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 = 3.6150127 3.6150127 3.6150127 Created orthogonal box = (0.0000000 -62.198645 0.0000000) to (31.097515 62.198645 3.6150127) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0428402 5.0428402 3.6150127 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -62.198645 0.0000000) to (31.097515 62.198645 3.6150127) create_atoms CPU = 0.003 seconds 594 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0428402 5.0428402 3.6150127 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -62.198645 0.0000000) to (31.097515 62.198645 3.6150127) create_atoms CPU = 0.002 seconds 594 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 36 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 12 atoms, new total = 1176 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_028979335952_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 9 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.051 | 5.051 | 5.051 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4127.2254 0 -4127.2254 3122.8412 25 0 -4147.5906 0 -4147.5906 -4801.3566 Loop time of 7.95674 on 1 procs for 25 steps with 1176 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 = -4127.22538448548 -4147.58809178595 -4147.59064324008 Force two-norm initial, final = 30.196572 0.17707417 Force max component initial, final = 8.3505830 0.055121647 Final line search alpha, max atom move = 1.0000000 0.055121647 Iterations, force evaluations = 25 43 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.9408 | 7.9408 | 7.9408 | 0.0 | 99.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0087513 | 0.0087513 | 0.0087513 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007168 | | | 0.09 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8324.00 ave 8324 max 8324 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: 155764.0 ave 155764 max 155764 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 155764 Ave neighs/atom = 132.45238 Neighbor list builds = 0 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.051 | 5.051 | 5.051 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -4147.5906 0 -4147.5906 -4801.3566 13984.483 28 0 -4147.6367 0 -4147.6367 -1554.8336 13952.039 Loop time of 1.21424 on 1 procs for 3 steps with 1176 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 = -4147.59064324008 -4147.6351388651 -4147.6366729658 Force two-norm initial, final = 48.963753 0.17855339 Force max component initial, final = 41.681689 0.052890542 Final line search alpha, max atom move = 0.00023365738 1.2358266e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2094 | 1.2094 | 1.2094 | 0.0 | 99.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011926 | 0.0011926 | 0.0011926 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003623 | | | 0.30 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8299.00 ave 8299 max 8299 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: 156272.0 ave 156272 max 156272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156272 Ave neighs/atom = 132.88435 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.189 | 5.189 | 5.189 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4147.6367 0 -4147.6367 -1554.8336 Loop time of 6.815e-06 on 1 procs for 0 steps with 1176 atoms 161.4% 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 | | 6.815e-06 | | |100.00 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8304.00 ave 8304 max 8304 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: 156312.0 ave 156312 max 156312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156312 Ave neighs/atom = 132.91837 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 ghost atom cutoff = 7 binsize = 3.5, bins = 9 36 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.189 | 5.189 | 5.189 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 -4147.6367 -4147.6367 31.035017 124.39729 3.6138886 -1554.8336 -1554.8336 -0.64600966 -4663.1996 -0.65528177 2.2765502 297.56041 Loop time of 9.502e-06 on 1 procs for 0 steps with 1176 atoms 242.1% 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 | | 9.502e-06 | | |100.00 Nlocal: 1176.00 ave 1176 max 1176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8304.00 ave 8304 max 8304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 78156.0 ave 78156 max 78156 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 156312.0 ave 156312 max 156312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 156312 Ave neighs/atom = 132.91837 Neighbor list builds = 0 Dangerous builds = 0 1176 -4147.6366729658 eV 2.27655015963864 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10