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 = 2.8665000 2.8665000 2.8665000 Created orthogonal box = (0.0000000 -38.028420 0.0000000) to (13.445077 38.028420 4.0538432) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8891189 4.3214114 4.0538432 Created 176 atoms using lattice units in orthogonal box = (0.0000000 -38.028420 0.0000000) to (13.445077 38.028420 4.0538432) create_atoms CPU = 0.001 seconds 176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8891189 4.3214114 4.0538432 Created 178 atoms using lattice units in orthogonal box = (0.0000000 -38.028420 0.0000000) to (13.445077 38.028420 4.0538432) create_atoms CPU = 0.000 seconds 178 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 4 20 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 7.673367000244601 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 352 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_960699513424_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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 4 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 4.460 | 4.460 | 4.460 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 5371.8466 0 5371.8466 11826121 72 0 -1498.0504 0 -1498.0504 9680.112 Loop time of 0.398846 on 1 procs for 72 steps with 352 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 = 5371.8465522571 -1498.04914768495 -1498.05035328823 Force two-norm initial, final = 44742.876 0.16466009 Force max component initial, final = 14537.244 0.038127944 Final line search alpha, max atom move = 1.0000000 0.038127944 Iterations, force evaluations = 72 141 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.3892 | 0.3892 | 0.3892 | 0.0 | 97.58 Neigh | 0.0032537 | 0.0032537 | 0.0032537 | 0.0 | 0.82 Comm | 0.0039171 | 0.0039171 | 0.0039171 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002479 | | | 0.62 Nlocal: 352.000 ave 352 max 352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3725.00 ave 3725 max 3725 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: 58584.0 ave 58584 max 58584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58584 Ave neighs/atom = 166.43182 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 4 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 72 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.460 | 4.460 | 4.460 Mbytes Step Temp E_pair E_mol TotEng Press Volume 72 0 -1498.0504 0 -1498.0504 9680.112 4145.4198 77 0 -1498.132 0 -1498.132 -55.482625 4168.0646 Loop time of 0.0229054 on 1 procs for 5 steps with 352 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 = -1498.05035328823 -1498.1318732904 -1498.13204840112 Force two-norm initial, final = 44.819453 0.59007590 Force max component initial, final = 33.100086 0.48585738 Final line search alpha, max atom move = 0.00049188420 0.00023898557 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.021831 | 0.021831 | 0.021831 | 0.0 | 95.31 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022213 | 0.00022213 | 0.00022213 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008518 | | | 3.72 Nlocal: 352.000 ave 352 max 352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3717.00 ave 3717 max 3717 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: 58536.0 ave 58536 max 58536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58536 Ave neighs/atom = 166.29545 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 4 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 4.598 | 4.598 | 4.598 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1498.132 0 -1498.132 -55.482625 Loop time of 1.589e-06 on 1 procs for 0 steps with 352 atoms 125.9% 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 | | 1.589e-06 | | |100.00 Nlocal: 352.000 ave 352 max 352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3717.00 ave 3717 max 3717 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: 58508.0 ave 58508 max 58508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58508 Ave neighs/atom = 166.21591 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 = 7.673367 ghost atom cutoff = 7.673367 binsize = 3.8366835, bins = 4 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.673367000244601 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) = 4.598 | 4.598 | 4.598 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 -1498.132 -1498.132 13.448324 76.346206 4.0595586 -55.482625 -55.482625 68.956837 -48.38104 -187.02367 2.3285312 247.57639 Loop time of 1.544e-06 on 1 procs for 0 steps with 352 atoms 194.3% 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 | | 1.544e-06 | | |100.00 Nlocal: 352.000 ave 352 max 352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3717.00 ave 3717 max 3717 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29254.0 ave 29254 max 29254 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 58508.0 ave 58508 max 58508 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 58508 Ave neighs/atom = 166.21591 Neighbor list builds = 0 Dangerous builds = 0 352 -1498.13204840112 eV 2.3285311692796 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00