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 = 3.5200244 3.5200244 3.5200244 Created orthogonal box = (0.0000000 -46.168207 0.0000000) to (32.643363 46.168207 4.9780662) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0731838 5.9047855 4.9780662 Created 694 atoms using lattice units in orthogonal box = (0.0000000 -46.168207 0.0000000) to (32.643363 46.168207 4.9780662) create_atoms CPU = 0.002 seconds 694 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0731838 5.9047855 4.9780662 Created 694 atoms using lattice units in orthogonal box = (0.0000000 -46.168207 0.0000000) to (32.643363 46.168207 4.9780662) create_atoms CPU = 0.001 seconds 694 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 8 22 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 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 1368 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_532072268679_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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 5.908 | 5.908 | 5.908 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6015.0738 0 -6015.0738 13959.72 58 0 -6064.6374 0 -6064.6374 -4171.4088 Loop time of 1.44533 on 1 procs for 58 steps with 1368 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 = -6015.07383599086 -6064.63145503568 -6064.63744148086 Force two-norm initial, final = 68.287866 0.26110265 Force max component initial, final = 13.797666 0.020327478 Final line search alpha, max atom move = 1.0000000 0.020327478 Iterations, force evaluations = 58 101 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.411 | 1.411 | 1.411 | 0.0 | 97.62 Neigh | 0.01821 | 0.01821 | 0.01821 | 0.0 | 1.26 Comm | 0.0087525 | 0.0087525 | 0.0087525 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007408 | | | 0.51 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9675.00 ave 9675 max 9675 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: 304848.0 ave 304848 max 304848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 304848 Ave neighs/atom = 222.84211 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.907 | 5.907 | 5.907 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -6064.6374 0 -6064.6374 -4171.4088 15004.743 59 0 -6064.6434 0 -6064.6434 -2832.065 14993.369 Loop time of 0.0491214 on 1 procs for 1 steps with 1368 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 = -6064.63744148088 -6064.63744148088 -6064.6434232022 Force two-norm initial, final = 21.475730 3.1258376 Force max component initial, final = 18.638592 2.6835898 Final line search alpha, max atom move = 5.3652121e-05 0.00014398029 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.047917 | 0.047917 | 0.047917 | 0.0 | 97.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00025701 | 0.00025701 | 0.00025701 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009471 | | | 1.93 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9666.00 ave 9666 max 9666 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: 305536.0 ave 305536 max 305536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 305536 Ave neighs/atom = 223.34503 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 6.045 | 6.045 | 6.045 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6064.6434 0 -6064.6434 -2832.065 Loop time of 2.457e-06 on 1 procs for 0 steps with 1368 atoms 203.5% 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 | | 2.457e-06 | | |100.00 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9666.00 ave 9666 max 9666 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: 305544.0 ave 305544 max 305544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 305544 Ave neighs/atom = 223.35088 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 = 8.4 ghost atom cutoff = 8.4 binsize = 4.2, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.4 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) = 6.045 | 6.045 | 6.045 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 -6064.6434 -6064.6434 32.634356 92.336413 4.9756657 -2832.065 -2832.065 286.68661 -8614.0176 -168.86399 2.2935151 925.01351 Loop time of 2.234e-06 on 1 procs for 0 steps with 1368 atoms 268.6% 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 | | 2.234e-06 | | |100.00 Nlocal: 1368.00 ave 1368 max 1368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9666.00 ave 9666 max 9666 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 152772.0 ave 152772 max 152772 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 305544.0 ave 305544 max 305544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 305544 Ave neighs/atom = 223.35088 Neighbor list builds = 0 Dangerous builds = 0 1368 -6027.3498255398 eV 2.29351513738022 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01