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 = 3.5181212 3.5181212 3.5181212 Created orthogonal box = (0.0000000 -49.504354 0.0000000) to (11.668288 49.504354 4.9753748) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3037673 6.0005278 4.9753748 Created 264 atoms using lattice units in orthogonal box = (0.0000000 -49.504354 0.0000000) to (11.668288 49.504354 4.9753748) create_atoms CPU = 0.001 seconds 264 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3037673 6.0005278 4.9753748 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -49.504354 0.0000000) to (11.668288 49.504354 4.9753748) create_atoms CPU = 0.001 seconds 266 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 3 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 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 524 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_222110751402_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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 3 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 4.957 | 4.957 | 4.957 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2225.1581 0 -2225.1581 38056.2 79 0 -2289.8357 0 -2289.8357 -5839.9141 Loop time of 1.23139 on 1 procs for 79 steps with 524 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2225.15807283486 -2289.83409105648 -2289.83573679673 Force two-norm initial, final = 205.02606 0.12862795 Force max component initial, final = 71.394418 0.025036848 Final line search alpha, max atom move = 1.0000000 0.025036848 Iterations, force evaluations = 79 154 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2109 | 1.2109 | 1.2109 | 0.0 | 98.33 Neigh | 0.0075774 | 0.0075774 | 0.0075774 | 0.0 | 0.62 Comm | 0.0079987 | 0.0079987 | 0.0079987 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00493 | | | 0.40 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6316.00 ave 6316 max 6316 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: 128992.0 ave 128992 max 128992 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 128992 Ave neighs/atom = 246.16794 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 3 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 79 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.956 | 4.956 | 4.956 Mbytes Step Temp E_pair E_mol TotEng Press Volume 79 0 -2289.8357 0 -2289.8357 -5839.9141 5747.8621 84 0 -2289.9349 0 -2289.9349 -203.66165 5728.6737 Loop time of 0.0596341 on 1 procs for 5 steps with 524 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 = -2289.83573679672 -2289.93400539754 -2289.93491425008 Force two-norm initial, final = 48.480834 1.4235461 Force max component initial, final = 47.034288 1.0556382 Final line search alpha, max atom move = 0.00037507150 0.00039593981 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.057823 | 0.057823 | 0.057823 | 0.0 | 96.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034267 | 0.00034267 | 0.00034267 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001468 | | | 2.46 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6178.00 ave 6178 max 6178 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: 129308.0 ave 129308 max 129308 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129308 Ave neighs/atom = 246.77099 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 3 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 5.093 | 5.093 | 5.093 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2289.9349 0 -2289.9349 -203.66165 Loop time of 2.066e-06 on 1 procs for 0 steps with 524 atoms 193.6% 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 | | 2.066e-06 | | |100.00 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6132.00 ave 6132 max 6132 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: 129428.0 ave 129428 max 129428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129428 Ave neighs/atom = 247.00000 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 3 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 5.093 | 5.093 | 5.093 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 -2289.9349 -2289.9349 11.672568 98.584435 4.9782802 -203.66165 -203.66165 -64.877726 -250.69742 -295.40982 2.2497063 248.02325 Loop time of 2.254e-06 on 1 procs for 0 steps with 524 atoms 177.5% 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 | | 2.254e-06 | | |100.00 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6132.00 ave 6132 max 6132 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 64714.0 ave 64714 max 64714 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 129428.0 ave 129428 max 129428 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 129428 Ave neighs/atom = 247.00000 Neighbor list builds = 0 Dangerous builds = 0 524 -2289.93491425008 eV 2.24970625704529 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01