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 -40.420136 0.0000000) to (28.581352 40.420136 4.9753748) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0627110 5.5118367 4.9753748 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -40.420136 0.0000000) to (28.581352 40.420136 4.9753748) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0627110 5.5118367 4.9753748 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -40.420136 0.0000000) to (28.581352 40.420136 4.9753748) create_atoms CPU = 0.001 seconds 532 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 = 7 19 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 12 atoms, new total = 1048 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 = 7 19 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) = 5.443 | 5.443 | 5.443 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4172.2546 0 -4172.2546 91863.888 75 0 -4579.7075 0 -4579.7075 -4981.2431 Loop time of 1.98756 on 1 procs for 75 steps with 1048 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 = -4172.2545808092 -4579.70378435578 -4579.70750964702 Force two-norm initial, final = 721.00120 0.18940932 Force max component initial, final = 175.25842 0.018877149 Final line search alpha, max atom move = 1.0000000 0.018877149 Iterations, force evaluations = 75 127 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9393 | 1.9393 | 1.9393 | 0.0 | 97.57 Neigh | 0.031062 | 0.031062 | 0.031062 | 0.0 | 1.56 Comm | 0.0096111 | 0.0096111 | 0.0096111 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007598 | | | 0.38 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8177.00 ave 8177 max 8177 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: 257768.0 ave 257768 max 257768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 257768 Ave neighs/atom = 245.96183 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 = 8.7 ghost atom cutoff = 8.7 binsize = 4.35, bins = 7 19 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 : 75 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.441 | 5.441 | 5.441 Mbytes Step Temp E_pair E_mol TotEng Press Volume 75 0 -4579.7075 0 -4579.7075 -4981.2431 11495.724 79 0 -4579.8468 0 -4579.8468 30.475937 11460.257 Loop time of 0.106722 on 1 procs for 4 steps with 1048 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 = -4579.70750964702 -4579.84647785728 -4579.84675713036 Force two-norm initial, final = 81.719237 1.1031634 Force max component initial, final = 59.670301 0.99960760 Final line search alpha, max atom move = 0.00026026643 0.00026016431 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10463 | 0.10463 | 0.10463 | 0.0 | 98.04 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00041526 | 0.00041526 | 0.00041526 | 0.0 | 0.39 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001674 | | | 1.57 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7839.00 ave 7839 max 7839 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: 258320.0 ave 258320 max 258320 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258320 Ave neighs/atom = 246.48855 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 = 7 19 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) = 5.584 | 5.584 | 5.584 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4579.8468 0 -4579.8468 30.475937 Loop time of 2.24e-06 on 1 procs for 0 steps with 1048 atoms 178.6% 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 | | 2.24e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8588.00 ave 8588 max 8588 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: 258696.0 ave 258696 max 258696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258696 Ave neighs/atom = 246.84733 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 = 7 19 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) = 5.584 | 5.584 | 5.584 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 -4579.8468 -4579.8468 28.625893 80.647954 4.9641163 30.475937 30.475937 9.0416244 -57.045571 139.43176 2.2798799 508.80363 Loop time of 2.519e-06 on 1 procs for 0 steps with 1048 atoms 198.5% 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 | | 2.519e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8588.00 ave 8588 max 8588 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 129348.0 ave 129348 max 129348 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 258696.0 ave 258696 max 258696 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 258696 Ave neighs/atom = 246.84733 Neighbor list builds = 0 Dangerous builds = 0 1048 -4579.84675713036 eV 2.27987987866426 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02