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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -37.447179 0.0000000) to (17.652769 37.447179 4.0498230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7163725 4.5987764 4.0498230 Created 227 atoms using lattice units in orthogonal box = (0.0000000 -37.447179 0.0000000) to (17.652769 37.447179 4.0498230) create_atoms CPU = 0.001 seconds 227 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7163725 4.5987764 4.0498230 Created 229 atoms using lattice units in orthogonal box = (0.0000000 -37.447179 0.0000000) to (17.652769 37.447179 4.0498230) create_atoms CPU = 0.001 seconds 229 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 7 27 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 456 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 7 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.453 | 4.453 | 4.453 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1619.7578 0 -1619.7578 118282.9 81 0 -1944.6333 0 -1944.6333 8884.6026 Loop time of 1.55511 on 1 procs for 81 steps with 456 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1619.75782848276 -1944.63185323246 -1944.63325672052 Force two-norm initial, final = 648.02203 0.21071087 Force max component initial, final = 165.10921 0.10273240 Final line search alpha, max atom move = 1.0000000 0.10273240 Iterations, force evaluations = 81 150 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5454 | 1.5454 | 1.5454 | 0.0 | 99.38 Neigh | 0.0022462 | 0.0022462 | 0.0022462 | 0.0 | 0.14 Comm | 0.00387 | 0.00387 | 0.00387 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003573 | | | 0.23 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2898.00 ave 2898 max 2898 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: 26612.0 ave 26612 max 26612 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26612 Ave neighs/atom = 58.359649 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 7 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.449 | 4.449 | 4.449 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -1944.6333 0 -1944.6333 8884.6026 5354.242 87 0 -1944.7823 0 -1944.7823 -131.22681 5380.3318 Loop time of 0.0929075 on 1 procs for 6 steps with 456 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 = -1944.63325672052 -1944.78221493262 -1944.78226518818 Force two-norm initial, final = 63.029664 1.0163065 Force max component initial, final = 56.440890 0.52852897 Final line search alpha, max atom move = 0.0024578916 0.0012990669 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.091887 | 0.091887 | 0.091887 | 0.0 | 98.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00018401 | 0.00018401 | 0.00018401 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008363 | | | 0.90 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2538.00 ave 2538 max 2538 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: 26588.0 ave 26588 max 26588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26588 Ave neighs/atom = 58.307018 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.587 | 4.587 | 4.587 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1944.7823 0 -1944.7823 -131.22681 Loop time of 1.766e-06 on 1 procs for 0 steps with 456 atoms 169.9% 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 | | 1.766e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2535.00 ave 2535 max 2535 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: 26568.0 ave 26568 max 26568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26568 Ave neighs/atom = 58.263158 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 7 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.587 | 4.587 | 4.587 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 -1944.7823 -1944.7823 17.677622 75.250066 4.0446257 -131.22681 -131.22681 -127.94066 -158.13495 -107.60481 2.2768606 357.10436 Loop time of 1.433e-06 on 1 procs for 0 steps with 456 atoms 139.6% 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 | | 1.433e-06 | | |100.00 Nlocal: 456.000 ave 456 max 456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2535.00 ave 2535 max 2535 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 13284.0 ave 13284 max 13284 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 26568.0 ave 26568 max 26568 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 26568 Ave neighs/atom = 58.263158 Neighbor list builds = 0 Dangerous builds = 0 456 -1944.78226518818 eV 2.27686063602213 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01