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 = 3.6582963 3.6582963 3.6582963 Created orthogonal box = (0.0000000 -47.416940 0.0000000) to (27.376183 47.416940 6.3363551) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8663249 5.6448738 6.3363551 Created 672 atoms using lattice units in orthogonal box = (0.0000000 -47.416940 0.0000000) to (27.376183 47.416940 6.3363551) create_atoms CPU = 0.002 seconds 672 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8663249 5.6448738 6.3363551 Created 676 atoms using lattice units in orthogonal box = (0.0000000 -47.416940 0.0000000) to (27.376183 47.416940 6.3363551) create_atoms CPU = 0.002 seconds 676 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 ghost atom cutoff = 8 binsize = 4, bins = 7 24 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 1344 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_942420706858_005#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 ghost atom cutoff = 8 binsize = 4, bins = 7 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.503 | 5.503 | 5.503 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4982.7519 0 -4982.7519 72834.022 564 0 -5442.8426 0 -5442.8426 -61877.673 Loop time of 14.1475 on 1 procs for 564 steps with 1344 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4982.75190066185 -5442.83755179083 -5442.84257469429 Force two-norm initial, final = 460.51129 0.23632986 Force max component initial, final = 81.543924 0.061114749 Final line search alpha, max atom move = 1.0000000 0.061114749 Iterations, force evaluations = 564 1092 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 13.785 | 13.785 | 13.785 | 0.0 | 97.43 Neigh | 0.16612 | 0.16612 | 0.16612 | 0.0 | 1.17 Comm | 0.10879 | 0.10879 | 0.10879 | 0.0 | 0.77 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08799 | | | 0.62 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7367.00 ave 7367 max 7367 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: 227016.0 ave 227016 max 227016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227016 Ave neighs/atom = 168.91071 Neighbor list builds = 10 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 ghost atom cutoff = 8 binsize = 4, bins = 7 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 564 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.500 | 5.500 | 5.500 Mbytes Step Temp E_pair E_mol TotEng Press Volume 564 0 -5442.8426 0 -5442.8426 -61877.673 16450.38 605 0 -5462.3305 0 -5462.3305 3185.3027 15724.899 Loop time of 0.589907 on 1 procs for 41 steps with 1344 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 = -5442.8425746943 -5462.32510308951 -5462.33052373472 Force two-norm initial, final = 1165.4870 55.219222 Force max component initial, final = 937.73453 34.336528 Final line search alpha, max atom move = 2.1509263e-05 0.00073855342 Iterations, force evaluations = 41 44 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.55379 | 0.55379 | 0.55379 | 0.0 | 93.88 Neigh | 0.015962 | 0.015962 | 0.015962 | 0.0 | 2.71 Comm | 0.003229 | 0.003229 | 0.003229 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01692 | | | 2.87 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7524.00 ave 7524 max 7524 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: 231536.0 ave 231536 max 231536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231536 Ave neighs/atom = 172.27381 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 7 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.639 | 5.639 | 5.639 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5462.3305 0 -5462.3305 3185.3027 Loop time of 2.396e-06 on 1 procs for 0 steps with 1344 atoms 166.9% 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 | | 2.396e-06 | | |100.00 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7523.00 ave 7523 max 7523 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: 232994.0 ave 232994 max 232994 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 232994 Ave neighs/atom = 173.35863 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 ghost atom cutoff = 8 binsize = 4, bins = 7 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.639 | 5.639 | 5.639 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 -5462.3305 -5462.3305 26.374813 94.021767 6.3411799 3185.3027 3185.3027 3370.508 3197.0019 2988.3981 2.1820725 4131.6275 Loop time of 2.65e-06 on 1 procs for 0 steps with 1344 atoms 264.2% 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 | | 2.65e-06 | | |100.00 Nlocal: 1344.00 ave 1344 max 1344 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7523.00 ave 7523 max 7523 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 116497.0 ave 116497 max 116497 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 232994.0 ave 232994 max 232994 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 232994 Ave neighs/atom = 173.35863 Neighbor list builds = 0 Dangerous builds = 0 1344 -5462.33052373472 eV 2.18207248610981 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15