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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -53.154354 0.0000000) to (37.583315 53.154354 4.9780317) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9342077 6.0610600 4.9780317 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -53.154354 0.0000000) to (37.583315 53.154354 4.9780317) create_atoms CPU = 0.002 seconds 916 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9342077 6.0610600 4.9780317 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -53.154354 0.0000000) to (37.583315 53.154354 4.9780317) create_atoms CPU = 0.002 seconds 916 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 25 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1816 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_266134052596_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 6.408 | 6.408 | 6.408 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8026.7709 0 -8026.7709 4002.3022 43 0 -8061.5143 0 -8061.5143 -2599.2516 Loop time of 1.8083 on 1 procs for 43 steps with 1816 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 = -8026.77087813473 -8061.50628933561 -8061.51428100396 Force two-norm initial, final = 27.252361 0.30779922 Force max component initial, final = 4.9883236 0.021685344 Final line search alpha, max atom move = 1.0000000 0.021685344 Iterations, force evaluations = 43 71 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7697 | 1.7697 | 1.7697 | 0.0 | 97.87 Neigh | 0.024709 | 0.024709 | 0.024709 | 0.0 | 1.37 Comm | 0.0076404 | 0.0076404 | 0.0076404 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00623 | | | 0.34 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12107.0 ave 12107 max 12107 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: 449544.0 ave 449544 max 449544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 449544 Ave neighs/atom = 247.54626 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.408 | 6.408 | 6.408 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -8061.5143 0 -8061.5143 -2599.2516 19889.396 45 0 -8061.5358 0 -8061.5358 -842.82077 19869.82 Loop time of 0.125656 on 1 procs for 2 steps with 1816 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 = -8061.51428100396 -8061.53400375198 -8061.53578139628 Force two-norm initial, final = 43.959670 0.31102071 Force max component initial, final = 42.093361 0.039051302 Final line search alpha, max atom move = 0.00010965483 4.2821638e-06 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12349 | 0.12349 | 0.12349 | 0.0 | 98.27 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00043401 | 0.00043401 | 0.00043401 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001734 | | | 1.38 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12116.0 ave 12116 max 12116 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: 449440.0 ave 449440 max 449440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 449440 Ave neighs/atom = 247.48899 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 6.546 | 6.546 | 6.546 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8061.5358 0 -8061.5358 -842.82077 Loop time of 2.127e-06 on 1 procs for 0 steps with 1816 atoms 141.0% 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 | | 2.127e-06 | | |100.00 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12116.0 ave 12116 max 12116 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: 449472.0 ave 449472 max 449472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 449472 Ave neighs/atom = 247.50661 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 6.546 | 6.546 | 6.546 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 -8061.5358 -8061.5358 37.544396 106.30871 4.9782874 -842.82077 -842.82077 0.11112022 -2525.4244 -3.1490116 2.3011817 603.94829 Loop time of 2.157e-06 on 1 procs for 0 steps with 1816 atoms 231.8% 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 | | 2.157e-06 | | |100.00 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12116.0 ave 12116 max 12116 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 224736.0 ave 224736 max 224736 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 449472.0 ave 449472 max 449472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 449472 Ave neighs/atom = 247.50661 Neighbor list builds = 0 Dangerous builds = 0 1816 -8061.53578139628 eV 2.30118166700886 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02