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 = 3.6110509 3.6110509 3.6110509 Created orthogonal box = (0.0000000 -41.487816 0.0000000) to (29.336316 41.487816 5.1067972) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4448964 5.6574295 5.1067972 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -41.487816 0.0000000) to (29.336316 41.487816 5.1067972) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4448964 5.6574295 5.1067972 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -41.487816 0.0000000) to (29.336316 41.487816 5.1067972) 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 17 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 10.319 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_984358344196_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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.254 | 6.254 | 6.254 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4171.3056 0 -4171.3056 25519.395 88 0 -4326.6456 0 -4326.6456 -4342.1528 Loop time of 2.83209 on 1 procs for 88 steps with 1048 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 = -4171.30557294491 -4326.64212464102 -4326.64557739764 Force two-norm initial, final = 221.01334 0.24683764 Force max component initial, final = 49.987615 0.021415872 Final line search alpha, max atom move = 1.0000000 0.021415872 Iterations, force evaluations = 88 168 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7636 | 2.7636 | 2.7636 | 0.0 | 97.58 Neigh | 0.042345 | 0.042345 | 0.042345 | 0.0 | 1.50 Comm | 0.015786 | 0.015786 | 0.015786 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01039 | | | 0.37 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10072.0 ave 10072 max 10072 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: 398128.0 ave 398128 max 398128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 398128 Ave neighs/atom = 379.89313 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 17 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 88 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.255 | 6.255 | 6.255 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -4326.6456 0 -4326.6456 -4342.1528 12430.963 92 0 -4326.8446 0 -4326.8446 -518.16385 12402.372 Loop time of 0.101947 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 = -4326.64557739768 -4326.84144321285 -4326.84462428899 Force two-norm initial, final = 99.435874 8.5058313 Force max component initial, final = 83.622131 7.9057260 Final line search alpha, max atom move = 0.00011187004 0.00088441388 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.099535 | 0.099535 | 0.099535 | 0.0 | 97.63 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0004351 | 0.0004351 | 0.0004351 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001977 | | | 1.94 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10102.0 ave 10102 max 10102 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: 398160.0 ave 398160 max 398160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 398160 Ave neighs/atom = 379.92366 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.393 | 6.393 | 6.393 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4326.8446 0 -4326.8446 -518.16385 Loop time of 1.938e-06 on 1 procs for 0 steps with 1048 atoms 154.8% 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 | | 1.938e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10142.0 ave 10142 max 10142 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: 398720.0 ave 398720 max 398720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 398720 Ave neighs/atom = 380.45802 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 = 10.319 ghost atom cutoff = 10.319 binsize = 5.1595, bins = 6 17 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 10.319 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) = 6.393 | 6.393 | 6.393 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 -4326.8446 -4326.8446 29.280942 82.744975 5.1189169 -518.16385 -518.16385 -1019.3582 -169.33813 -365.7952 2.311869 749.2459 Loop time of 2.4e-06 on 1 procs for 0 steps with 1048 atoms 250.0% 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 | | 2.4e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10142.0 ave 10142 max 10142 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 199360.0 ave 199360 max 199360 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 398720.0 ave 398720 max 398720 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 398720 Ave neighs/atom = 380.45802 Neighbor list builds = 0 Dangerous builds = 0 1048 -4326.84462428899 eV 2.31186902837871 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03