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 = 3.1582519 3.1582519 3.1582519 Created orthogonal box = (0.0000000 -45.984842 0.0000000) to (22.992421 45.984842 3.1582519) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.9043734 3.9043734 3.1582519 Created 212 atoms using lattice units in orthogonal box = (0.0000000 -45.984842 0.0000000) to (22.992421 45.984842 3.1582519) create_atoms CPU = 0.002 seconds 212 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.9043734 3.9043734 3.1582519 Created 213 atoms using lattice units in orthogonal box = (0.0000000 -45.984842 0.0000000) to (22.992421 45.984842 3.1582519) create_atoms CPU = 0.001 seconds 213 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 6 22 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 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 425 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_228581001644_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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 6 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.481 | 4.481 | 4.481 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2492.2059 0 -2492.2059 108624.04 62 0 -2691.2228 0 -2691.2228 23154.439 Loop time of 0.855611 on 1 procs for 62 steps with 425 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 = -2492.20591118132 -2691.22030831286 -2691.2227953335 Force two-norm initial, final = 259.26588 0.29146312 Force max component initial, final = 85.647724 0.098492471 Final line search alpha, max atom move = 0.90414580 0.089051554 Iterations, force evaluations = 62 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.82304 | 0.82304 | 0.82304 | 0.0 | 96.19 Neigh | 0.0099374 | 0.0099374 | 0.0099374 | 0.0 | 1.16 Comm | 0.013783 | 0.013783 | 0.013783 | 0.0 | 1.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008854 | | | 1.03 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5223.00 ave 5223 max 5223 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: 70612.0 ave 70612 max 70612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70612 Ave neighs/atom = 166.14588 Neighbor list builds = 1 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 6 22 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 62 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.481 | 4.481 | 4.481 Mbytes Step Temp E_pair E_mol TotEng Press Volume 62 0 -2691.2228 0 -2691.2228 23154.439 6678.4576 167 0 -2699.016 0 -2699.016 -984.19569 6731.5215 Loop time of 1.05332 on 1 procs for 105 steps with 425 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 = -2691.22279533351 -2699.01343945728 -2699.01603978389 Force two-norm initial, final = 226.58120 8.3280886 Force max component initial, final = 177.94576 5.2162652 Final line search alpha, max atom move = 0.00013920075 0.00072610806 Iterations, force evaluations = 105 128 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.95963 | 0.95963 | 0.95963 | 0.0 | 91.11 Neigh | 0.028731 | 0.028731 | 0.028731 | 0.0 | 2.73 Comm | 0.016357 | 0.016357 | 0.016357 | 0.0 | 1.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0486 | | | 4.61 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5163.00 ave 5163 max 5163 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: 69048.0 ave 69048 max 69048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69048 Ave neighs/atom = 162.46588 Neighbor list builds = 3 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 6 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.619 | 4.619 | 4.619 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2699.016 0 -2699.016 -984.19569 Loop time of 6.856e-06 on 1 procs for 0 steps with 425 atoms 204.2% 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 | | 6.856e-06 | | |100.00 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5151.00 ave 5151 max 5151 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: 68708.0 ave 68708 max 68708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68708 Ave neighs/atom = 161.66588 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 6 23 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.619 | 4.619 | 4.619 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 -2699.016 -2699.016 23.612049 95.167666 2.9956436 -984.19569 -984.19569 -1064.9474 -1284.6994 -602.9403 2.6430883 542.5396 Loop time of 6.656e-06 on 1 procs for 0 steps with 425 atoms 300.5% 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 | | 6.656e-06 | | |100.00 Nlocal: 425.000 ave 425 max 425 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5151.00 ave 5151 max 5151 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34354.0 ave 34354 max 34354 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 68708.0 ave 68708 max 68708 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68708 Ave neighs/atom = 161.66588 Neighbor list builds = 0 Dangerous builds = 0 425 -2699.01603978388 eV 2.64308829703157 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02