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 = 3.6584036 3.6584036 3.6584036 Created orthogonal box = (0.0000000 -69.026621 0.0000000) to (34.513311 69.026621 3.6584036) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0412701 5.0412701 3.6584036 Created 712 atoms using lattice units in orthogonal box = (0.0000000 -69.026621 0.0000000) to (34.513311 69.026621 3.6584036) create_atoms CPU = 0.002 seconds 712 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0412701 5.0412701 3.6584036 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -69.026621 0.0000000) to (34.513311 69.026621 3.6584036) create_atoms CPU = 0.002 seconds 714 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 38 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1426 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_143977152728_005#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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.110 | 5.110 | 5.110 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5089.6201 0 -5089.6201 80387.962 179 0 -5547.2828 0 -5547.2828 -454.68417 Loop time of 8.08888 on 1 procs for 179 steps with 1426 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 = -5089.62007349122 -5547.27758661715 -5547.2828037402 Force two-norm initial, final = 947.07242 0.26322929 Force max component initial, final = 248.50038 0.050835559 Final line search alpha, max atom move = 1.0000000 0.050835559 Iterations, force evaluations = 179 346 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.9016 | 7.9016 | 7.9016 | 0.0 | 97.69 Neigh | 0.050644 | 0.050644 | 0.050644 | 0.0 | 0.63 Comm | 0.077374 | 0.077374 | 0.077374 | 0.0 | 0.96 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05923 | | | 0.73 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9702.00 ave 9702 max 9702 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: 196996.0 ave 196996 max 196996 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 196996 Ave neighs/atom = 138.14586 Neighbor list builds = 2 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 179 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.487 | 5.487 | 5.487 Mbytes Step Temp E_pair E_mol TotEng Press Volume 179 0 -5547.2828 0 -5547.2828 -454.68417 17431.102 232 0 -5567.7563 0 -5567.7563 -255.61292 17440.952 Loop time of 1.48037 on 1 procs for 53 steps with 1426 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -5547.28280374017 -5567.75230777058 -5567.75630762535 Force two-norm initial, final = 580.72264 7.1773788 Force max component initial, final = 414.23410 4.8582533 Final line search alpha, max atom move = 0.00016179231 0.00078602801 Iterations, force evaluations = 53 54 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.2772 | 1.2772 | 1.2772 | 0.0 | 86.27 Neigh | 0.14873 | 0.14873 | 0.14873 | 0.0 | 10.05 Comm | 0.013318 | 0.013318 | 0.013318 | 0.0 | 0.90 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04113 | | | 2.78 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8786.00 ave 8786 max 8786 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: 202296.0 ave 202296 max 202296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202296 Ave neighs/atom = 141.86255 Neighbor list builds = 6 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.621 | 5.621 | 5.621 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5567.7563 0 -5567.7563 -255.61292 Loop time of 6.375e-06 on 1 procs for 0 steps with 1426 atoms 188.2% 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 | | 6.375e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8786.00 ave 8786 max 8786 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: 202136.0 ave 202136 max 202136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202136 Ave neighs/atom = 141.75035 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.621 | 5.621 | 5.621 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 -5567.7563 -5567.7563 34.612407 131.63367 3.8279954 -255.61292 -255.61292 -156.64465 -425.5403 -184.6538 2.1700169 483.87295 Loop time of 7.558e-06 on 1 procs for 0 steps with 1426 atoms 251.4% 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 | | 7.558e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8786.00 ave 8786 max 8786 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 101068.0 ave 101068 max 101068 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 202136.0 ave 202136 max 202136 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 202136 Ave neighs/atom = 141.75035 Neighbor list builds = 0 Dangerous builds = 0 1426 -5567.75630762535 eV 2.1700169438715 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11