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 = 3.6133157 3.6133157 3.6133157 Created orthogonal box = (0.0000000 -65.043295 0.0000000) to (45.990000 65.043295 5.1100000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2455556 6.0221928 5.1100000 Created 1299 atoms using lattice units in orthogonal box = (0.0000000 -65.043295 0.0000000) to (45.990000 65.043295 5.1100000) create_atoms CPU = 0.010 seconds 1299 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2455556 6.0221928 5.1100000 Created 1299 atoms using lattice units in orthogonal box = (0.0000000 -65.043295 0.0000000) to (45.990000 65.043295 5.1100000) create_atoms CPU = 0.010 seconds 1299 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 41 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 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 15 atoms, new total = 2583 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_353393547686_001#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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.731 | 5.731 | 5.731 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9043.2751 0 -9043.2751 9976.7523 41 0 -9121.3985 0 -9121.3985 -678.4839 Loop time of 10.5688 on 1 procs for 41 steps with 2583 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 = -9043.27508138395 -9121.39062147184 -9121.39853720465 Force two-norm initial, final = 80.989539 0.25717858 Force max component initial, final = 14.894495 0.046692052 Final line search alpha, max atom move = 1.0000000 0.046692052 Iterations, force evaluations = 41 67 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 10.491 | 10.491 | 10.491 | 0.0 | 99.26 Neigh | 0.039635 | 0.039635 | 0.039635 | 0.0 | 0.38 Comm | 0.01878 | 0.01878 | 0.01878 | 0.0 | 0.18 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0193 | | | 0.18 Nlocal: 2583.00 ave 2583 max 2583 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11027.0 ave 11027 max 11027 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: 222946.0 ave 222946 max 222946 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 222946 Ave neighs/atom = 86.312815 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 41 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.731 | 5.731 | 5.731 Mbytes Step Temp E_pair E_mol TotEng Press Volume 41 0 -9121.3985 0 -9121.3985 -678.4839 30571.507 42 0 -9121.403 0 -9121.403 -563.32987 30569.008 Loop time of 0.466307 on 1 procs for 1 steps with 2583 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 = -9121.39853720465 -9121.39853720465 -9121.40304354827 Force two-norm initial, final = 16.068954 1.1202455 Force max component initial, final = 12.474218 0.87952040 Final line search alpha, max atom move = 8.0165349e-05 7.0507059e-05 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.46335 | 0.46335 | 0.46335 | 0.0 | 99.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00076416 | 0.00076416 | 0.00076416 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002193 | | | 0.47 Nlocal: 2583.00 ave 2583 max 2583 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11022.0 ave 11022 max 11022 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: 223392.0 ave 223392 max 223392 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223392 Ave neighs/atom = 86.485482 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.869 | 5.869 | 5.869 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9121.403 0 -9121.403 -563.32987 Loop time of 6.766e-06 on 1 procs for 0 steps with 2583 atoms 177.4% 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 | | 6.766e-06 | | |100.00 Nlocal: 2583.00 ave 2583 max 2583 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11022.0 ave 11022 max 11022 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: 223408.0 ave 223408 max 223408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223408 Ave neighs/atom = 86.491676 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 = 6.5 ghost atom cutoff = 6.5 binsize = 3.25, bins = 15 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.5 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) = 5.869 | 5.869 | 5.869 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 -9121.403 -9121.403 46.006183 130.08659 5.107785 -563.32987 -563.32987 46.113461 -1769.9154 33.812357 2.3697287 1297.6651 Loop time of 7.006e-06 on 1 procs for 0 steps with 2583 atoms 299.7% 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 | | 7.006e-06 | | |100.00 Nlocal: 2583.00 ave 2583 max 2583 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11022.0 ave 11022 max 11022 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 111704.0 ave 111704 max 111704 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 223408.0 ave 223408 max 223408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 223408 Ave neighs/atom = 86.491676 Neighbor list builds = 0 Dangerous builds = 0 2583 -9121.40304354827 eV 2.36972866833863 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:12