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 = 3.6110986 3.6110986 3.6110986 Created orthogonal box = (0.0000000 -40.858528 0.0000000) to (17.690698 40.858528 6.2546062) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.8968993 5.1068646 6.2546062 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -40.858528 0.0000000) to (17.690698 40.858528 6.2546062) create_atoms CPU = 0.001 seconds 396 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.8968993 5.1068646 6.2546062 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -40.858528 0.0000000) to (17.690698 40.858528 6.2546062) create_atoms CPU = 0.001 seconds 396 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 ghost atom cutoff = 6 binsize = 3, bins = 6 28 3 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 31 atoms, new total = 761 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_179158257180_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 ghost atom cutoff = 6 binsize = 3, bins = 6 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.559 | 4.559 | 4.559 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3128.6978 0 -3128.6978 31846.302 309 0 -3228.9565 0 -3228.9565 -6102.9012 Loop time of 14.0857 on 1 procs for 309 steps with 761 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 = -3128.6977584533 -3228.95381337135 -3228.9565377231 Force two-norm initial, final = 79.627653 0.16562903 Force max component initial, final = 15.167819 0.046211632 Final line search alpha, max atom move = 1.0000000 0.046211632 Iterations, force evaluations = 309 569 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.004 | 14.004 | 14.004 | 0.0 | 99.42 Neigh | 0.046278 | 0.046278 | 0.046278 | 0.0 | 0.33 Comm | 0.016772 | 0.016772 | 0.016772 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01846 | | | 0.13 Nlocal: 761.000 ave 761 max 761 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3517.00 ave 3517 max 3517 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: 50424.0 ave 50424 max 50424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50424 Ave neighs/atom = 66.260184 Neighbor list builds = 10 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 ghost atom cutoff = 6 binsize = 3, bins = 6 28 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 309 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.558 | 4.558 | 4.558 Mbytes Step Temp E_pair E_mol TotEng Press Volume 309 0 -3228.9565 0 -3228.9565 -6102.9012 9041.8572 312 0 -3228.9798 0 -3228.9798 -6599.7964 9044.6927 Loop time of 0.139497 on 1 procs for 3 steps with 761 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 = -3228.95653772309 -3228.97976801257 -3228.97979610441 Force two-norm initial, final = 21.918569 0.20666200 Force max component initial, final = 18.748063 0.044487325 Final line search alpha, max atom move = 0.0011192876 4.9794110e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13862 | 0.13862 | 0.13862 | 0.0 | 99.37 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00015169 | 0.00015169 | 0.00015169 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.000727 | | | 0.52 Nlocal: 761.000 ave 761 max 761 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3517.00 ave 3517 max 3517 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: 50356.0 ave 50356 max 50356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50356 Ave neighs/atom = 66.170828 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 ghost atom cutoff = 6 binsize = 3, bins = 6 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.696 | 4.696 | 4.696 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3228.9798 0 -3228.9798 -6599.7964 Loop time of 1.631e-06 on 1 procs for 0 steps with 761 atoms 122.6% 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 | | 1.631e-06 | | |100.00 Nlocal: 761.000 ave 761 max 761 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3511.00 ave 3511 max 3511 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: 50370.0 ave 50370 max 50370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50370 Ave neighs/atom = 66.189225 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 ghost atom cutoff = 6 binsize = 3, bins = 6 28 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.696 | 4.696 | 4.696 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 -3228.9798 -3228.9798 17.666829 81.717055 6.2650207 -6599.7964 -6599.7964 -5.2498633 -19788.533 -5.6066713 2.3082804 1643.9816 Loop time of 1.477e-06 on 1 procs for 0 steps with 761 atoms 203.1% 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 | | 1.477e-06 | | |100.00 Nlocal: 761.000 ave 761 max 761 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3511.00 ave 3511 max 3511 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 25185.0 ave 25185 max 25185 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 50370.0 ave 50370 max 50370 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 50370 Ave neighs/atom = 66.189225 Neighbor list builds = 0 Dangerous builds = 0 761 -3228.97979610441 eV 2.30828040668529 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:14