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 = 3.6390874 3.6390874 3.6390874 Created orthogonal box = (0.0000000 -58.678521 0.0000000) to (29.339261 58.678521 3.6390874) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0623592 4.0623592 3.6390874 Created 520 atoms using lattice units in orthogonal box = (0.0000000 -58.678521 0.0000000) to (29.339261 58.678521 3.6390874) create_atoms CPU = 0.001 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0623592 4.0623592 3.6390874 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.678521 0.0000000) to (29.339261 58.678521 3.6390874) create_atoms CPU = 0.000 seconds 522 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 25 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 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 1036 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_609260676108_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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 5.864 | 5.864 | 5.864 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2566.9886 0 -2566.9886 150940.23 56 0 -3390.8368 0 -3390.8368 -364.01627 Loop time of 1.87289 on 1 procs for 56 steps with 1036 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2566.98855390384 -3390.8339876537 -3390.83676995108 Force two-norm initial, final = 2147.8067 0.13509589 Force max component initial, final = 725.83629 0.0098547365 Final line search alpha, max atom move = 1.0000000 0.0098547365 Iterations, force evaluations = 56 97 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8348 | 1.8348 | 1.8348 | 0.0 | 97.97 Neigh | 0.017924 | 0.017924 | 0.017924 | 0.0 | 0.96 Comm | 0.012532 | 0.012532 | 0.012532 | 0.0 | 0.67 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007592 | | | 0.41 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11876.0 ave 11876 max 11876 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: 329144.0 ave 329144 max 329144 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 329144 Ave neighs/atom = 317.70656 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 25 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 56 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.865 | 5.865 | 5.865 Mbytes Step Temp E_pair E_mol TotEng Press Volume 56 0 -3390.8368 0 -3390.8368 -364.01627 12529.992 60 0 -3390.8647 0 -3390.8647 27.736684 12526.982 Loop time of 0.133744 on 1 procs for 4 steps with 1036 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 = -3390.83676995109 -3390.86433814597 -3390.86468407234 Force two-norm initial, final = 15.857212 0.58568744 Force max component initial, final = 10.821791 0.55642379 Final line search alpha, max atom move = 0.00014686213 8.1717585e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13029 | 0.13029 | 0.13029 | 0.0 | 97.42 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00063651 | 0.00063651 | 0.00063651 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002819 | | | 2.11 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11892.0 ave 11892 max 11892 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: 329192.0 ave 329192 max 329192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 329192 Ave neighs/atom = 317.75290 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.003 | 6.003 | 6.003 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3390.8647 0 -3390.8647 27.736684 Loop time of 2.056e-06 on 1 procs for 0 steps with 1036 atoms 145.9% 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 | | 2.056e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11892.0 ave 11892 max 11892 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: 329268.0 ave 329268 max 329268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 329268 Ave neighs/atom = 317.82625 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 = 9.6 ghost atom cutoff = 9.6 binsize = 4.8, bins = 7 25 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.6 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) = 6.003 | 6.003 | 6.003 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 -3390.8647 -3390.8647 29.424174 117.23847 3.6313831 27.736684 27.736684 -0.38983745 71.093607 12.506283 2.3076436 200.81405 Loop time of 2.4e-06 on 1 procs for 0 steps with 1036 atoms 208.3% 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 | | 2.4e-06 | | |100.00 Nlocal: 1036.00 ave 1036 max 1036 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11892.0 ave 11892 max 11892 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 164634.0 ave 164634 max 164634 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 329268.0 ave 329268 max 329268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 329268 Ave neighs/atom = 317.82625 Neighbor list builds = 0 Dangerous builds = 0 1036 -3390.86468407234 eV 2.30764355271458 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02