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 = 3.1582519 3.1582519 3.1582519 Created orthogonal box = (0.0000000 -51.315520 0.0000000) to (10.474737 51.315520 7.7361057) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.7612439 4.6650473 5.1574038 Created 263 atoms using lattice units in orthogonal box = (0.0000000 -51.315520 0.0000000) to (10.474737 51.315520 7.7361057) create_atoms CPU = 0.002 seconds 263 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.7612439 4.6650473 5.1574038 Created 265 atoms using lattice units in orthogonal box = (0.0000000 -51.315520 0.0000000) to (10.474737 51.315520 7.7361057) create_atoms CPU = 0.002 seconds 265 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 3 25 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 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 523 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_228581001644_004#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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 3 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.571 | 4.571 | 4.571 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3120.6374 0 -3120.6374 56331.927 325 0 -3317.0525 0 -3317.0525 -12324.323 Loop time of 5.7797 on 1 procs for 325 steps with 523 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3120.63742738054 -3317.04922580236 -3317.05248678997 Force two-norm initial, final = 430.57848 0.33332041 Force max component initial, final = 152.22494 0.078948959 Final line search alpha, max atom move = 0.87490942 0.069073188 Iterations, force evaluations = 325 635 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.568 | 5.568 | 5.568 | 0.0 | 96.34 Neigh | 0.07881 | 0.07881 | 0.07881 | 0.0 | 1.36 Comm | 0.077569 | 0.077569 | 0.077569 | 0.0 | 1.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05534 | | | 0.96 Nlocal: 523.000 ave 523 max 523 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4576.00 ave 4576 max 4576 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: 85880.0 ave 85880 max 85880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85880 Ave neighs/atom = 164.20650 Neighbor list builds = 6 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 3 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 325 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.572 | 4.572 | 4.572 Mbytes Step Temp E_pair E_mol TotEng Press Volume 325 0 -3317.0525 0 -3317.0525 -12324.323 8316.5699 335 0 -3318.1609 0 -3318.1609 190.81393 8278.1694 Loop time of 0.132761 on 1 procs for 10 steps with 523 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3317.05248678999 -3318.16056858164 -3318.16090238705 Force two-norm initial, final = 231.49758 2.2825425 Force max component initial, final = 214.14554 1.1443491 Final line search alpha, max atom move = 0.00031339983 0.00035863883 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12586 | 0.12586 | 0.12586 | 0.0 | 94.80 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.001453 | 0.001453 | 0.001453 | 0.0 | 1.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005453 | | | 4.11 Nlocal: 523.000 ave 523 max 523 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4569.00 ave 4569 max 4569 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: 86002.0 ave 86002 max 86002 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 86002 Ave neighs/atom = 164.43977 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 3 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.710 | 4.710 | 4.710 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3318.1609 0 -3318.1609 190.81393 Loop time of 6.665e-06 on 1 procs for 0 steps with 523 atoms 195.0% 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 | | 6.665e-06 | | |100.00 Nlocal: 523.000 ave 523 max 523 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4616.00 ave 4616 max 4616 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: 85972.0 ave 85972 max 85972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85972 Ave neighs/atom = 164.38241 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 = 8.48804 ghost atom cutoff = 8.48804 binsize = 4.24402, bins = 3 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.48804 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) = 4.710 | 4.710 | 4.710 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 -3318.1609 -3318.1609 10.454433 103.18387 7.6740042 190.81393 190.81393 208.09568 144.64399 219.70211 2.5703814 990.61462 Loop time of 8.64e-06 on 1 procs for 0 steps with 523 atoms 243.1% 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 | | 8.64e-06 | | |100.00 Nlocal: 523.000 ave 523 max 523 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4616.00 ave 4616 max 4616 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 42986.0 ave 42986 max 42986 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 85972.0 ave 85972 max 85972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 85972 Ave neighs/atom = 164.38241 Neighbor list builds = 0 Dangerous builds = 0 523 -3318.16090238705 eV 2.57038144339177 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06