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 = 3.5181212 3.5181212 3.5181212 Created orthogonal box = (0.0000000 -42.513139 0.0000000) to (52.063440 42.513139 8.6176019) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9923847 5.2409121 5.7450679 Created 1754 atoms using lattice units in orthogonal box = (0.0000000 -42.513139 0.0000000) to (52.063440 42.513139 8.6176019) create_atoms CPU = 0.002 seconds 1754 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9923847 5.2409121 5.7450679 Created 1754 atoms using lattice units in orthogonal box = (0.0000000 -42.513139 0.0000000) to (52.063440 42.513139 8.6176019) create_atoms CPU = 0.002 seconds 1754 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 12 20 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 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 52 atoms, new total = 3456 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_222110751402_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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 12 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 12.19 | 12.19 | 12.19 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15017.972 0 -15017.972 4804.6736 52 0 -15097.346 0 -15097.346 -13591.804 Loop time of 4.26845 on 1 procs for 52 steps with 3456 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 = -15017.9722040629 -15097.3323994016 -15097.3460927307 Force two-norm initial, final = 115.15341 0.38462181 Force max component initial, final = 22.401461 0.067922873 Final line search alpha, max atom move = 1.0000000 0.067922873 Iterations, force evaluations = 52 95 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.193 | 4.193 | 4.193 | 0.0 | 98.23 Neigh | 0.048412 | 0.048412 | 0.048412 | 0.0 | 1.13 Comm | 0.012669 | 0.012669 | 0.012669 | 0.0 | 0.30 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01433 | | | 0.34 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13592.0 ave 13592 max 13592 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: 846056.0 ave 846056 max 846056 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 846056 Ave neighs/atom = 244.80787 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 12 20 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 52 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 12.19 | 12.19 | 12.19 Mbytes Step Temp E_pair E_mol TotEng Press Volume 52 0 -15097.346 0 -15097.346 -13591.804 38148.06 57 0 -15098.351 0 -15098.351 -2867.7055 37908.462 Loop time of 0.312209 on 1 procs for 5 steps with 3456 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 = -15097.3460927306 -15098.3453973931 -15098.3505300213 Force two-norm initial, final = 426.46952 2.1669718 Force max component initial, final = 346.27301 1.5623172 Final line search alpha, max atom move = 6.0018269e-05 9.3767576e-05 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30767 | 0.30767 | 0.30767 | 0.0 | 98.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00069791 | 0.00069791 | 0.00069791 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003837 | | | 1.23 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13543.0 ave 13543 max 13543 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: 846320.0 ave 846320 max 846320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 846320 Ave neighs/atom = 244.88426 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 12 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 11.71 | 11.71 | 11.71 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15098.351 0 -15098.351 -2867.7055 Loop time of 1.781e-06 on 1 procs for 0 steps with 3456 atoms 224.6% 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 | | 1.781e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13581.0 ave 13581 max 13581 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: 847988.0 ave 847988 max 847988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 847988 Ave neighs/atom = 245.36690 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 12 20 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.7 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) = 11.71 | 11.71 | 11.71 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 -15098.351 -15098.351 51.839265 85.026278 8.6005092 -2867.7055 -2867.7055 -65.746008 -8477.9807 -59.389897 2.1624762 1349.3423 Loop time of 1.987e-06 on 1 procs for 0 steps with 3456 atoms 251.6% 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 | | 1.987e-06 | | |100.00 Nlocal: 3456.00 ave 3456 max 3456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13581.0 ave 13581 max 13581 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 423994.0 ave 423994 max 423994 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 847988.0 ave 847988 max 847988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 847988 Ave neighs/atom = 245.36690 Neighbor list builds = 0 Dangerous builds = 0 3456 -15098.3505300213 eV 2.16247619187256 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05