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 = 3.5200000 3.5200000 3.5200000 Created orthogonal box = (0.0000000 -35.550258 0.0000000) to (25.137828 35.550258 4.9780318) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4360873 5.5765110 4.9780318 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -35.550258 0.0000000) to (25.137828 35.550258 4.9780318) create_atoms CPU = 0.003 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4360873 5.5765110 4.9780318 Created 410 atoms using lattice units in orthogonal box = (0.0000000 -35.550258 0.0000000) to (25.137828 35.550258 4.9780318) create_atoms CPU = 0.002 seconds 410 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 17 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 808 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_103383163946_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 4.988 | 4.988 | 4.988 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3380.438 0 -3380.438 65054.578 53 0 -3576.2101 0 -3576.2101 -2393.9489 Loop time of 1.9527 on 1 procs for 53 steps with 808 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 = -3380.43800818127 -3576.20671574184 -3576.21009981864 Force two-norm initial, final = 512.59503 0.18998129 Force max component initial, final = 158.05463 0.013796833 Final line search alpha, max atom move = 1.0000000 0.013796833 Iterations, force evaluations = 53 91 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8739 | 1.8739 | 1.8739 | 0.0 | 95.96 Neigh | 0.052615 | 0.052615 | 0.052615 | 0.0 | 2.69 Comm | 0.014816 | 0.014816 | 0.014816 | 0.0 | 0.76 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01141 | | | 0.58 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6385.00 ave 6385 max 6385 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: 180660.0 ave 180660 max 180660 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180660 Ave neighs/atom = 223.58911 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 17 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.989 | 4.989 | 4.989 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -3576.2101 0 -3576.2101 -2393.9489 8897.2986 56 0 -3576.2362 0 -3576.2362 1.0467573 8885.4069 Loop time of 0.158292 on 1 procs for 3 steps with 808 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 = -3576.21009981865 -3576.23503745172 -3576.23620503393 Force two-norm initial, final = 29.694489 0.22640266 Force max component initial, final = 21.355183 0.022357597 Final line search alpha, max atom move = 0.00027327683 6.1098133e-06 Iterations, force evaluations = 3 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15377 | 0.15377 | 0.15377 | 0.0 | 97.14 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010256 | 0.0010256 | 0.0010256 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003495 | | | 2.21 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6338.00 ave 6338 max 6338 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: 180328.0 ave 180328 max 180328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180328 Ave neighs/atom = 223.17822 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.127 | 5.127 | 5.127 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3576.2362 0 -3576.2362 1.0467573 Loop time of 6.395e-06 on 1 procs for 0 steps with 808 atoms 172.0% 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 | | 6.395e-06 | | |100.00 Nlocal: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6347.00 ave 6347 max 6347 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: 180376.0 ave 180376 max 180376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180376 Ave neighs/atom = 223.23762 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 6 17 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 5.127 | 5.127 | 5.127 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 -3576.2362 -3576.2362 25.092821 71.174052 4.9751495 1.0467573 1.0467573 3.8695419 -0.20964257 -0.51962753 2.2241748 455.69631 Loop time of 6.766e-06 on 1 procs for 0 steps with 808 atoms 280.8% 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: 808.000 ave 808 max 808 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6347.00 ave 6347 max 6347 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 90188.0 ave 90188 max 90188 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 180376.0 ave 180376 max 180376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 180376 Ave neighs/atom = 223.23762 Neighbor list builds = 0 Dangerous builds = 0 808 -3554.23330138273 eV 2.22417483796028 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02