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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -38.487462 0.0000000) to (27.212197 38.487462 5.0973115) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2514766 6.0763986 5.0973115 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.487462 0.0000000) to (27.212197 38.487462 5.0973115) create_atoms CPU = 0.001 seconds 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2514766 6.0763986 5.0973115 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -38.487462 0.0000000) to (27.212197 38.487462 5.0973115) create_atoms CPU = 0.001 seconds 458 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 9 26 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 20 atoms, new total = 896 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.568 | 4.568 | 4.568 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3765.4576 0 -3765.4576 -6126.2798 44 0 -3787.5604 0 -3787.5604 -22854.446 Loop time of 2.24284 on 1 procs for 44 steps with 896 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 = -3765.4575888103 -3787.55691454877 -3787.5603819409 Force two-norm initial, final = 17.712459 0.17861540 Force max component initial, final = 6.0765059 0.040370720 Final line search alpha, max atom move = 1.0000000 0.040370720 Iterations, force evaluations = 44 74 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.2316 | 2.2316 | 2.2316 | 0.0 | 99.50 Neigh | 0.0048102 | 0.0048102 | 0.0048102 | 0.0 | 0.21 Comm | 0.0028267 | 0.0028267 | 0.0028267 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003549 | | | 0.16 Nlocal: 896.000 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3988.00 ave 3988 max 3988 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: 69496.0 ave 69496 max 69496 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69496 Ave neighs/atom = 77.562500 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 9 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 44 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.568 | 4.568 | 4.568 Mbytes Step Temp E_pair E_mol TotEng Press Volume 44 0 -3787.5604 0 -3787.5604 -22854.446 10677.118 66 0 -3789.8057 0 -3789.8057 -183.53816 10520.804 Loop time of 0.741102 on 1 procs for 22 steps with 896 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3787.56038194091 -3789.80466202754 -3789.80568923518 Force two-norm initial, final = 249.62031 0.67069862 Force max component initial, final = 234.65597 0.11667211 Final line search alpha, max atom move = 0.00042325494 4.9382047e-05 Iterations, force evaluations = 22 23 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.73612 | 0.73612 | 0.73612 | 0.0 | 99.33 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00074825 | 0.00074825 | 0.00074825 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004238 | | | 0.57 Nlocal: 896.000 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3988.00 ave 3988 max 3988 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: 69432.0 ave 69432 max 69432 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69432 Ave neighs/atom = 77.491071 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.706 | 4.706 | 4.706 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3789.8057 0 -3789.8057 -183.53816 Loop time of 1.867e-06 on 1 procs for 0 steps with 896 atoms 160.7% 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 | | 1.867e-06 | | |100.00 Nlocal: 896.000 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4016.00 ave 4016 max 4016 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: 69544.0 ave 69544 max 69544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69544 Ave neighs/atom = 77.616071 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 9 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 4.706 | 4.706 | 4.706 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 -3789.8057 -3789.8057 26.628666 76.974924 5.1327515 -183.53816 -183.53816 12.15239 -544.87574 -17.891121 2.3310592 852.05497 Loop time of 2.01e-06 on 1 procs for 0 steps with 896 atoms 199.0% 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 | | 2.01e-06 | | |100.00 Nlocal: 896.000 ave 896 max 896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4016.00 ave 4016 max 4016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 34772.0 ave 34772 max 34772 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 69544.0 ave 69544 max 69544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 69544 Ave neighs/atom = 77.616071 Neighbor list builds = 0 Dangerous builds = 0 896 -3789.80568923518 eV 2.33105917001275 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03