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 = 3.6583649 3.6583649 3.6583649 Created orthogonal box = (0.0000000 -48.533694 0.0000000) to (29.720697 48.533694 8.9611272) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4037630 5.5151925 5.9740848 Created 1056 atoms using lattice units in orthogonal box = (0.0000000 -48.533694 0.0000000) to (29.720697 48.533694 8.9611272) create_atoms CPU = 0.002 seconds 1056 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4037630 5.5151925 5.9740848 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -48.533694 0.0000000) to (29.720697 48.533694 8.9611272) create_atoms CPU = 0.001 seconds 1080 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 = 8 26 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 24 atoms, new total = 2112 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_469343973171_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 8 26 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) = 5.963 | 5.963 | 5.963 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8365.3367 0 -8365.3367 10661.328 228 0 -8465.4018 0 -8465.4018 -79391.586 Loop time of 6.38967 on 1 procs for 228 steps with 2112 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 = -8365.3367027124 -8465.39430605732 -8465.40183206757 Force two-norm initial, final = 64.167968 0.27358077 Force max component initial, final = 5.4691062 0.011208928 Final line search alpha, max atom move = 1.0000000 0.011208928 Iterations, force evaluations = 228 451 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.2596 | 6.2596 | 6.2596 | 0.0 | 97.96 Neigh | 0.063574 | 0.063574 | 0.063574 | 0.0 | 0.99 Comm | 0.029459 | 0.029459 | 0.029459 | 0.0 | 0.46 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03705 | | | 0.58 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7737.00 ave 7737 max 7737 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: 319728.0 ave 319728 max 319728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 319728 Ave neighs/atom = 151.38636 Neighbor list builds = 3 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 = 8 26 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 : 228 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.964 | 5.964 | 5.964 Mbytes Step Temp E_pair E_mol TotEng Press Volume 228 0 -8465.4018 0 -8465.4018 -79391.586 25852.049 281 0 -8532.4788 0 -8532.4788 18.112959 24423.738 Loop time of 0.858431 on 1 procs for 53 steps with 2112 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 = -8465.40183206754 -8532.47719434332 -8532.47876858496 Force two-norm initial, final = 2435.4397 8.9117072 Force max component initial, final = 1886.5660 5.8848797 Final line search alpha, max atom move = 0.00093737198 0.0055163213 Iterations, force evaluations = 53 54 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.7922 | 0.7922 | 0.7922 | 0.0 | 92.28 Neigh | 0.041978 | 0.041978 | 0.041978 | 0.0 | 4.89 Comm | 0.0037654 | 0.0037654 | 0.0037654 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02049 | | | 2.39 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8104.00 ave 8104 max 8104 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: 339552.0 ave 339552 max 339552 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 339552 Ave neighs/atom = 160.77273 Neighbor list builds = 2 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 = 8 27 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) = 6.105 | 6.105 | 6.105 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8532.4788 0 -8532.4788 18.112959 Loop time of 1.836e-06 on 1 procs for 0 steps with 2112 atoms 163.4% 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 | | 1.836e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8139.00 ave 8139 max 8139 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: 334896.0 ave 334896 max 334896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 334896 Ave neighs/atom = 158.56818 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 = 8 27 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) = 6.105 | 6.105 | 6.105 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 -8532.4788 -8532.4788 28.353858 98.861125 8.7131348 18.112959 18.112959 -368.2892 58.685876 363.9422 2.430448 6940.2756 Loop time of 2.271e-06 on 1 procs for 0 steps with 2112 atoms 220.2% 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 | | 2.271e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8139.00 ave 8139 max 8139 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 167448.0 ave 167448 max 167448 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 334896.0 ave 334896 max 334896 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 334896 Ave neighs/atom = 158.56818 Neighbor list builds = 0 Dangerous builds = 0 2112 -8532.47876858497 eV 2.43044802766305 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07