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 = 4.0320000 4.0320000 4.0320000 Created orthogonal box = (0.0000000 -79.829527 0.0000000) to (48.885402 79.829527 9.8763426) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6534138 5.7021090 6.5842284 Created 2352 atoms using lattice units in orthogonal box = (0.0000000 -79.829527 0.0000000) to (48.885402 79.829527 9.8763426) create_atoms CPU = 0.011 seconds 2352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6534138 5.7021090 6.5842284 Created 2358 atoms using lattice units in orthogonal box = (0.0000000 -79.829527 0.0000000) to (48.885402 79.829527 9.8763426) create_atoms CPU = 0.003 seconds 2358 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 12 36 3 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 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 4704 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_519613893196_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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 12 36 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 12.30 | 12.30 | 12.30 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15390.473 0 -15390.473 12344.297 71 0 -15774.825 0 -15774.825 3139.5034 Loop time of 5.12094 on 1 procs for 71 steps with 4704 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 = -15390.4734860717 -15774.8098595499 -15774.8251930437 Force two-norm initial, final = 328.78714 0.30954278 Force max component initial, final = 52.997144 0.025651399 Final line search alpha, max atom move = 1.0000000 0.025651399 Iterations, force evaluations = 71 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.9721 | 4.9721 | 4.9721 | 0.0 | 97.09 Neigh | 0.097544 | 0.097544 | 0.097544 | 0.0 | 1.90 Comm | 0.021249 | 0.021249 | 0.021249 | 0.0 | 0.41 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03 | | | 0.59 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14897.0 ave 14897 max 14897 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: 826020.0 ave 826020 max 826020 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 826020 Ave neighs/atom = 175.59949 Neighbor list builds = 2 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 12 36 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 71 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.30 | 12.30 | 12.30 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -15774.825 0 -15774.825 3139.5034 77084.824 76 0 -15775.38 0 -15775.38 -235.12007 77403.892 Loop time of 0.30835 on 1 procs for 5 steps with 4704 atoms 98.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -15774.8251930436 -15775.3722709955 -15775.3804282413 Force two-norm initial, final = 290.97122 22.618169 Force max component initial, final = 251.54113 18.152964 Final line search alpha, max atom move = 3.6334827e-05 0.00065958480 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30086 | 0.30086 | 0.30086 | 0.0 | 97.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00096634 | 0.00096634 | 0.00096634 | 0.0 | 0.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00652 | | | 2.11 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15274.0 ave 15274 max 15274 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: 826104.0 ave 826104 max 826104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 826104 Ave neighs/atom = 175.61735 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 12 37 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 11.82 | 11.82 | 11.82 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15775.38 0 -15775.38 -235.12007 Loop time of 2.194e-06 on 1 procs for 0 steps with 4704 atoms 182.3% 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 | | 2.194e-06 | | |100.00 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15268.0 ave 15268 max 15268 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: 825420.0 ave 825420 max 825420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 825420 Ave neighs/atom = 175.47194 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 = 8.875 ghost atom cutoff = 8.875 binsize = 4.4375, bins = 12 37 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.875 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) = 11.82 | 11.82 | 11.82 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 -15775.38 -15775.38 48.893687 160.38965 9.8703754 -235.12007 -235.12007 -375.81032 -56.186323 -273.36356 2.5316256 2262.9408 Loop time of 2.025e-06 on 1 procs for 0 steps with 4704 atoms 345.7% 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 | | 2.025e-06 | | |100.00 Nlocal: 4704.00 ave 4704 max 4704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 15268.0 ave 15268 max 15268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 412710.0 ave 412710 max 412710 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 825420.0 ave 825420 max 825420 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 825420 Ave neighs/atom = 175.47194 Neighbor list builds = 0 Dangerous builds = 0 4704 -15775.3804282413 eV 2.53162555160155 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06