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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -49.713793 0.0000000) to (24.855355 49.713793 3.0829274) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.4415107 3.4415107 3.0829274 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -49.713793 0.0000000) to (24.855355 49.713793 3.0829274) create_atoms CPU = 0.001 seconds 261 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.4415107 3.4415107 3.0829274 Created 261 atoms using lattice units in orthogonal box = (0.0000000 -49.713793 0.0000000) to (24.855355 49.713793 3.0829274) create_atoms CPU = 0.000 seconds 261 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 30 1 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 6 atoms, new total = 516 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_152208847456_001#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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.248 | 5.248 | 5.248 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3251.5849 0 -3251.5849 34218.56 108 0 -3348.5912 0 -3348.5912 -12000.439 Loop time of 28.2688 on 1 procs for 108 steps with 516 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 = -3251.58486601754 -3348.58802259513 -3348.59121833911 Force two-norm initial, final = 205.83252 0.26362776 Force max component initial, final = 56.547211 0.051669397 Final line search alpha, max atom move = 1.0000000 0.051669397 Iterations, force evaluations = 108 201 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 28.193 | 28.193 | 28.193 | 0.0 | 99.73 Neigh | 0.063234 | 0.063234 | 0.063234 | 0.0 | 0.22 Comm | 0.0071066 | 0.0071066 | 0.0071066 | 0.0 | 0.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005684 | | | 0.02 Nlocal: 516.000 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4004.00 ave 4004 max 4004 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: 37772.0 ave 37772 max 37772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37772 Ave neighs/atom = 73.201550 Neighbor list builds = 3 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 108 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.245 | 5.245 | 5.245 Mbytes Step Temp E_pair E_mol TotEng Press Volume 108 0 -3348.5912 0 -3348.5912 -12000.439 7618.863 123 0 -3349.0528 0 -3349.0528 -331.89586 7571.8985 Loop time of 2.5301 on 1 procs for 15 steps with 516 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 = -3348.59121833911 -3349.05145041838 -3349.05277707961 Force two-norm initial, final = 78.016020 0.93572571 Force max component initial, final = 74.973194 0.24115048 Final line search alpha, max atom move = 0.00058966697 0.00014219847 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5264 | 2.5264 | 2.5264 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00059748 | 0.00059748 | 0.00059748 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003091 | | | 0.12 Nlocal: 516.000 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4014.00 ave 4014 max 4014 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: 37764.0 ave 37764 max 37764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37764 Ave neighs/atom = 73.186047 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 30 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.383 | 5.383 | 5.383 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3349.0528 0 -3349.0528 -331.89586 Loop time of 1.865e-06 on 1 procs for 0 steps with 516 atoms 160.9% 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 | | 1.865e-06 | | |100.00 Nlocal: 516.000 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4004.00 ave 4004 max 4004 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: 38422.0 ave 38422 max 38422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38422 Ave neighs/atom = 74.461240 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 8 30 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.383 | 5.383 | 5.383 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 -3349.0528 -3349.0528 25.072386 99.427586 3.0374016 -331.89586 -331.89586 -51.471805 -989.99535 45.779579 2.5715568 709.88772 Loop time of 1.755e-06 on 1 procs for 0 steps with 516 atoms 170.9% 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 | | 1.755e-06 | | |100.00 Nlocal: 516.000 ave 516 max 516 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4004.00 ave 4004 max 4004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19211.0 ave 19211 max 19211 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 38422.0 ave 38422 max 38422 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 38422 Ave neighs/atom = 74.461240 Neighbor list builds = 0 Dangerous builds = 0 516 -3349.05277707961 eV 2.57155677251656 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:31