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 = 3.5200010 3.5200010 3.5200010 Created orthogonal box = (0.0000000 -49.530804 0.0000000) to (11.674523 49.530804 4.9780331) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3066012 6.0037339 4.9780331 Created 264 atoms using lattice units in orthogonal box = (0.0000000 -49.530804 0.0000000) to (11.674523 49.530804 4.9780331) create_atoms CPU = 0.001 seconds 264 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3066012 6.0037339 4.9780331 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -49.530804 0.0000000) to (11.674523 49.530804 4.9780331) 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 4 27 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 7.6 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_267721408934_005#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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 4 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.548 | 4.548 | 4.548 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2274.2211 0 -2274.2211 27202.934 93 0 -2324.8666 0 -2324.8666 -3589.7956 Loop time of 0.885111 on 1 procs for 93 steps with 524 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2274.22110562402 -2324.86454247407 -2324.86664769678 Force two-norm initial, final = 153.11858 0.17470660 Force max component initial, final = 53.572703 0.041045683 Final line search alpha, max atom move = 1.0000000 0.041045683 Iterations, force evaluations = 93 180 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.86648 | 0.86648 | 0.86648 | 0.0 | 97.89 Neigh | 0.0054735 | 0.0054735 | 0.0054735 | 0.0 | 0.62 Comm | 0.0079377 | 0.0079377 | 0.0079377 | 0.0 | 0.90 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005221 | | | 0.59 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5499.00 ave 5499 max 5499 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: 90972.0 ave 90972 max 90972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 90972 Ave neighs/atom = 173.61069 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 4 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 93 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.548 | 4.548 | 4.548 Mbytes Step Temp E_pair E_mol TotEng Press Volume 93 0 -2324.8666 0 -2324.8666 -3589.7956 5757.0803 95 0 -2324.8842 0 -2324.8842 22.068122 5745.3869 Loop time of 0.0200671 on 1 procs for 2 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 = -2324.86664769676 -2324.88278156084 -2324.88420556893 Force two-norm initial, final = 24.004129 0.33319952 Force max component initial, final = 19.339634 0.18206734 Final line search alpha, max atom move = 0.00027074953 4.9294646e-05 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.019359 | 0.019359 | 0.019359 | 0.0 | 96.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00016064 | 0.00016064 | 0.00016064 | 0.0 | 0.80 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0005476 | | | 2.73 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5311.00 ave 5311 max 5311 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: 91012.0 ave 91012 max 91012 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91012 Ave neighs/atom = 173.68702 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 4 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.686 | 4.686 | 4.686 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2324.8842 0 -2324.8842 22.068122 Loop time of 1.546e-06 on 1 procs for 0 steps with 524 atoms 194.0% 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 | | 1.546e-06 | | |100.00 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5311.00 ave 5311 max 5311 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: 91044.0 ave 91044 max 91044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91044 Ave neighs/atom = 173.74809 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 4 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 4.686 | 4.686 | 4.686 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 -2324.8842 -2324.8842 11.667148 98.920574 4.9781495 22.068122 22.068122 -32.990946 48.422262 50.773052 2.3214594 252.62163 Loop time of 2.085e-06 on 1 procs for 0 steps with 524 atoms 143.9% 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 | | 2.085e-06 | | |100.00 Nlocal: 524.000 ave 524 max 524 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5311.00 ave 5311 max 5311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 45522.0 ave 45522 max 45522 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 91044.0 ave 91044 max 91044 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91044 Ave neighs/atom = 173.74809 Neighbor list builds = 0 Dangerous builds = 0 524 -2305.78324409552 eV 2.32145943593092 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01