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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -59.156140 0.0000000) to (41.827152 59.156140 5.1100000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2428586 5.7386779 5.1100000 Created 1079 atoms using lattice units in orthogonal box = (0.0000000 -59.156140 0.0000000) to (41.827152 59.156140 5.1100000) create_atoms CPU = 0.016 seconds 1079 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2428586 5.7386779 5.1100000 Created 1079 atoms using lattice units in orthogonal box = (0.0000000 -59.156140 0.0000000) to (41.827152 59.156140 5.1100000) create_atoms CPU = 0.012 seconds 1079 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 ghost atom cutoff = 6 binsize = 3, bins = 14 40 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 30 atoms, new total = 2128 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_087820130586_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 14 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.217 | 5.217 | 5.217 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7475.5979 0 -7475.5979 4260.2811 39 0 -7516.1912 0 -7516.1912 -7058.6893 Loop time of 5.3059 on 1 procs for 39 steps with 2128 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 = -7475.59793351566 -7516.18556161062 -7516.19118876195 Force two-norm initial, final = 36.689203 0.19973526 Force max component initial, final = 10.006743 0.036105637 Final line search alpha, max atom move = 1.0000000 0.036105637 Iterations, force evaluations = 39 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.2488 | 5.2488 | 5.2488 | 0.0 | 98.92 Neigh | 0.027726 | 0.027726 | 0.027726 | 0.0 | 0.52 Comm | 0.013327 | 0.013327 | 0.013327 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01601 | | | 0.30 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7653.00 ave 7653 max 7653 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: 164438.0 ave 164438 max 164438 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164438 Ave neighs/atom = 77.273496 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 14 40 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.217 | 5.217 | 5.217 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -7516.1912 0 -7516.1912 -7058.6893 25287.682 43 0 -7516.3642 0 -7516.3642 -2620.9039 25207.087 Loop time of 0.564661 on 1 procs for 4 steps with 2128 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 = -7516.19118876193 -7516.36259321283 -7516.36419087652 Force two-norm initial, final = 121.45354 0.24155256 Force max component initial, final = 112.15214 0.040368174 Final line search alpha, max atom move = 8.5378197e-05 3.4465619e-06 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.55878 | 0.55878 | 0.55878 | 0.0 | 98.96 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011834 | 0.0011834 | 0.0011834 | 0.0 | 0.21 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004701 | | | 0.83 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7653.00 ave 7653 max 7653 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: 164552.0 ave 164552 max 164552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164552 Ave neighs/atom = 77.327068 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 ghost atom cutoff = 6 binsize = 3, bins = 14 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.355 | 5.355 | 5.355 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7516.3642 0 -7516.3642 -2620.9039 Loop time of 6.084e-06 on 1 procs for 0 steps with 2128 atoms 197.2% 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 | | 6.084e-06 | | |100.00 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7653.00 ave 7653 max 7653 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: 164576.0 ave 164576 max 164576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164576 Ave neighs/atom = 77.338346 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 ghost atom cutoff = 6 binsize = 3, bins = 14 40 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 5.355 | 5.355 | 5.355 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 -7516.3642 -7516.3642 41.81853 118.31228 5.0947641 -2620.9039 -2620.9039 -1.9766138 -7860.4656 -0.2695892 2.3985168 912.78987 Loop time of 7.066e-06 on 1 procs for 0 steps with 2128 atoms 268.9% 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 | | 7.066e-06 | | |100.00 Nlocal: 2128.00 ave 2128 max 2128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7653.00 ave 7653 max 7653 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 82288.0 ave 82288 max 82288 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 164576.0 ave 164576 max 164576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 164576 Ave neighs/atom = 77.338346 Neighbor list builds = 0 Dangerous builds = 0 2128 -7516.36419087652 eV 2.3985168008372 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06