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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -30.842533 0.0000000) to (15.421267 30.842533 2.8636573) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7223747 3.7223747 2.8636573 Created 116 atoms using lattice units in orthogonal box = (0.0000000 -30.842533 0.0000000) to (15.421267 30.842533 2.8636573) create_atoms CPU = 0.001 seconds 116 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7223747 3.7223747 2.8636573 Created 117 atoms using lattice units in orthogonal box = (0.0000000 -30.842533 0.0000000) to (15.421267 30.842533 2.8636573) create_atoms CPU = 0.001 seconds 117 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 23 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 233 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_058735400462_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.390 | 4.390 | 4.390 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -942.85814 0 -942.85814 66543.18 29 0 -991.97356 0 -991.97356 19518.907 Loop time of 0.708724 on 1 procs for 29 steps with 233 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 = -942.858141514782 -991.972708882243 -991.973558086738 Force two-norm initial, final = 124.69712 0.098804023 Force max component initial, final = 59.306706 0.021864648 Final line search alpha, max atom move = 1.0000000 0.021864648 Iterations, force evaluations = 29 48 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.70369 | 0.70369 | 0.70369 | 0.0 | 99.29 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026083 | 0.0026083 | 0.0026083 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002426 | | | 0.34 Nlocal: 233.000 ave 233 max 233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2147.00 ave 2147 max 2147 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: 13668.0 ave 13668 max 13668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13668 Ave neighs/atom = 58.660944 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 29 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.390 | 4.390 | 4.390 Mbytes Step Temp E_pair E_mol TotEng Press Volume 29 0 -991.97356 0 -991.97356 19518.907 2724.088 52 0 -992.57338 0 -992.57338 -66.219404 2753.5137 Loop time of 0.407274 on 1 procs for 23 steps with 233 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 = -991.973558086738 -992.573361511736 -992.57338076304 Force two-norm initial, final = 72.860580 0.32860764 Force max component initial, final = 69.603527 0.16658595 Final line search alpha, max atom move = 0.0033084850 0.00055114712 Iterations, force evaluations = 23 27 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39841 | 0.39841 | 0.39841 | 0.0 | 97.82 Neigh | 0.0024884 | 0.0024884 | 0.0024884 | 0.0 | 0.61 Comm | 0.0014637 | 0.0014637 | 0.0014637 | 0.0 | 0.36 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004913 | | | 1.21 Nlocal: 233.000 ave 233 max 233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2127.00 ave 2127 max 2127 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: 13494.0 ave 13494 max 13494 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13494 Ave neighs/atom = 57.914163 Neighbor list builds = 1 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.528 | 4.528 | 4.528 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -992.57338 0 -992.57338 -66.219404 Loop time of 6.636e-06 on 1 procs for 0 steps with 233 atoms 195.9% 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 | | 6.636e-06 | | |100.00 Nlocal: 233.000 ave 233 max 233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2127.00 ave 2127 max 2127 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: 13492.0 ave 13492 max 13492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13492 Ave neighs/atom = 57.905579 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.528 | 4.528 | 4.528 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 -992.57338 -992.57338 15.429174 62.843927 2.8397574 -66.219404 -66.219404 -96.980431 -41.003845 -60.673936 2.2786876 197.33149 Loop time of 6.435e-06 on 1 procs for 0 steps with 233 atoms 186.5% 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 | | 6.435e-06 | | |100.00 Nlocal: 233.000 ave 233 max 233 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2127.00 ave 2127 max 2127 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 6746.00 ave 6746 max 6746 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 13492.0 ave 13492 max 13492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 13492 Ave neighs/atom = 57.905579 Neighbor list builds = 0 Dangerous builds = 0 233 -992.57338076304 eV 2.27868756308451 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01