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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -46.530958 0.0000000) to (32.902356 46.530958 5.7275650) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9852055 6.3451307 5.7275650 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -46.530958 0.0000000) to (32.902356 46.530958 5.7275650) create_atoms CPU = 0.004 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9852055 6.3451307 5.7275650 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -46.530958 0.0000000) to (32.902356 46.530958 5.7275650) create_atoms CPU = 0.003 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 25 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 7.65 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_418978237058_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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.001 | 5.001 | 5.001 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3426.1518 0 -3426.1518 10597.899 82 0 -3516.5685 0 -3516.5685 571.16848 Loop time of 1.95158 on 1 procs for 82 steps with 1048 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 = -3426.15180184699 -3516.56506972942 -3516.56849897532 Force two-norm initial, final = 101.91200 0.13016854 Force max component initial, final = 24.751717 0.016701716 Final line search alpha, max atom move = 1.0000000 0.016701716 Iterations, force evaluations = 82 150 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.8738 | 1.8738 | 1.8738 | 0.0 | 96.01 Neigh | 0.036831 | 0.036831 | 0.036831 | 0.0 | 1.89 Comm | 0.020842 | 0.020842 | 0.020842 | 0.0 | 1.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02015 | | | 1.03 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5615.00 ave 5615 max 5615 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: 135328.0 ave 135328 max 135328 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 135328 Ave neighs/atom = 129.12977 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.001 | 5.001 | 5.001 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -3516.5685 0 -3516.5685 571.16848 17537.554 86 0 -3516.6121 0 -3516.6121 1.7744784 17551.52 Loop time of 0.0942066 on 1 procs for 4 steps with 1048 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 = -3516.56849897533 -3516.61197778408 -3516.61214352072 Force two-norm initial, final = 25.700932 0.34092289 Force max component initial, final = 23.777741 0.22018895 Final line search alpha, max atom move = 0.00045357363 9.9871902e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.090057 | 0.090057 | 0.090057 | 0.0 | 95.59 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00091717 | 0.00091717 | 0.00091717 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003233 | | | 3.43 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5655.00 ave 5655 max 5655 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: 136104.0 ave 136104 max 136104 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136104 Ave neighs/atom = 129.87023 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.138 | 5.138 | 5.138 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3516.6121 0 -3516.6121 1.7744784 Loop time of 6.665e-06 on 1 procs for 0 steps with 1048 atoms 180.0% 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 | | 6.665e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5655.00 ave 5655 max 5655 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: 136008.0 ave 136008 max 136008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136008 Ave neighs/atom = 129.77863 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 9 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 5.138 | 5.138 | 5.138 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 -3516.6121 -3516.6121 32.896976 93.337751 5.7161212 1.7744784 1.7744784 -20.096486 8.5318731 16.888048 2.5847065 796.95029 Loop time of 9.381e-06 on 1 procs for 0 steps with 1048 atoms 458.4% 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 | | 9.381e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5655.00 ave 5655 max 5655 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 68004.0 ave 68004 max 68004 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 136008.0 ave 136008 max 136008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 136008 Ave neighs/atom = 129.77863 Neighbor list builds = 0 Dangerous builds = 0 1048 -3516.61214352072 eV 2.58470649343739 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02