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 = 4.0445274 4.0445274 4.0445274 Created orthogonal box = (0.0000000 -80.081601 0.0000000) to (49.037288 80.081601 9.9070283) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6709789 5.7198254 6.6046855 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -80.081601 0.0000000) to (49.037288 80.081601 9.9070283) create_atoms CPU = 0.003 seconds 2358 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6709789 5.7198254 6.6046855 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -80.081601 0.0000000) to (49.037288 80.081601 9.9070283) create_atoms CPU = 0.003 seconds 2358 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 10 33 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 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 48 atoms, new total = 4668 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_722733117926_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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 13.63 | 13.63 | 13.63 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15405.442 0 -15405.442 -1290.5221 21 0 -15431.531 0 -15431.531 -2133.9133 Loop time of 2.1199 on 1 procs for 21 steps with 4668 atoms 99.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15405.4423547746 -15431.5183068141 -15431.5312918754 Force two-norm initial, final = 28.090296 0.27165425 Force max component initial, final = 5.4189826 0.023216044 Final line search alpha, max atom move = 1.0000000 0.023216044 Iterations, force evaluations = 21 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1038 | 2.1038 | 2.1038 | 0.0 | 99.24 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0074123 | 0.0074123 | 0.0074123 | 0.0 | 0.35 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008725 | | | 0.41 Nlocal: 4668.00 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 17924.0 ave 17924 max 17924 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: 1.15000e+06 ave 1.15e+06 max 1.15e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1149996 Ave neighs/atom = 246.35733 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 21 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 13.63 | 13.63 | 13.63 Mbytes Step Temp E_pair E_mol TotEng Press Volume 21 0 -15431.531 0 -15431.531 -2133.9133 77809.494 24 0 -15431.689 0 -15431.689 -127.00121 77624.028 Loop time of 0.364449 on 1 procs for 3 steps with 4668 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15431.5312918752 -15431.6832088005 -15431.6885859566 Force two-norm initial, final = 161.26703 0.31914351 Force max component initial, final = 138.75117 0.087868239 Final line search alpha, max atom move = 5.6121449e-05 4.9312928e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35933 | 0.35933 | 0.35933 | 0.0 | 98.60 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00080532 | 0.00080532 | 0.00080532 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004311 | | | 1.18 Nlocal: 4668.00 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18030.0 ave 18030 max 18030 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: 1.14918e+06 ave 1.14918e+06 max 1.14918e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1149180 Ave neighs/atom = 246.18252 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 13.14 | 13.14 | 13.14 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15431.689 0 -15431.689 -127.00121 Loop time of 1.95e-06 on 1 procs for 0 steps with 4668 atoms 153.8% 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 | | 1.95e-06 | | |100.00 Nlocal: 4668.00 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18039.0 ave 18039 max 18039 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: 1.14937e+06 ave 1.14937e+06 max 1.14937e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1149372 Ave neighs/atom = 246.22365 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 = 10 ghost atom cutoff = 10 binsize = 5, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10 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) = 13.14 | 13.14 | 13.14 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 -15431.689 -15431.689 49.0214 160.1632 9.8866173 -127.00121 -127.00121 -1.8130316 -379.92057 0.72995687 2.5608074 2329.5358 Loop time of 2.464e-06 on 1 procs for 0 steps with 4668 atoms 243.5% 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 | | 2.464e-06 | | |100.00 Nlocal: 4668.00 ave 4668 max 4668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 18039.0 ave 18039 max 18039 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 574686.0 ave 574686 max 574686 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 1.14937e+06 ave 1.14937e+06 max 1.14937e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1149372 Ave neighs/atom = 246.22365 Neighbor list builds = 0 Dangerous builds = 0 4668 -15431.6885859566 eV 2.56080735755324 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03