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 = 4.0320734 4.0320734 4.0320734 Created orthogonal box = (0.0000000 -43.050763 0.0000000) to (30.441486 43.050763 5.7022129) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8746728 6.7974889 5.7022129 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -43.050763 0.0000000) to (30.441486 43.050763 5.7022129) create_atoms CPU = 0.001 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8746728 6.7974889 5.7022129 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -43.050763 0.0000000) to (30.441486 43.050763 5.7022129) 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 6 atoms, new total = 908 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_020851069572_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 4.967 | 4.967 | 4.967 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2979.9217 0 -2979.9217 5474.1779 64 0 -3041.5284 0 -3041.5284 2195.8726 Loop time of 1.16785 on 1 procs for 64 steps with 908 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2979.92169334271 -3041.5255318607 -3041.52841033291 Force two-norm initial, final = 34.488998 0.13484623 Force max component initial, final = 6.9744491 0.023882876 Final line search alpha, max atom move = 1.0000000 0.023882876 Iterations, force evaluations = 64 115 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1344 | 1.1344 | 1.1344 | 0.0 | 97.13 Neigh | 0.014898 | 0.014898 | 0.014898 | 0.0 | 1.28 Comm | 0.0096948 | 0.0096948 | 0.0096948 | 0.0 | 0.83 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008869 | | | 0.76 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5097.00 ave 5097 max 5097 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: 118216.0 ave 118216 max 118216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118216 Ave neighs/atom = 130.19383 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 8 23 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 64 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.967 | 4.967 | 4.967 Mbytes Step Temp E_pair E_mol TotEng Press Volume 64 0 -3041.5284 0 -3041.5284 2195.8726 14945.833 72 0 -3041.7812 0 -3041.7812 -10.914566 14986.257 Loop time of 0.105417 on 1 procs for 8 steps with 908 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 = -3041.5284103329 -3041.77902302115 -3041.78118767296 Force two-norm initial, final = 65.438571 0.52203414 Force max component initial, final = 65.311783 0.32936955 Final line search alpha, max atom move = 0.00024173428 7.9619912e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10092 | 0.10092 | 0.10092 | 0.0 | 95.73 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00080731 | 0.00080731 | 0.00080731 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003691 | | | 3.50 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5098.00 ave 5098 max 5098 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: 118900.0 ave 118900 max 118900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118900 Ave neighs/atom = 130.94714 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.105 | 5.105 | 5.105 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3041.7812 0 -3041.7812 -10.914566 Loop time of 3.097e-06 on 1 procs for 0 steps with 908 atoms 129.2% 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 | | 3.097e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5112.00 ave 5112 max 5112 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: 118668.0 ave 118668 max 118668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118668 Ave neighs/atom = 130.69163 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 8 23 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.105 | 5.105 | 5.105 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 -3041.7812 -3041.7812 30.344585 86.761283 5.6922767 -10.914566 -10.914566 -35.100716 -22.828901 25.185918 2.6792806 858.52717 Loop time of 3.045e-06 on 1 procs for 0 steps with 908 atoms 131.4% 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 | | 3.045e-06 | | |100.00 Nlocal: 908.000 ave 908 max 908 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5112.00 ave 5112 max 5112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 59334.0 ave 59334 max 59334 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 118668.0 ave 118668 max 118668 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 118668 Ave neighs/atom = 130.69163 Neighbor list builds = 0 Dangerous builds = 0 908 -3041.78118767296 eV 2.67928063415355 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01