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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -45.224615 0.0000000) to (9.0441141 45.224615 4.0446508) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4264684 5.4264684 4.0446508 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -45.224615 0.0000000) to (9.0441141 45.224615 4.0446508) create_atoms CPU = 0.001 seconds 102 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4264684 5.4264684 4.0446508 Created 102 atoms using lattice units in orthogonal box = (0.0000000 -45.224615 0.0000000) to (9.0441141 45.224615 4.0446508) create_atoms CPU = 0.001 seconds 102 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 3 28 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 198 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_099716416216_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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 3 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.402 | 4.402 | 4.402 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -656.20854 0 -656.20854 5125.0163 52 0 -662.7365 0 -662.7365 -2655.6846 Loop time of 1.89525 on 1 procs for 52 steps with 198 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 = -656.208536731125 -662.73585753869 -662.73650232876 Force two-norm initial, final = 17.751774 0.051748661 Force max component initial, final = 8.2887213 0.0086334152 Final line search alpha, max atom move = 1.0000000 0.0086334152 Iterations, force evaluations = 52 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.885 | 1.885 | 1.885 | 0.0 | 99.46 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0059078 | 0.0059078 | 0.0059078 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00435 | | | 0.23 Nlocal: 198.000 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2262.00 ave 2262 max 2262 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: 15160.0 ave 15160 max 15160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15160 Ave neighs/atom = 76.565657 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 3 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.402 | 4.402 | 4.402 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -662.7365 0 -662.7365 -2655.6846 3308.6584 55 0 -662.75054 0 -662.75054 474.06109 3295.3473 Loop time of 0.110576 on 1 procs for 3 steps with 198 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 = -662.73650232876 -662.750079700308 -662.750544199224 Force two-norm initial, final = 9.8433950 0.75537391 Force max component initial, final = 7.8644002 0.75073340 Final line search alpha, max atom move = 0.00065393715 0.00049093246 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10922 | 0.10922 | 0.10922 | 0.0 | 98.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027822 | 0.00027822 | 0.00027822 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001076 | | | 0.97 Nlocal: 198.000 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2262.00 ave 2262 max 2262 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: 15080.0 ave 15080 max 15080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15080 Ave neighs/atom = 76.161616 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 3 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.540 | 4.540 | 4.540 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -662.75054 0 -662.75054 474.06109 Loop time of 8.449e-06 on 1 procs for 0 steps with 198 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 | | 8.449e-06 | | |100.00 Nlocal: 198.000 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2262.00 ave 2262 max 2262 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: 15080.0 ave 15080 max 15080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15080 Ave neighs/atom = 76.161616 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 3 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 4.540 | 4.540 | 4.540 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 -662.75054 -662.75054 9.0312221 90.44923 4.0341291 474.06109 474.06109 364.48142 1088.4274 -30.725594 2.573817 155.83432 Loop time of 7.077e-06 on 1 procs for 0 steps with 198 atoms 296.7% 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 | | 7.077e-06 | | |100.00 Nlocal: 198.000 ave 198 max 198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2262.00 ave 2262 max 2262 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 7540.00 ave 7540 max 7540 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 15080.0 ave 15080 max 15080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 15080 Ave neighs/atom = 76.161616 Neighbor list builds = 0 Dangerous builds = 0 198 -662.750544199224 eV 2.57381698147234 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02