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 = 4.0452705 4.0452705 4.0452705 Created orthogonal box = (0.0000000 -69.597465 0.0000000) to (34.798732 69.597465 4.0452705) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6430377 5.6430377 4.0452705 Created 592 atoms using lattice units in orthogonal box = (0.0000000 -69.597465 0.0000000) to (34.798732 69.597465 4.0452705) create_atoms CPU = 0.001 seconds 592 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6430377 5.6430377 4.0452705 Created 594 atoms using lattice units in orthogonal box = (0.0000000 -69.597465 0.0000000) to (34.798732 69.597465 4.0452705) create_atoms CPU = 0.001 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, 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, cut 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1186 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_658278549784_005#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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 5.479 | 5.479 | 5.479 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3919.7265 0 -3919.7265 19458.216 97 0 -4037.0007 0 -4037.0007 4844.714 Loop time of 2.37757 on 1 procs for 97 steps with 1186 atoms 98.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3919.72649770352 -4036.99759059988 -4037.00067605694 Force two-norm initial, final = 137.19037 0.12014967 Force max component initial, final = 25.429323 0.022245251 Final line search alpha, max atom move = 1.0000000 0.022245251 Iterations, force evaluations = 97 165 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.3049 | 2.3049 | 2.3049 | 0.0 | 96.94 Neigh | 0.042211 | 0.042211 | 0.042211 | 0.0 | 1.78 Comm | 0.0183 | 0.0183 | 0.0183 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01219 | | | 0.51 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10238.0 ave 10238 max 10238 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: 258812.0 ave 258812 max 258812 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258812 Ave neighs/atom = 218.22260 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 8 30 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 97 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.479 | 5.479 | 5.479 Mbytes Step Temp E_pair E_mol TotEng Press Volume 97 0 -4037.0007 0 -4037.0007 4844.714 19594.51 105 0 -4037.3672 0 -4037.3672 -54.43868 19712.64 Loop time of 0.162625 on 1 procs for 8 steps with 1186 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 = -4037.00067605696 -4037.36343607565 -4037.36716504407 Force two-norm initial, final = 116.45154 1.4218220 Force max component initial, final = 103.86434 1.0722148 Final line search alpha, max atom move = 0.00018389370 0.00019717355 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14269 | 0.14269 | 0.14269 | 0.0 | 87.74 Neigh | 0.014687 | 0.014687 | 0.014687 | 0.0 | 9.03 Comm | 0.0010721 | 0.0010721 | 0.0010721 | 0.0 | 0.66 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004178 | | | 2.57 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10250.0 ave 10250 max 10250 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: 259980.0 ave 259980 max 259980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 259980 Ave neighs/atom = 219.20742 Neighbor list builds = 1 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 8 30 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 5.617 | 5.617 | 5.617 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4037.3672 0 -4037.3672 -54.43868 Loop time of 1.954e-06 on 1 procs for 0 steps with 1186 atoms 153.5% 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 | | 1.954e-06 | | |100.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10250.0 ave 10250 max 10250 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: 260020.0 ave 260020 max 260020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 260020 Ave neighs/atom = 219.24115 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 = 9.5 ghost atom cutoff = 9.5 binsize = 4.75, bins = 8 30 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.5 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) = 5.617 | 5.617 | 5.617 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 -4037.3672 -4037.3672 34.81048 140.28154 4.0367722 -54.43868 -54.43868 -1.9348245 -74.418308 -86.962908 2.5113601 396.10663 Loop time of 2.484e-06 on 1 procs for 0 steps with 1186 atoms 201.3% 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 | | 2.484e-06 | | |100.00 Nlocal: 1186.00 ave 1186 max 1186 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10250.0 ave 10250 max 10250 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130010.0 ave 130010 max 130010 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 260020.0 ave 260020 max 260020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 260020 Ave neighs/atom = 219.24115 Neighbor list builds = 0 Dangerous builds = 0 1186 -4037.36716504407 eV 2.51136005943784 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03