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 = 3.6149251 3.6149251 3.6149251 Created orthogonal box = (0.0000000 -38.427181 0.0000000) to (38.427181 38.427181 3.6149251) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1009532 5.1009532 3.6149251 Created 452 atoms using lattice units in orthogonal box = (0.0000000 -38.427181 0.0000000) to (38.427181 38.427181 3.6149251) create_atoms CPU = 0.003 seconds 452 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1009532 5.1009532 3.6149251 Created 454 atoms using lattice units in orthogonal box = (0.0000000 -38.427181 0.0000000) to (38.427181 38.427181 3.6149251) create_atoms CPU = 0.002 seconds 454 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 = 11 21 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 906 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 = 11 21 1 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) = 4.977 | 4.977 | 4.977 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2971.8334 0 -2971.8334 79514.411 78 0 -3199.5513 0 -3199.5513 6309.5333 Loop time of 2.22694 on 1 procs for 78 steps with 906 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -2971.83340554514 -3199.54832721566 -3199.55129840138 Force two-norm initial, final = 296.40287 0.16077294 Force max component initial, final = 52.768796 0.026630103 Final line search alpha, max atom move = 1.0000000 0.026630103 Iterations, force evaluations = 78 136 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.1506 | 2.1506 | 2.1506 | 0.0 | 96.57 Neigh | 0.034701 | 0.034701 | 0.034701 | 0.0 | 1.56 Comm | 0.022947 | 0.022947 | 0.022947 | 0.0 | 1.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01865 | | | 0.84 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6684.00 ave 6684 max 6684 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: 133920.0 ave 133920 max 133920 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133920 Ave neighs/atom = 147.81457 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 21 1 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 : 78 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.977 | 4.977 | 4.977 Mbytes Step Temp E_pair E_mol TotEng Press Volume 78 0 -3199.5513 0 -3199.5513 6309.5333 10675.945 83 0 -3199.737 0 -3199.737 240.63003 10721.849 Loop time of 0.106502 on 1 procs for 5 steps with 906 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 = -3199.55129840138 -3199.73518417653 -3199.73695741727 Force two-norm initial, final = 84.730041 3.2353169 Force max component initial, final = 71.446459 2.9372251 Final line search alpha, max atom move = 0.00017573970 0.00051618704 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10226 | 0.10226 | 0.10226 | 0.0 | 96.02 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0009652 | 0.0009652 | 0.0009652 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003277 | | | 3.08 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6679.00 ave 6679 max 6679 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: 133536.0 ave 133536 max 133536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133536 Ave neighs/atom = 147.39073 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 = 11 21 1 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) = 5.115 | 5.115 | 5.115 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3199.737 0 -3199.737 240.63003 Loop time of 6.295e-06 on 1 procs for 0 steps with 906 atoms 190.6% 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 | | 6.295e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6684.00 ave 6684 max 6684 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: 132600.0 ave 132600 max 132600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132600 Ave neighs/atom = 146.35762 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 = 11 21 1 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) = 5.115 | 5.115 | 5.115 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 -3199.737 -3199.737 38.358642 77.173973 3.6218929 240.63003 240.63003 123.0515 159.08012 439.75846 2.3111087 153.32586 Loop time of 6.866e-06 on 1 procs for 0 steps with 906 atoms 247.6% 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 | | 6.866e-06 | | |100.00 Nlocal: 906.000 ave 906 max 906 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6684.00 ave 6684 max 6684 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 66300.0 ave 66300 max 66300 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 132600.0 ave 132600 max 132600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 132600 Ave neighs/atom = 146.35762 Neighbor list builds = 0 Dangerous builds = 0 906 -3199.74148741727 eV 2.31110873767072 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03