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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -67.308115 0.0000000) to (33.654058 67.308115 3.5673230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9157612 4.9157612 3.5673230 Created 712 atoms using lattice units in orthogonal box = (0.0000000 -67.308115 0.0000000) to (33.654058 67.308115 3.5673230) create_atoms CPU = 0.003 seconds 712 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9157612 4.9157612 3.5673230 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -67.308115 0.0000000) to (33.654058 67.308115 3.5673230) create_atoms CPU = 0.002 seconds 714 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 = 13 49 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 = 1426 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 49 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) = 4.683 | 4.683 | 4.683 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5631.735 0 -5631.735 57473.598 91 0 -6010.3448 0 -6010.3448 31192.566 Loop time of 16.7314 on 1 procs for 91 steps with 1426 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 = -5631.73496348628 -6010.3390717147 -6010.34482579562 Force two-norm initial, final = 556.37610 0.28001980 Force max component initial, final = 148.60710 0.023386697 Final line search alpha, max atom move = 1.0000000 0.023386697 Iterations, force evaluations = 91 168 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.662 | 16.662 | 16.662 | 0.0 | 99.58 Neigh | 0.014449 | 0.014449 | 0.014449 | 0.0 | 0.09 Comm | 0.027583 | 0.027583 | 0.027583 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02759 | | | 0.16 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6782.00 ave 6782 max 6782 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: 80252.0 ave 80252 max 80252 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 80252 Ave neighs/atom = 56.277700 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 13 49 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 : 91 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.683 | 4.683 | 4.683 Mbytes Step Temp E_pair E_mol TotEng Press Volume 91 0 -6010.3448 0 -6010.3448 31192.566 16161.337 99 0 -6012.1492 0 -6012.1492 289.73405 16294.235 Loop time of 0.990043 on 1 procs for 8 steps with 1426 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 = -6010.34482579562 -6012.14448016617 -6012.1492209739 Force two-norm initial, final = 581.02121 10.721954 Force max component initial, final = 447.69314 8.1253085 Final line search alpha, max atom move = 4.6908364e-05 0.00038114493 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.96797 | 0.96797 | 0.96797 | 0.0 | 97.77 Neigh | 0.014238 | 0.014238 | 0.014238 | 0.0 | 1.44 Comm | 0.0019293 | 0.0019293 | 0.0019293 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005902 | | | 0.60 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6778.00 ave 6778 max 6778 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: 78696.0 ave 78696 max 78696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78696 Ave neighs/atom = 55.186536 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 = 13 49 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) = 4.821 | 4.821 | 4.821 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6012.1492 0 -6012.1492 289.73405 Loop time of 6.205e-06 on 1 procs for 0 steps with 1426 atoms 193.4% 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 | | 6.205e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6790.00 ave 6790 max 6790 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: 78612.0 ave 78612 max 78612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78612 Ave neighs/atom = 55.127630 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 = 13 49 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) = 4.821 | 4.821 | 4.821 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 -6012.1492 -6012.1492 33.736846 135.58172 3.5622825 289.73405 289.73405 -444.63732 516.02453 797.81495 2.2909071 393.85299 Loop time of 6.775e-06 on 1 procs for 0 steps with 1426 atoms 265.7% 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 | | 6.775e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6790.00 ave 6790 max 6790 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 39306.0 ave 39306 max 39306 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 78612.0 ave 78612 max 78612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 78612 Ave neighs/atom = 55.127630 Neighbor list builds = 0 Dangerous builds = 0 1426 -6012.1492209739 eV 2.2909071405342 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18