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 = 2.8638485 2.8638485 2.8638485 Created orthogonal box = (0.0000000 -51.549273 0.0000000) to (36.450841 51.549273 4.0500934) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9501142 4.7730809 4.0500934 Created 648 atoms using lattice units in orthogonal box = (0.0000000 -51.549273 0.0000000) to (36.450841 51.549273 4.0500934) create_atoms CPU = 0.002 seconds 648 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9501142 4.7730809 4.0500934 Created 650 atoms using lattice units in orthogonal box = (0.0000000 -51.549273 0.0000000) to (36.450841 51.549273 4.0500934) create_atoms CPU = 0.002 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 7 18 1 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 1290 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_147603128437_004#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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 7 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 11.41 | 11.41 | 11.41 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4950.7236 0 -4950.7236 43441.142 107 0 -5373.0205 0 -5373.0205 -4281.4343 Loop time of 6.35906 on 1 procs for 107 steps with 1290 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4950.7235649232 -5373.01586633064 -5373.02048148946 Force two-norm initial, final = 615.03386 0.29660943 Force max component initial, final = 200.47488 0.052033777 Final line search alpha, max atom move = 1.0000000 0.052033777 Iterations, force evaluations = 107 178 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.142 | 6.142 | 6.142 | 0.0 | 96.59 Neigh | 0.17248 | 0.17248 | 0.17248 | 0.0 | 2.71 Comm | 0.028973 | 0.028973 | 0.028973 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01562 | | | 0.25 Nlocal: 1290.00 ave 1290 max 1290 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15804.0 ave 15804 max 15804 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: 780352.0 ave 780352 max 780352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 780352 Ave neighs/atom = 604.92403 Neighbor list builds = 5 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 7 18 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 107 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.41 | 11.41 | 11.41 Mbytes Step Temp E_pair E_mol TotEng Press Volume 107 0 -5373.0205 0 -5373.0205 -4281.4343 15220.367 112 0 -5373.2744 0 -5373.2744 -20.538699 15181.945 Loop time of 0.264272 on 1 procs for 5 steps with 1290 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 = -5373.0204814894 -5373.27418959748 -5373.27444550246 Force two-norm initial, final = 125.31853 0.50727424 Force max component initial, final = 114.04364 0.20542557 Final line search alpha, max atom move = 0.00029495191 6.0590663e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25988 | 0.25988 | 0.25988 | 0.0 | 98.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0009006 | 0.0009006 | 0.0009006 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003493 | | | 1.32 Nlocal: 1290.00 ave 1290 max 1290 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15785.0 ave 15785 max 15785 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: 780404.0 ave 780404 max 780404 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 780404 Ave neighs/atom = 604.96434 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 7 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 10.92 | 10.92 | 10.92 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5373.2744 0 -5373.2744 -20.538699 Loop time of 1.924e-06 on 1 procs for 0 steps with 1290 atoms 155.9% 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 | | 1.924e-06 | | |100.00 Nlocal: 1290.00 ave 1290 max 1290 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15804.0 ave 15804 max 15804 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: 780804.0 ave 780804 max 780804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 780804 Ave neighs/atom = 605.27442 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 7 18 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 10.92 | 10.92 | 10.92 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 -5373.2744 -5373.2744 36.510976 103.06745 4.0344325 -20.538699 -20.538699 -21.714674 -20.929752 -18.971672 2.315344 637.28402 Loop time of 2.323e-06 on 1 procs for 0 steps with 1290 atoms 258.3% 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 | | 2.323e-06 | | |100.00 Nlocal: 1290.00 ave 1290 max 1290 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15804.0 ave 15804 max 15804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 390402.0 ave 390402 max 390402 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 780804.0 ave 780804 max 780804 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 780804 Ave neighs/atom = 605.27442 Neighbor list builds = 0 Dangerous builds = 0 1290 -5373.27444550246 eV 2.31534402311478 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07