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 = 4.0709491 4.0709491 4.0709491 Created orthogonal box = (0.0000000 -55.970368 0.0000000) to (15.232097 55.970368 9.9717481) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5280415 6.2184775 6.6478321 Created 508 atoms using lattice units in orthogonal box = (0.0000000 -55.970368 0.0000000) to (15.232097 55.970368 9.9717481) create_atoms CPU = 0.001 seconds 508 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5280415 6.2184775 6.6478321 Created 508 atoms using lattice units in orthogonal box = (0.0000000 -55.970368 0.0000000) to (15.232097 55.970368 9.9717481) create_atoms CPU = 0.001 seconds 508 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 37 4 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1000 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 37 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.519 | 4.519 | 4.519 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3342.5605 0 -3342.5605 1944.054 52 0 -3357.6445 0 -3357.6445 -3194.2684 Loop time of 2.59955 on 1 procs for 52 steps with 1000 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 = -3342.56050996584 -3357.64268122185 -3357.64453592143 Force two-norm initial, final = 19.804620 0.20339574 Force max component initial, final = 4.4106303 0.019440863 Final line search alpha, max atom move = 1.0000000 0.019440863 Iterations, force evaluations = 52 98 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.5872 | 2.5872 | 2.5872 | 0.0 | 99.53 Neigh | 0.0047106 | 0.0047106 | 0.0047106 | 0.0 | 0.18 Comm | 0.0031289 | 0.0031289 | 0.0031289 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004492 | | | 0.17 Nlocal: 1000.00 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3485.00 ave 3485 max 3485 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: 53760.0 ave 53760 max 53760 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53760 Ave neighs/atom = 53.760000 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 37 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.518 | 4.518 | 4.518 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -3357.6445 0 -3357.6445 -3194.2684 17002.749 55 0 -3357.6984 0 -3357.6984 -250.83596 16951.852 Loop time of 0.157295 on 1 procs for 3 steps with 1000 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 = -3357.64453592142 -3357.69835171059 -3357.69836535589 Force two-norm initial, final = 51.582647 0.41039982 Force max component initial, final = 36.651918 0.33674189 Final line search alpha, max atom move = 0.0070820351 0.0023848179 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15633 | 0.15633 | 0.15633 | 0.0 | 99.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015561 | 0.00015561 | 0.00015561 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008069 | | | 0.51 Nlocal: 1000.00 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3418.00 ave 3418 max 3418 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: 53752.0 ave 53752 max 53752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53752 Ave neighs/atom = 53.752000 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 37 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.656 | 4.656 | 4.656 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3357.6984 0 -3357.6984 -250.83596 Loop time of 1.564e-06 on 1 procs for 0 steps with 1000 atoms 127.9% 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 | | 1.564e-06 | | |100.00 Nlocal: 1000.00 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3430.00 ave 3430 max 3430 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: 53752.0 ave 53752 max 53752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53752 Ave neighs/atom = 53.752000 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 5 37 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.656 | 4.656 | 4.656 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 -3357.6984 -3357.6984 15.209875 111.94074 9.9564228 -250.83596 -250.83596 -4.214661 -780.07093 31.777694 2.5381492 567.65128 Loop time of 2.892e-06 on 1 procs for 0 steps with 1000 atoms 172.9% 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 | | 2.892e-06 | | |100.00 Nlocal: 1000.00 ave 1000 max 1000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3430.00 ave 3430 max 3430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 26876.0 ave 26876 max 26876 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 53752.0 ave 53752 max 53752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 53752 Ave neighs/atom = 53.752000 Neighbor list builds = 0 Dangerous builds = 0 1000 -3357.69836535589 eV 2.53814922450646 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03