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 = 3.6135806 3.6135806 3.6135806 Created orthogonal box = (0.0000000 -37.899553 0.0000000) to (46.417283 37.899553 8.8514286) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9076542 5.5126623 5.9009524 Created 1318 atoms using lattice units in orthogonal box = (0.0000000 -37.899553 0.0000000) to (46.417283 37.899553 8.8514286) create_atoms CPU = 0.005 seconds 1318 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9076542 5.5126623 5.9009524 Created 1324 atoms using lattice units in orthogonal box = (0.0000000 -37.899553 0.0000000) to (46.417283 37.899553 8.8514286) create_atoms CPU = 0.005 seconds 1324 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, 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 7.50679 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 14 atoms, new total = 2628 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_426403318662_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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 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) = 6.070 | 6.070 | 6.070 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7456.6412 0 -7456.6412 160899.89 72 0 -9263.1788 0 -9263.1788 741.05635 Loop time of 4.62036 on 1 procs for 72 steps with 2628 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 = -7456.64120377087 -9263.1711936379 -9263.17880773773 Force two-norm initial, final = 2681.7820 0.29403087 Force max component initial, final = 367.59151 0.070882765 Final line search alpha, max atom move = 1.0000000 0.070882765 Iterations, force evaluations = 72 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.3892 | 4.3892 | 4.3892 | 0.0 | 95.00 Neigh | 0.16938 | 0.16938 | 0.16938 | 0.0 | 3.67 Comm | 0.026587 | 0.026587 | 0.026587 | 0.0 | 0.58 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03516 | | | 0.76 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8488.00 ave 8488 max 8488 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: 370158.0 ave 370158 max 370158 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 370158 Ave neighs/atom = 140.85160 Neighbor list builds = 3 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.068 | 6.068 | 6.068 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -9263.1788 0 -9263.1788 741.05635 31142.766 75 0 -9263.306 0 -9263.306 -376.39066 31167.566 Loop time of 0.175176 on 1 procs for 3 steps with 2628 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 = -9263.17880773774 -9263.29733652433 -9263.30596168988 Force two-norm initial, final = 78.778586 13.309171 Force max component initial, final = 65.994240 9.5181128 Final line search alpha, max atom move = 5.2669777e-05 0.00050131688 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17048 | 0.17048 | 0.17048 | 0.0 | 97.32 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00097985 | 0.00097985 | 0.00097985 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003715 | | | 2.12 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8488.00 ave 8488 max 8488 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: 370288.0 ave 370288 max 370288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 370288 Ave neighs/atom = 140.90107 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 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) = 6.206 | 6.206 | 6.206 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9263.306 0 -9263.306 -376.39066 Loop time of 6.054e-06 on 1 procs for 0 steps with 2628 atoms 181.7% 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 | | 6.054e-06 | | |100.00 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8488.00 ave 8488 max 8488 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: 370014.0 ave 370014 max 370014 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 370014 Ave neighs/atom = 140.79680 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 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) = 6.206 | 6.206 | 6.206 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 -9263.306 -9263.306 46.428975 75.990308 8.8339631 -376.39066 -376.39066 -428.47541 -212.38105 -488.31553 2.3150532 1467.3266 Loop time of 6.675e-06 on 1 procs for 0 steps with 2628 atoms 239.7% 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 | | 6.675e-06 | | |100.00 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8488.00 ave 8488 max 8488 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 185007.0 ave 185007 max 185007 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 370014.0 ave 370014 max 370014 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 370014 Ave neighs/atom = 140.79680 Neighbor list builds = 0 Dangerous builds = 0 2628 -9263.31910168988 eV 2.31505323056524 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05