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 = 3.5600001 3.5600001 3.5600001 Created orthogonal box = (0.0000000 -65.643159 0.0000000) to (32.821579 65.643159 3.5600001) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0197710 5.0197710 3.5600001 Created 680 atoms using lattice units in orthogonal box = (0.0000000 -65.643159 0.0000000) to (32.821579 65.643159 3.5600001) create_atoms CPU = 0.003 seconds 680 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0197710 5.0197710 3.5600001 Created 682 atoms using lattice units in orthogonal box = (0.0000000 -65.643159 0.0000000) to (32.821579 65.643159 3.5600001) create_atoms CPU = 0.002 seconds 682 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 = 9 34 1 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 0 atoms, new total = 1362 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 = 9 34 1 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) = 5.514 | 5.514 | 5.514 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5815.4126 0 -5815.4126 36282.517 33 0 -5982.2121 0 -5982.2121 14819.723 Loop time of 1.64492 on 1 procs for 33 steps with 1362 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 = -5815.4125626641 -5982.206932621 -5982.2121439446 Force two-norm initial, final = 310.50118 0.37906257 Force max component initial, final = 126.18712 0.070042699 Final line search alpha, max atom move = 1.0000000 0.070042699 Iterations, force evaluations = 33 57 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6201 | 1.6201 | 1.6201 | 0.0 | 98.49 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.01479 | 0.01479 | 0.01479 | 0.0 | 0.90 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009985 | | | 0.61 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11015.0 ave 11015 max 11015 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: 240124.0 ave 240124 max 240124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 240124 Ave neighs/atom = 176.30250 Neighbor list builds = 0 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 = 9 34 1 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 : 33 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.514 | 5.514 | 5.514 Mbytes Step Temp E_pair E_mol TotEng Press Volume 33 0 -5982.2121 0 -5982.2121 14819.723 15340.127 45 0 -5983.1446 0 -5983.1446 248.34501 15455.973 Loop time of 0.439608 on 1 procs for 12 steps with 1362 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 = -5982.21214394459 -5983.14314743239 -5983.14464515038 Force two-norm initial, final = 261.87067 5.5609594 Force max component initial, final = 210.85192 4.1531391 Final line search alpha, max atom move = 9.2126363e-05 0.00038261360 Iterations, force evaluations = 12 13 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.39262 | 0.39262 | 0.39262 | 0.0 | 89.31 Neigh | 0.031311 | 0.031311 | 0.031311 | 0.0 | 7.12 Comm | 0.0041671 | 0.0041671 | 0.0041671 | 0.0 | 0.95 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01151 | | | 2.62 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10970.0 ave 10970 max 10970 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: 238640.0 ave 238640 max 238640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238640 Ave neighs/atom = 175.21292 Neighbor list builds = 1 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 = 9 34 1 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) = 5.652 | 5.652 | 5.652 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5983.1446 0 -5983.1446 248.34501 Loop time of 7.868e-06 on 1 procs for 0 steps with 1362 atoms 190.6% 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 | | 7.868e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10970.0 ave 10970 max 10970 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: 238536.0 ave 238536 max 238536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238536 Ave neighs/atom = 175.13656 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 = 9 34 1 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) = 5.652 | 5.652 | 5.652 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 -5983.1446 -5983.1446 32.98307 132.43717 3.5383059 248.34501 248.34501 432.63542 373.20941 -60.809798 2.3172337 158.78392 Loop time of 6.425e-06 on 1 procs for 0 steps with 1362 atoms 264.6% 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 | | 6.425e-06 | | |100.00 Nlocal: 1362.00 ave 1362 max 1362 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10970.0 ave 10970 max 10970 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 119268.0 ave 119268 max 119268 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 238536.0 ave 238536 max 238536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 238536 Ave neighs/atom = 175.13656 Neighbor list builds = 0 Dangerous builds = 0 1362 -5983.14464515038 eV 2.31723367650949 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02