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 = 2.8638485 2.8638485 2.8638485 Created orthogonal box = (0.0000000 -40.297921 0.0000000) to (9.4983110 40.297921 4.0500934) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.3174141 4.8845964 4.0500934 Created 132 atoms using lattice units in orthogonal box = (0.0000000 -40.297921 0.0000000) to (9.4983110 40.297921 4.0500934) create_atoms CPU = 0.001 seconds 132 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.3174141 4.8845964 4.0500934 Created 134 atoms using lattice units in orthogonal box = (0.0000000 -40.297921 0.0000000) to (9.4983110 40.297921 4.0500934) create_atoms CPU = 0.000 seconds 134 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 14 1 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 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 264 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_147603128437_004#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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 4.942 | 4.942 | 4.942 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1029.5275 0 -1029.5275 52078.675 78 0 -1100.0397 0 -1100.0397 3844.9792 Loop time of 1.10796 on 1 procs for 78 steps with 264 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 = -1029.52747025524 -1100.03894392279 -1100.03974542028 Force two-norm initial, final = 145.05353 0.11224265 Force max component initial, final = 46.195359 0.011522392 Final line search alpha, max atom move = 1.0000000 0.011522392 Iterations, force evaluations = 78 145 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.085 | 1.085 | 1.085 | 0.0 | 97.93 Neigh | 0.0082858 | 0.0082858 | 0.0082858 | 0.0 | 0.75 Comm | 0.010417 | 0.010417 | 0.010417 | 0.0 | 0.94 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00427 | | | 0.39 Nlocal: 264.000 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8136.00 ave 8136 max 8136 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: 159752.0 ave 159752 max 159752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159752 Ave neighs/atom = 605.12121 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 14 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.943 | 4.943 | 4.943 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -1100.0397 0 -1100.0397 3844.9792 3100.4452 103 0 -1101.1435 0 -1101.1435 85.456733 3105.6121 Loop time of 0.226976 on 1 procs for 25 steps with 264 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 = -1100.03974542028 -1101.14325347429 -1101.1434769954 Force two-norm initial, final = 86.700229 0.80115401 Force max component initial, final = 61.295014 0.47557863 Final line search alpha, max atom move = 0.0011168924 0.00053117017 Iterations, force evaluations = 25 28 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21097 | 0.21097 | 0.21097 | 0.0 | 92.95 Neigh | 0.0078542 | 0.0078542 | 0.0078542 | 0.0 | 3.46 Comm | 0.0018345 | 0.0018345 | 0.0018345 | 0.0 | 0.81 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006319 | | | 2.78 Nlocal: 264.000 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8346.00 ave 8346 max 8346 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: 160064.0 ave 160064 max 160064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160064 Ave neighs/atom = 606.30303 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.082 | 5.082 | 5.082 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1101.1435 0 -1101.1435 85.456733 Loop time of 1.692e-06 on 1 procs for 0 steps with 264 atoms 177.3% 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 | | 1.692e-06 | | |100.00 Nlocal: 264.000 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8346.00 ave 8346 max 8346 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: 159944.0 ave 159944 max 159944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159944 Ave neighs/atom = 605.84848 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 = 11.97749 ghost atom cutoff = 11.97749 binsize = 5.988745, bins = 2 14 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 11.97749 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) = 5.082 | 5.082 | 5.082 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 -1101.1435 -1101.1435 9.305009 81.553128 4.0925104 85.456733 85.456733 55.271087 -46.820124 247.91924 2.437104 279.18956 Loop time of 1.869e-06 on 1 procs for 0 steps with 264 atoms 214.0% 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 | | 1.869e-06 | | |100.00 Nlocal: 264.000 ave 264 max 264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8346.00 ave 8346 max 8346 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 79972.0 ave 79972 max 79972 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 159944.0 ave 159944 max 159944 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 159944 Ave neighs/atom = 605.84848 Neighbor list builds = 0 Dangerous builds = 0 264 -1101.1434769954 eV 2.43710399419193 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01