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 = 3.4919386 3.4919386 3.4919386 Created orthogonal box = (0.0000000 -49.135931 0.0000000) to (11.581450 49.135931 4.9383469) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2642955 5.9558705 4.9383469 Created 264 atoms using lattice units in orthogonal box = (0.0000000 -49.135931 0.0000000) to (11.581450 49.135931 4.9383469) create_atoms CPU = 0.001 seconds 264 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2642955 5.9558705 4.9383469 Created 266 atoms using lattice units in orthogonal box = (0.0000000 -49.135931 0.0000000) to (11.581450 49.135931 4.9383469) create_atoms CPU = 0.001 seconds 266 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 4 29 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 6.853417482829597 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 528 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_108408461881_001#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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 4 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 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) = 4.529 | 4.529 | 4.529 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2233.7498 0 -2233.7498 56105.544 63 0 -2337.3839 0 -2337.3839 9497.5706 Loop time of 0.693877 on 1 procs for 63 steps with 528 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2233.74978214115 -2337.38171104427 -2337.38391650536 Force two-norm initial, final = 246.94467 0.18889437 Force max component initial, final = 75.044136 0.033309128 Final line search alpha, max atom move = 1.0000000 0.033309128 Iterations, force evaluations = 63 120 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.6825 | 0.6825 | 0.6825 | 0.0 | 98.36 Neigh | 0.004292 | 0.004292 | 0.004292 | 0.0 | 0.62 Comm | 0.0042361 | 0.0042361 | 0.0042361 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002853 | | | 0.41 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4516.00 ave 4516 max 4516 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: 70256.0 ave 70256 max 70256 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70256 Ave neighs/atom = 133.06061 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 4 29 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.532 | 4.532 | 4.532 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -2337.3839 0 -2337.3839 9497.5706 5620.4841 69 0 -2337.548 0 -2337.548 109.46409 5649.1631 Loop time of 0.0528877 on 1 procs for 6 steps with 528 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 = -2337.38391650536 -2337.54776985023 -2337.54795776916 Force two-norm initial, final = 70.200293 1.0386652 Force max component initial, final = 65.792069 0.96314195 Final line search alpha, max atom move = 0.00045778908 0.00044091586 Iterations, force evaluations = 6 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.051319 | 0.051319 | 0.051319 | 0.0 | 97.03 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00032119 | 0.00032119 | 0.00032119 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001248 | | | 2.36 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4728.00 ave 4728 max 4728 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: 70280.0 ave 70280 max 70280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70280 Ave neighs/atom = 133.10606 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 4 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 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) = 4.670 | 4.670 | 4.670 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2337.548 0 -2337.548 109.46409 Loop time of 1.698e-06 on 1 procs for 0 steps with 528 atoms 117.8% 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 | | 1.698e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4728.00 ave 4728 max 4728 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: 70276.0 ave 70276 max 70276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70276 Ave neighs/atom = 133.09848 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 = 6.8534175 ghost atom cutoff = 6.8534175 binsize = 3.4267087, bins = 4 29 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.853417482829597 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) = 4.670 | 4.670 | 4.670 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 -2337.548 -2337.548 11.582354 98.759797 4.9386371 109.46409 109.46409 -17.648069 72.864631 273.17569 2.2930152 247.84388 Loop time of 1.683e-06 on 1 procs for 0 steps with 528 atoms 118.8% 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 | | 1.683e-06 | | |100.00 Nlocal: 528.000 ave 528 max 528 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4728.00 ave 4728 max 4728 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35138.0 ave 35138 max 35138 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 70276.0 ave 70276 max 70276 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 70276 Ave neighs/atom = 133.09848 Neighbor list builds = 0 Dangerous builds = 0 528 -2337.54795776916 eV 2.29301524220324 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00