Loop time of 4.338e-06 on 1 procs for 0 steps with 3319 atoms 230.5% 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 | | 4.338e-06 | | |100.00 Nlocal: 3319.00 ave 3319 max 3319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11560.0 ave 11560 max 11560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 331602.0 ave 331602 max 331602 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 663204.0 ave 663204 max 663204 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 663204 Ave neighs/atom = 199.82043 Neighbor list builds = 0 Dangerous builds = 0 3319 -11642.424107891 eV 2.29233596196868 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:26