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 = 2.8603420 2.8603420 2.8603420 Created orthogonal box = (0.0000000 -43.193077 0.0000000) to (30.540095 43.193077 4.0451344) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8221203 4.1674771 4.0451344 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -43.193077 0.0000000) to (30.540095 43.193077 4.0451344) create_atoms CPU = 0.001 seconds 458 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8221203 4.1674771 4.0451344 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -43.193077 0.0000000) to (30.540095 43.193077 4.0451344) create_atoms CPU = 0.001 seconds 458 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 23 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 9 atoms, new total = 907 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_657255834688_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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 4.984 | 4.984 | 4.984 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3804.2786 0 -3804.2786 15226.477 259 0 -3967.7531 0 -3967.7531 -6794.7829 Loop time of 3.3737 on 1 procs for 259 steps with 907 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 = -3804.27858421228 -3967.74932643078 -3967.75309644257 Force two-norm initial, final = 116.28521 0.33651754 Force max component initial, final = 31.650678 0.10910257 Final line search alpha, max atom move = 0.91281558 0.099590522 Iterations, force evaluations = 259 454 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.2354 | 3.2354 | 3.2354 | 0.0 | 95.90 Neigh | 0.097109 | 0.097109 | 0.097109 | 0.0 | 2.88 Comm | 0.022971 | 0.022971 | 0.022971 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01824 | | | 0.54 Nlocal: 907.000 ave 907 max 907 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6374.00 ave 6374 max 6374 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: 143302.0 ave 143302 max 143302 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 143302 Ave neighs/atom = 157.99559 Neighbor list builds = 11 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 259 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.986 | 4.986 | 4.986 Mbytes Step Temp E_pair E_mol TotEng Press Volume 259 0 -3967.7531 0 -3967.7531 -6794.7829 10672.041 270 0 -3968.5301 0 -3968.5301 -409.49292 10616.611 Loop time of 0.0939554 on 1 procs for 11 steps with 907 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 = -3967.75309644258 -3968.52697111615 -3968.53005180971 Force two-norm initial, final = 132.56812 1.5781419 Force max component initial, final = 123.77950 0.26556572 Final line search alpha, max atom move = 0.00014832791 3.9390810e-05 Iterations, force evaluations = 11 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.090674 | 0.090674 | 0.090674 | 0.0 | 96.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00058446 | 0.00058446 | 0.00058446 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002697 | | | 2.87 Nlocal: 907.000 ave 907 max 907 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6366.00 ave 6366 max 6366 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: 142904.0 ave 142904 max 142904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 142904 Ave neighs/atom = 157.55678 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.124 | 5.124 | 5.124 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3968.5301 0 -3968.5301 -409.49292 Loop time of 1.588e-06 on 1 procs for 0 steps with 907 atoms 125.9% 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 | | 1.588e-06 | | |100.00 Nlocal: 907.000 ave 907 max 907 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6383.00 ave 6383 max 6383 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: 143962.0 ave 143962 max 143962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 143962 Ave neighs/atom = 158.72326 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 5.124 | 5.124 | 5.124 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 -3968.5301 -3968.5301 30.214305 86.386155 4.067515 -409.49292 -409.49292 39.649588 -1247.488 -20.640312 2.2752662 5734.5583 Loop time of 1.602e-06 on 1 procs for 0 steps with 907 atoms 249.7% 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 | | 1.602e-06 | | |100.00 Nlocal: 907.000 ave 907 max 907 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6383.00 ave 6383 max 6383 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 71981.0 ave 71981 max 71981 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 143962.0 ave 143962 max 143962 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 143962 Ave neighs/atom = 158.72326 Neighbor list builds = 0 Dangerous builds = 0 907 -3968.53005180971 eV 2.27526622963061 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03