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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -46.564820 0.0000000) to (38.020017 46.564820 7.7074639) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.6873993 4.4651198 5.1383093 Created 876 atoms using lattice units in orthogonal box = (0.0000000 -46.564820 0.0000000) to (38.020017 46.564820 7.7074639) create_atoms CPU = 0.001 seconds 876 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.6873993 4.4651198 5.1383093 Created 878 atoms using lattice units in orthogonal box = (0.0000000 -46.564820 0.0000000) to (38.020017 46.564820 7.7074639) create_atoms CPU = 0.001 seconds 878 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 29 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1738 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_356501945107_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.061 | 5.061 | 5.061 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10041.126 0 -10041.126 157858.67 222 0 -11763.554 0 -11763.554 -9260.9315 Loop time of 18.3372 on 1 procs for 222 steps with 1738 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 = -10041.1261566848 -11763.5449367753 -11763.5540297405 Force two-norm initial, final = 1694.5877 0.58307400 Force max component initial, final = 494.28523 0.13074562 Final line search alpha, max atom move = 0.92563307 0.12102247 Iterations, force evaluations = 222 422 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 18.237 | 18.237 | 18.237 | 0.0 | 99.45 Neigh | 0.049619 | 0.049619 | 0.049619 | 0.0 | 0.27 Comm | 0.021159 | 0.021159 | 0.021159 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02979 | | | 0.16 Nlocal: 1738.00 ave 1738 max 1738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5353.00 ave 5353 max 5353 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: 111360.0 ave 111360 max 111360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111360 Ave neighs/atom = 64.073648 Neighbor list builds = 5 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 29 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 222 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.073 | 5.073 | 5.073 Mbytes Step Temp E_pair E_mol TotEng Press Volume 222 0 -11763.554 0 -11763.554 -9260.9315 27290.515 225 0 -11763.869 0 -11763.869 -4.3555756 27193.26 Loop time of 0.262147 on 1 procs for 3 steps with 1738 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 = -11763.5540297405 -11763.8599838191 -11763.8686989738 Force two-norm initial, final = 278.17416 1.3171661 Force max component initial, final = 195.14561 1.0240805 Final line search alpha, max atom move = 4.1978206e-05 4.2989063e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.26041 | 0.26041 | 0.26041 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025721 | 0.00025721 | 0.00025721 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001478 | | | 0.56 Nlocal: 1738.00 ave 1738 max 1738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5753.00 ave 5753 max 5753 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: 111380.0 ave 111380 max 111380 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111380 Ave neighs/atom = 64.085155 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.211 | 5.211 | 5.211 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11763.869 0 -11763.869 -4.3555756 Loop time of 2.176e-06 on 1 procs for 0 steps with 1738 atoms 183.8% 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 | | 2.176e-06 | | |100.00 Nlocal: 1738.00 ave 1738 max 1738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5758.00 ave 5758 max 5758 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: 111448.0 ave 111448 max 111448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111448 Ave neighs/atom = 64.124281 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 12 29 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.211 | 5.211 | 5.211 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 -11763.869 -11763.869 37.941413 93.01926 7.7050401 -4.3555756 -4.3555756 24.653743 -60.265412 22.544943 2.4659582 1353.5276 Loop time of 2.163e-06 on 1 procs for 0 steps with 1738 atoms 184.9% 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 | | 2.163e-06 | | |100.00 Nlocal: 1738.00 ave 1738 max 1738 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5758.00 ave 5758 max 5758 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 55724.0 ave 55724 max 55724 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 111448.0 ave 111448 max 111448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 111448 Ave neighs/atom = 64.124281 Neighbor list builds = 0 Dangerous builds = 0 1738 -11763.8686989738 eV 2.46595824762973 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19