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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -56.641208 0.0000000) to (40.049157 56.641208 4.4499063) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4387744 5.2442649 4.4499063 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -56.641208 0.0000000) to (40.049157 56.641208 4.4499063) create_atoms CPU = 0.006 seconds 650 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4387744 5.2442649 4.4499063 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -56.641208 0.0000000) to (40.049157 56.641208 4.4499063) create_atoms CPU = 0.006 seconds 650 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 40 2 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1296 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.633 | 4.633 | 4.633 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8735.9354 0 -8735.9354 18752.744 19 0 -8798.2475 0 -8798.2475 4912.4523 Loop time of 2.2963 on 1 procs for 19 steps with 1296 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 = -8735.93541194359 -8798.24235729831 -8798.24750458015 Force two-norm initial, final = 42.423345 0.26325574 Force max component initial, final = 8.6249547 0.047686557 Final line search alpha, max atom move = 1.0000000 0.047686557 Iterations, force evaluations = 19 29 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2874 | 2.2874 | 2.2874 | 0.0 | 99.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0037093 | 0.0037093 | 0.0037093 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005179 | | | 0.23 Nlocal: 1296.00 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5131.00 ave 5131 max 5131 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: 74832.0 ave 74832 max 74832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74832 Ave neighs/atom = 57.740741 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.633 | 4.633 | 4.633 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -8798.2475 0 -8798.2475 4912.4523 20188.626 21 0 -8798.2964 0 -8798.2964 896.81672 20219.061 Loop time of 0.460987 on 1 procs for 2 steps with 1296 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 = -8798.24750458015 -8798.29396246542 -8798.29641113476 Force two-norm initial, final = 82.983693 0.26862956 Force max component initial, final = 69.829759 0.047694433 Final line search alpha, max atom move = 0.00010978588 5.2361754e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.45729 | 0.45729 | 0.45729 | 0.0 | 99.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00064853 | 0.00064853 | 0.00064853 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003044 | | | 0.66 Nlocal: 1296.00 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5139.00 ave 5139 max 5139 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: 74832.0 ave 74832 max 74832 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74832 Ave neighs/atom = 57.740741 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.771 | 4.771 | 4.771 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8798.2964 0 -8798.2964 896.81672 Loop time of 6.245e-06 on 1 procs for 0 steps with 1296 atoms 176.1% 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 | | 6.245e-06 | | |100.00 Nlocal: 1296.00 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5139.00 ave 5139 max 5139 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: 74816.0 ave 74816 max 74816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74816 Ave neighs/atom = 57.728395 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 14 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.771 | 4.771 | 4.771 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 -8798.2964 -8798.2964 40.097801 113.28242 4.4512083 896.81672 896.81672 -0.21849836 2691.6944 -1.0257016 2.4490847 591.54011 Loop time of 6.716e-06 on 1 procs for 0 steps with 1296 atoms 297.8% 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 | | 6.716e-06 | | |100.00 Nlocal: 1296.00 ave 1296 max 1296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5139.00 ave 5139 max 5139 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 37408.0 ave 37408 max 37408 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 74816.0 ave 74816 max 74816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 74816 Ave neighs/atom = 57.728395 Neighbor list builds = 0 Dangerous builds = 0 1296 -8798.29641113476 eV 2.44908468870363 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03