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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -47.869310 0.0000000) to (58.622738 47.869310 9.9090513) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6997415 6.1541055 6.6060342 Created 1684 atoms using lattice units in orthogonal box = (0.0000000 -47.869310 0.0000000) to (58.622738 47.869310 9.9090513) create_atoms CPU = 0.002 seconds 1684 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6997415 6.1541055 6.6060342 Created 1684 atoms using lattice units in orthogonal box = (0.0000000 -47.869310 0.0000000) to (58.622738 47.869310 9.9090513) create_atoms CPU = 0.002 seconds 1684 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 19 31 4 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 56 atoms, new total = 3312 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 19 31 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.218 | 5.218 | 5.218 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11075.003 0 -11075.003 -2771.1236 25 0 -11092.512 0 -11092.512 -7083.9506 Loop time of 3.03289 on 1 procs for 25 steps with 3312 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -11075.0025396872 -11092.5029328268 -11092.5118832201 Force two-norm initial, final = 11.060398 0.20707886 Force max component initial, final = 3.0954580 0.022107081 Final line search alpha, max atom move = 1.0000000 0.022107081 Iterations, force evaluations = 25 34 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.0069 | 3.0069 | 3.0069 | 0.0 | 99.14 Neigh | 0.016524 | 0.016524 | 0.016524 | 0.0 | 0.54 Comm | 0.0030264 | 0.0030264 | 0.0030264 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006422 | | | 0.21 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6905.00 ave 6905 max 6905 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: 178910.0 ave 178910 max 178910 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 178910 Ave neighs/atom = 54.018720 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 19 31 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 25 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.218 | 5.218 | 5.218 Mbytes Step Temp E_pair E_mol TotEng Press Volume 25 0 -11092.512 0 -11092.512 -7083.9506 55614.154 31 0 -11093.427 0 -11093.427 -1393.9571 55171.741 Loop time of 1.57418 on 1 procs for 6 steps with 3312 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 = -11092.5118832201 -11093.424749824 -11093.4273696536 Force two-norm initial, final = 316.17364 0.25172240 Force max component initial, final = 242.01174 0.030426417 Final line search alpha, max atom move = 0.00011049322 3.3619129e-06 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.5658 | 1.5658 | 1.5658 | 0.0 | 99.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010331 | 0.0010331 | 0.0010331 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007348 | | | 0.47 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6905.00 ave 6905 max 6905 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: 179180.0 ave 179180 max 179180 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179180 Ave neighs/atom = 54.100242 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 19 31 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.356 | 5.356 | 5.356 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11093.427 0 -11093.427 -1393.9571 Loop time of 3.734e-06 on 1 procs for 0 steps with 3312 atoms 214.2% 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 | | 3.734e-06 | | |100.00 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6905.00 ave 6905 max 6905 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: 179324.0 ave 179324 max 179324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179324 Ave neighs/atom = 54.143720 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 19 31 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.356 | 5.356 | 5.356 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 -11093.427 -11093.427 58.44963 95.738621 9.8593381 -1393.9571 -1393.9571 -0.88096803 -4180.466 -0.52429616 2.6065371 1834.7244 Loop time of 2.437e-06 on 1 procs for 0 steps with 3312 atoms 246.2% 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 | | 2.437e-06 | | |100.00 Nlocal: 3312.00 ave 3312 max 3312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6905.00 ave 6905 max 6905 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 89662.0 ave 89662 max 89662 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 179324.0 ave 179324 max 179324 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179324 Ave neighs/atom = 54.143720 Neighbor list builds = 0 Dangerous builds = 0 3312 -11093.4273696536 eV 2.60653707613334 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05