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 = 2.8636458 2.8636458 2.8636458 Created orthogonal box = (0.0000000 -43.620617 0.0000000) to (21.808876 43.620617 2.8636458) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 3.7601511 3.7601511 2.8636458 Created 234 atoms using lattice units in orthogonal box = (0.0000000 -43.620617 0.0000000) to (21.808876 43.620617 2.8636458) create_atoms CPU = 0.002 seconds 234 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 3.7601511 3.7601511 2.8636458 Created 234 atoms using lattice units in orthogonal box = (0.0000000 -43.620617 0.0000000) to (21.808876 43.620617 2.8636458) create_atoms CPU = 0.001 seconds 234 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 26 1 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 460 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_110119204723_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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.477 | 4.477 | 4.477 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1955.1283 0 -1955.1283 1932.6246 15 0 -1963.9487 0 -1963.9487 -6857.1253 Loop time of 3.55025 on 1 procs for 15 steps with 460 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 = -1955.12834825567 -1963.94682884618 -1963.94867708557 Force two-norm initial, final = 21.878493 0.12610170 Force max component initial, final = 7.3989306 0.029739987 Final line search alpha, max atom move = 1.0000000 0.029739987 Iterations, force evaluations = 15 25 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.5451 | 3.5451 | 3.5451 | 0.0 | 99.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0028414 | 0.0028414 | 0.0028414 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002357 | | | 0.07 Nlocal: 460.000 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4280.00 ave 4280 max 4280 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: 51096.0 ave 51096 max 51096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51096 Ave neighs/atom = 111.07826 Neighbor list builds = 0 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 26 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 15 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.477 | 4.477 | 4.477 Mbytes Step Temp E_pair E_mol TotEng Press Volume 15 0 -1963.9487 0 -1963.9487 -6857.1253 5448.4677 21 0 -1964.0509 0 -1964.0509 1826.3994 5420.5774 Loop time of 1.15056 on 1 procs for 6 steps with 460 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 = -1963.94867708557 -1964.05045709439 -1964.05086388385 Force two-norm initial, final = 47.098207 0.15720999 Force max component initial, final = 40.288879 0.027913045 Final line search alpha, max atom move = 0.00029292020 8.1762949e-06 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.147 | 1.147 | 1.147 | 0.0 | 99.69 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0008807 | 0.0008807 | 0.0008807 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002726 | | | 0.24 Nlocal: 460.000 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4264.00 ave 4264 max 4264 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: 51040.0 ave 51040 max 51040 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51040 Ave neighs/atom = 110.95652 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.615 | 4.615 | 4.615 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1964.0509 0 -1964.0509 1826.3994 Loop time of 6.616e-06 on 1 procs for 0 steps with 460 atoms 166.3% 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 | | 6.616e-06 | | |100.00 Nlocal: 460.000 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4264.00 ave 4264 max 4264 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: 51056.0 ave 51056 max 51056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51056 Ave neighs/atom = 110.99130 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 7 26 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 4.615 | 4.615 | 4.615 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 -1964.0509 -1964.0509 21.804601 87.241233 2.8495455 1826.3994 1826.3994 -2.5221912 5480.8747 0.84565021 2.2872752 246.39726 Loop time of 7.297e-06 on 1 procs for 0 steps with 460 atoms 301.5% 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 | | 7.297e-06 | | |100.00 Nlocal: 460.000 ave 460 max 460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4264.00 ave 4264 max 4264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25528.0 ave 25528 max 25528 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 51056.0 ave 51056 max 51056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 51056 Ave neighs/atom = 110.99130 Neighbor list builds = 0 Dangerous builds = 0 460 -1964.05086388385 eV 2.28727519693607 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05