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 -38.796531 0.0000000) to (13.715533 38.796531 4.4499063) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0530909 4.0835141 4.4499063 Created 154 atoms using lattice units in orthogonal box = (0.0000000 -38.796531 0.0000000) to (13.715533 38.796531 4.4499063) create_atoms CPU = 0.002 seconds 154 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0530909 4.0835141 4.4499063 Created 154 atoms using lattice units in orthogonal box = (0.0000000 -38.796531 0.0000000) to (13.715533 38.796531 4.4499063) create_atoms CPU = 0.001 seconds 154 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 5 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 304 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.414 | 4.414 | 4.414 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2027.1916 0 -2027.1916 28672.684 52 0 -2057.1438 0 -2057.1438 11429.015 Loop time of 1.84113 on 1 procs for 52 steps with 304 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 = -2027.19164965246 -2057.14278058222 -2057.14379435348 Force two-norm initial, final = 25.836268 0.17000282 Force max component initial, final = 7.3228459 0.022424980 Final line search alpha, max atom move = 1.0000000 0.022424980 Iterations, force evaluations = 52 93 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8279 | 1.8279 | 1.8279 | 0.0 | 99.28 Neigh | 0.0030584 | 0.0030584 | 0.0030584 | 0.0 | 0.17 Comm | 0.0052017 | 0.0052017 | 0.0052017 | 0.0 | 0.28 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004945 | | | 0.27 Nlocal: 304.000 ave 304 max 304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1964.00 ave 1964 max 1964 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: 17444.0 ave 17444 max 17444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17444 Ave neighs/atom = 57.381579 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 5 27 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.414 | 4.414 | 4.414 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -2057.1438 0 -2057.1438 11429.015 4735.7245 55 0 -2057.1966 0 -2057.1966 2432.8685 4751.8122 Loop time of 0.124177 on 1 procs for 3 steps with 304 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 = -2057.14379435348 -2057.19651246308 -2057.19658806578 Force two-norm initial, final = 43.887673 0.18303503 Force max component initial, final = 32.534305 0.033832329 Final line search alpha, max atom move = 0.0014550433 4.9227505e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12255 | 0.12255 | 0.12255 | 0.0 | 98.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032265 | 0.00032265 | 0.00032265 | 0.0 | 0.26 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001306 | | | 1.05 Nlocal: 304.000 ave 304 max 304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1971.00 ave 1971 max 1971 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: 17464.0 ave 17464 max 17464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17464 Ave neighs/atom = 57.447368 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.552 | 4.552 | 4.552 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2057.1966 0 -2057.1966 2432.8685 Loop time of 6.194e-06 on 1 procs for 0 steps with 304 atoms 209.9% 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 | | 6.194e-06 | | |100.00 Nlocal: 304.000 ave 304 max 304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1963.00 ave 1963 max 1963 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: 17464.0 ave 17464 max 17464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17464 Ave neighs/atom = 57.447368 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 5 27 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.552 | 4.552 | 4.552 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 -2057.1966 -2057.1966 13.735792 77.593061 4.4584374 2432.8685 2432.8685 5.1661639 7304.8685 -11.429172 2.2126302 256.73287 Loop time of 7.377e-06 on 1 procs for 0 steps with 304 atoms 203.3% 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 | | 7.377e-06 | | |100.00 Nlocal: 304.000 ave 304 max 304 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 1963.00 ave 1963 max 1963 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 8732.00 ave 8732 max 8732 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 17464.0 ave 17464 max 17464 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 17464 Ave neighs/atom = 57.447368 Neighbor list builds = 0 Dangerous builds = 0 304 -2057.19658806578 eV 2.21263022485641 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02