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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -53.058356 0.0000000) to (37.515063 53.058356 5.7209934) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.9795465 6.7860164 5.7209934 Created 691 atoms using lattice units in orthogonal box = (0.0000000 -53.058356 0.0000000) to (37.515063 53.058356 5.7209934) create_atoms CPU = 0.002 seconds 691 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.9795465 6.7860164 5.7209934 Created 691 atoms using lattice units in orthogonal box = (0.0000000 -53.058356 0.0000000) to (37.515063 53.058356 5.7209934) create_atoms CPU = 0.002 seconds 691 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 13 34 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 1358 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 13 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.661 | 4.661 | 4.661 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4541.2135 0 -4541.2135 -2482.0778 66 0 -4549.3248 0 -4549.3248 -5409.0919 Loop time of 5.2781 on 1 procs for 66 steps with 1358 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 = -4541.21346918839 -4549.32101442047 -4549.32477303856 Force two-norm initial, final = 4.2734690 0.15560505 Force max component initial, final = 0.72258456 0.022757652 Final line search alpha, max atom move = 1.0000000 0.022757652 Iterations, force evaluations = 66 125 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2535 | 5.2535 | 5.2535 | 0.0 | 99.53 Neigh | 0.0063697 | 0.0063697 | 0.0063697 | 0.0 | 0.12 Comm | 0.008473 | 0.008473 | 0.008473 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009743 | | | 0.18 Nlocal: 1358.00 ave 1358 max 1358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5212.00 ave 5212 max 5212 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: 73394.0 ave 73394 max 73394 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73394 Ave neighs/atom = 54.045655 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 13 34 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 66 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.662 | 4.662 | 4.662 Mbytes Step Temp E_pair E_mol TotEng Press Volume 66 0 -4549.3248 0 -4549.3248 -5409.0919 22775.132 70 0 -4549.5063 0 -4549.5063 -1401.3528 22648.989 Loop time of 0.297526 on 1 procs for 4 steps with 1358 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 = -4549.32477303857 -4549.50606924909 -4549.5063288392 Force two-norm initial, final = 91.530542 0.19022881 Force max component initial, final = 67.936235 0.025204791 Final line search alpha, max atom move = 0.00066205638 1.6686993e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.29547 | 0.29547 | 0.29547 | 0.0 | 99.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00030856 | 0.00030856 | 0.00030856 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001751 | | | 0.59 Nlocal: 1358.00 ave 1358 max 1358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5249.00 ave 5249 max 5249 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: 73516.0 ave 73516 max 73516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73516 Ave neighs/atom = 54.135493 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.799 | 4.799 | 4.799 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4549.5063 0 -4549.5063 -1401.3528 Loop time of 2.191e-06 on 1 procs for 0 steps with 1358 atoms 182.6% 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 | | 2.191e-06 | | |100.00 Nlocal: 1358.00 ave 1358 max 1358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5249.00 ave 5249 max 5249 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: 73586.0 ave 73586 max 73586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73586 Ave neighs/atom = 54.187040 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 12 34 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 4.799 | 4.799 | 4.799 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 -4549.5063 -4549.5063 37.425572 106.11671 5.7029109 -1401.3528 -1401.3528 -0.58833583 -4204.2514 0.78132942 2.66686 1051.9342 Loop time of 2.166e-06 on 1 procs for 0 steps with 1358 atoms 184.7% 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 | | 2.166e-06 | | |100.00 Nlocal: 1358.00 ave 1358 max 1358 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5249.00 ave 5249 max 5249 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 36793.0 ave 36793 max 36793 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 73586.0 ave 73586 max 73586 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 73586 Ave neighs/atom = 54.187040 Neighbor list builds = 0 Dangerous builds = 0 1358 -4549.5063288392 eV 2.66685998312211 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05