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 = 4.0320382 4.0320382 4.0320382 Created orthogonal box = (0.0000000 -51.635283 0.0000000) to (36.511659 51.635283 5.7021631) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2336979 6.9266843 5.7021631 Created 655 atoms using lattice units in orthogonal box = (0.0000000 -51.635283 0.0000000) to (36.511659 51.635283 5.7021631) create_atoms CPU = 0.005 seconds 655 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2336979 6.9266843 5.7021631 Created 659 atoms using lattice units in orthogonal box = (0.0000000 -51.635283 0.0000000) to (36.511659 51.635283 5.7021631) create_atoms CPU = 0.004 seconds 659 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 9 24 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 8.68 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 1311 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_019873715786_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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.473 | 5.473 | 5.473 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4311.4317 0 -4311.4317 8650.9471 71 0 -4394.9919 0 -4394.9919 3248.8908 Loop time of 3.23878 on 1 procs for 71 steps with 1311 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 = -4311.43167198084 -4394.98787890762 -4394.9918767072 Force two-norm initial, final = 48.809173 0.15451414 Force max component initial, final = 7.1019152 0.034938512 Final line search alpha, max atom move = 1.0000000 0.034938512 Iterations, force evaluations = 71 123 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1299 | 3.1299 | 3.1299 | 0.0 | 96.64 Neigh | 0.063591 | 0.063591 | 0.063591 | 0.0 | 1.96 Comm | 0.024279 | 0.024279 | 0.024279 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02097 | | | 0.65 Nlocal: 1311.00 ave 1311 max 1311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8274.00 ave 8274 max 8274 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: 227188.0 ave 227188 max 227188 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227188 Ave neighs/atom = 173.29367 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 9 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.476 | 5.476 | 5.476 Mbytes Step Temp E_pair E_mol TotEng Press Volume 71 0 -4394.9919 0 -4394.9919 3248.8908 21500.46 79 0 -4395.3196 0 -4395.3196 13.031012 21579.164 Loop time of 0.258482 on 1 procs for 8 steps with 1311 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 = -4394.99187670721 -4395.31960637275 -4395.31962771636 Force two-norm initial, final = 104.21170 0.52905703 Force max component initial, final = 101.98570 0.39098354 Final line search alpha, max atom move = 0.0011520657 0.00045043872 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25071 | 0.25071 | 0.25071 | 0.0 | 97.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00168 | 0.00168 | 0.00168 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006087 | | | 2.36 Nlocal: 1311.00 ave 1311 max 1311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8291.00 ave 8291 max 8291 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: 227342.0 ave 227342 max 227342 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227342 Ave neighs/atom = 173.41114 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.614 | 5.614 | 5.614 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4395.3196 0 -4395.3196 13.031012 Loop time of 8.69e-06 on 1 procs for 0 steps with 1311 atoms 506.3% 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 | | 8.69e-06 | | |100.00 Nlocal: 1311.00 ave 1311 max 1311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8285.00 ave 8285 max 8285 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: 227118.0 ave 227118 max 227118 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227118 Ave neighs/atom = 173.24027 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 = 8.68 ghost atom cutoff = 8.68 binsize = 4.34, bins = 9 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.68 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) = 5.614 | 5.614 | 5.614 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 -4395.3196 -4395.3196 36.428614 103.99302 5.6962334 13.031012 13.031012 -5.07633 29.232224 14.937142 2.6475646 801.60766 Loop time of 7.397e-06 on 1 procs for 0 steps with 1311 atoms 256.9% 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 | | 7.397e-06 | | |100.00 Nlocal: 1311.00 ave 1311 max 1311 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8285.00 ave 8285 max 8285 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113559.0 ave 113559 max 113559 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 227118.0 ave 227118 max 227118 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227118 Ave neighs/atom = 173.24027 Neighbor list builds = 0 Dangerous builds = 0 1311 -4395.31962771636 eV 2.64756457865608 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04