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 = 3.6150001 3.6150001 3.6150001 Created orthogonal box = (0.0000000 -36.869527 0.0000000) to (18.432956 36.869527 3.6150001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.2537591 4.2537591 3.6150001 Created 209 atoms using lattice units in orthogonal box = (0.0000000 -36.869527 0.0000000) to (18.432956 36.869527 3.6150001) create_atoms CPU = 0.001 seconds 209 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.2537591 4.2537591 3.6150001 Created 209 atoms using lattice units in orthogonal box = (0.0000000 -36.869527 0.0000000) to (18.432956 36.869527 3.6150001) create_atoms CPU = 0.000 seconds 209 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 17 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 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 412 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_266134052596_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 4.498 | 4.498 | 4.498 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1431.3313 0 -1431.3313 16542.625 50 0 -1451.135 0 -1451.135 -5281.7829 Loop time of 0.463981 on 1 procs for 50 steps with 412 atoms 97.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1431.33133536159 -1451.13364977404 -1451.13499970534 Force two-norm initial, final = 38.306443 0.11368988 Force max component initial, final = 13.607628 0.020518480 Final line search alpha, max atom move = 1.0000000 0.020518480 Iterations, force evaluations = 50 92 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.4574 | 0.4574 | 0.4574 | 0.0 | 98.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0042016 | 0.0042016 | 0.0042016 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002379 | | | 0.51 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5528.00 ave 5528 max 5528 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: 91742.0 ave 91742 max 91742 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 91742 Ave neighs/atom = 222.67476 Neighbor list builds = 0 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 50 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.499 | 4.499 | 4.499 Mbytes Step Temp E_pair E_mol TotEng Press Volume 50 0 -1451.135 0 -1451.135 -5281.7829 4913.612 53 0 -1451.1609 0 -1451.1609 -804.35084 4897.633 Loop time of 0.0327209 on 1 procs for 3 steps with 412 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 = -1451.13499970534 -1451.16011580125 -1451.16090097583 Force two-norm initial, final = 21.171665 0.12222972 Force max component initial, final = 16.590400 0.025096239 Final line search alpha, max atom move = 0.00083736017 2.1014591e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.031335 | 0.031335 | 0.031335 | 0.0 | 95.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027236 | 0.00027236 | 0.00027236 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001114 | | | 3.40 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5588.00 ave 5588 max 5588 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: 92288.0 ave 92288 max 92288 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92288 Ave neighs/atom = 224.00000 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 4.637 | 4.637 | 4.637 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1451.1609 0 -1451.1609 -804.35084 Loop time of 1.776e-06 on 1 procs for 0 steps with 412 atoms 168.9% 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 | | 1.776e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5588.00 ave 5588 max 5588 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: 92340.0 ave 92340 max 92340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92340 Ave neighs/atom = 224.12621 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 5 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.72488399972482 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) = 4.637 | 4.637 | 4.637 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 -1451.1609 -1451.1609 18.385069 73.739054 3.6126295 -804.35084 -804.35084 2.3807249 -2413.8538 -1.5794336 2.3482771 201.48055 Loop time of 2.012e-06 on 1 procs for 0 steps with 412 atoms 198.8% 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 | | 2.012e-06 | | |100.00 Nlocal: 412.000 ave 412 max 412 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5588.00 ave 5588 max 5588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 46170.0 ave 46170 max 46170 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 92340.0 ave 92340 max 92340 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 92340 Ave neighs/atom = 224.12621 Neighbor list builds = 0 Dangerous builds = 0 412 -1451.16090097583 eV 2.34827714024412 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00