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 = 3.6784521 3.6784521 3.6784521 Created orthogonal box = (0.0000000 -66.215817 0.0000000) to (46.819052 66.215817 5.2021169) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.3581429 6.1307536 5.2021169 Created 1300 atoms using lattice units in orthogonal box = (0.0000000 -66.215817 0.0000000) to (46.819052 66.215817 5.2021169) create_atoms CPU = 0.003 seconds 1300 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.3581429 6.1307536 5.2021169 Created 1300 atoms using lattice units in orthogonal box = (0.0000000 -66.215817 0.0000000) to (46.819052 66.215817 5.2021169) create_atoms CPU = 0.003 seconds 1300 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 16 43 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 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 19 atoms, new total = 2581 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_024705128470_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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 16 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.709 | 5.709 | 5.709 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10820.294 0 -10820.294 5156.9279 589 0 -10912.022 0 -10912.022 -58134.826 Loop time of 7.86808 on 1 procs for 589 steps with 2581 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 = -10820.2937074153 -10912.0121500516 -10912.0218220583 Force two-norm initial, final = 54.120015 0.32818144 Force max component initial, final = 12.289945 0.053004777 Final line search alpha, max atom move = 0.89594204 0.047489208 Iterations, force evaluations = 589 1107 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.3621 | 7.3621 | 7.3621 | 0.0 | 93.57 Neigh | 0.29615 | 0.29615 | 0.29615 | 0.0 | 3.76 Comm | 0.10176 | 0.10176 | 0.10176 | 0.0 | 1.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1081 | | | 1.37 Nlocal: 2581.00 ave 2581 max 2581 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9429.00 ave 9429 max 9429 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: 171886.0 ave 171886 max 171886 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171886 Ave neighs/atom = 66.596668 Neighbor list builds = 21 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 16 43 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 589 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.324 | 5.324 | 5.324 Mbytes Step Temp E_pair E_mol TotEng Press Volume 589 0 -10912.022 0 -10912.022 -58134.826 32254.808 629 0 -10957.243 0 -10957.243 2018.6347 30828.477 Loop time of 0.323201 on 1 procs for 40 steps with 2581 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 = -10912.0218220583 -10957.2411468502 -10957.2427389156 Force two-norm initial, final = 2231.2605 5.1638937 Force max component initial, final = 2072.3152 3.1110759 Final line search alpha, max atom move = 8.5941880e-05 0.00026737171 Iterations, force evaluations = 40 41 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30248 | 0.30248 | 0.30248 | 0.0 | 93.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0029801 | 0.0029801 | 0.0029801 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01774 | | | 5.49 Nlocal: 2581.00 ave 2581 max 2581 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9432.00 ave 9432 max 9432 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: 171776.0 ave 171776 max 171776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 171776 Ave neighs/atom = 66.554049 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 16 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.465 | 5.465 | 5.465 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10957.243 0 -10957.243 2018.6347 Loop time of 1.709e-06 on 1 procs for 0 steps with 2581 atoms 117.0% 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 | | 1.709e-06 | | |100.00 Nlocal: 2581.00 ave 2581 max 2581 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9776.00 ave 9776 max 9776 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: 176492.0 ave 176492 max 176492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176492 Ave neighs/atom = 68.381248 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 = 6.1615 ghost atom cutoff = 6.1615 binsize = 3.08075, bins = 16 43 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1615 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) = 5.465 | 5.465 | 5.465 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 -10957.243 -10957.243 46.566513 132.43163 4.9990401 2018.6347 2018.6347 -89.005284 6300.2822 -155.37295 2.3355802 5576.3351 Loop time of 1.757e-06 on 1 procs for 0 steps with 2581 atoms 227.7% 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 | | 1.757e-06 | | |100.00 Nlocal: 2581.00 ave 2581 max 2581 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9776.00 ave 9776 max 9776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 88246.0 ave 88246 max 88246 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 176492.0 ave 176492 max 176492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176492 Ave neighs/atom = 68.381248 Neighbor list builds = 0 Dangerous builds = 0 2581 -10957.2424808156 eV 2.33558024170434 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08