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 = 3.5192937 3.5192937 3.5192937 Created orthogonal box = (0.0000000 -41.640844 0.0000000) to (50.999410 41.640844 8.6204737) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8285040 5.3538228 5.7469825 Created 1663 atoms using lattice units in orthogonal box = (0.0000000 -41.640844 0.0000000) to (50.999410 41.640844 8.6204737) create_atoms CPU = 0.003 seconds 1663 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8285040 5.3538228 5.7469825 Created 1687 atoms using lattice units in orthogonal box = (0.0000000 -41.640844 0.0000000) to (50.999410 41.640844 8.6204737) create_atoms CPU = 0.002 seconds 1687 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 22 3 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 31 atoms, new total = 3319 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_715003088863_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.001 | 7.001 | 7.001 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14588.315 0 -14588.315 9381.6049 140 0 -14697.532 0 -14697.532 -8195.5687 Loop time of 7.56459 on 1 procs for 140 steps with 3319 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 = -14588.3153955879 -14697.5184341247 -14697.5321246697 Force two-norm initial, final = 99.946687 0.50999688 Force max component initial, final = 13.177051 0.10828586 Final line search alpha, max atom move = 0.74531771 0.080707369 Iterations, force evaluations = 140 273 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 7.3522 | 7.3522 | 7.3522 | 0.0 | 97.19 Neigh | 0.14187 | 0.14187 | 0.14187 | 0.0 | 1.88 Comm | 0.029418 | 0.029418 | 0.029418 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04113 | | | 0.54 Nlocal: 3319.00 ave 3319 max 3319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10570.0 ave 10570 max 10570 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: 576018.0 ave 576018 max 576018 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 576018 Ave neighs/atom = 173.55167 Neighbor list builds = 4 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 140 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.997 | 6.997 | 6.997 Mbytes Step Temp E_pair E_mol TotEng Press Volume 140 0 -14697.532 0 -14697.532 -8195.5687 36613.884 143 0 -14697.992 0 -14697.992 -0.20466521 36443.158 Loop time of 0.16123 on 1 procs for 3 steps with 3319 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 = -14697.5321246698 -14697.9859729886 -14697.9919055114 Force two-norm initial, final = 327.38420 1.5222314 Force max component initial, final = 223.06264 0.99879310 Final line search alpha, max atom move = 5.6250620e-05 5.6182731e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15803 | 0.15803 | 0.15803 | 0.0 | 98.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049132 | 0.00049132 | 0.00049132 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002707 | | | 1.68 Nlocal: 3319.00 ave 3319 max 3319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10582.0 ave 10582 max 10582 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: 576114.0 ave 576114 max 576114 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 576114 Ave neighs/atom = 173.58060 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.135 | 7.135 | 7.135 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -14697.992 0 -14697.992 -0.20466521 Loop time of 1.776e-06 on 1 procs for 0 steps with 3319 atoms 168.9% 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 | | 1.776e-06 | | |100.00 Nlocal: 3319.00 ave 3319 max 3319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10582.0 ave 10582 max 10582 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: 576536.0 ave 576536 max 576536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 576536 Ave neighs/atom = 173.70774 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 7.135 | 7.135 | 7.135 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 -14697.992 -14697.992 50.944303 83.082736 8.6101276 -0.20466521 -0.20466521 -41.841758 -2.6301891 43.857952 2.0707278 1641.841 Loop time of 2.091e-06 on 1 procs for 0 steps with 3319 atoms 286.9% 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 | | 2.091e-06 | | |100.00 Nlocal: 3319.00 ave 3319 max 3319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10582.0 ave 10582 max 10582 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 288268.0 ave 288268 max 288268 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 576536.0 ave 576536 max 576536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 576536 Ave neighs/atom = 173.70774 Neighbor list builds = 0 Dangerous builds = 0 3319 -14697.9919055114 eV 2.07072776154406 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:08