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 -42.476759 0.0000000) to (52.023193 42.476759 9.9204336) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.6211336 6.1784377 6.6136224 Created 1320 atoms using lattice units in orthogonal box = (0.0000000 -42.476759 0.0000000) to (52.023193 42.476759 9.9204336) create_atoms CPU = 0.003 seconds 1320 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.6211336 6.1784377 6.6136224 Created 1326 atoms using lattice units in orthogonal box = (0.0000000 -42.476759 0.0000000) to (52.023193 42.476759 9.9204336) create_atoms CPU = 0.002 seconds 1326 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 13 21 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 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 18 atoms, new total = 2628 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_751354403791_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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 6.042 | 6.042 | 6.042 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8650.0553 0 -8650.0553 2921.2201 100 0 -8799.3541 0 -8799.3541 818.50565 Loop time of 3.11769 on 1 procs for 100 steps with 2628 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8650.05532847365 -8799.34563153199 -8799.35411311853 Force two-norm initial, final = 64.030663 0.23212676 Force max component initial, final = 8.5630959 0.035277354 Final line search alpha, max atom move = 1.0000000 0.035277354 Iterations, force evaluations = 100 176 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.9956 | 2.9956 | 2.9956 | 0.0 | 96.08 Neigh | 0.079085 | 0.079085 | 0.079085 | 0.0 | 2.54 Comm | 0.017775 | 0.017775 | 0.017775 | 0.0 | 0.57 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02526 | | | 0.81 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8395.00 ave 8395 max 8395 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: 366636.0 ave 366636 max 366636 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 366636 Ave neighs/atom = 139.51142 Neighbor list builds = 3 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 13 21 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 100 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.042 | 6.042 | 6.042 Mbytes Step Temp E_pair E_mol TotEng Press Volume 100 0 -8799.3541 0 -8799.3541 818.50565 43843.885 105 0 -8799.6006 0 -8799.6006 56.675925 43885.279 Loop time of 0.12488 on 1 procs for 5 steps with 2628 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 = -8799.35411311852 -8799.59818162096 -8799.60061081276 Force two-norm initial, final = 95.995463 2.7255531 Force max component initial, final = 88.835863 1.7985264 Final line search alpha, max atom move = 0.00015625931 0.00028103649 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12102 | 0.12102 | 0.12102 | 0.0 | 96.91 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052921 | 0.00052921 | 0.00052921 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003329 | | | 2.67 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8393.00 ave 8393 max 8393 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: 366576.0 ave 366576 max 366576 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 366576 Ave neighs/atom = 139.48858 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 6.180 | 6.180 | 6.180 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8799.6006 0 -8799.6006 56.675925 Loop time of 2.388e-06 on 1 procs for 0 steps with 2628 atoms 167.5% 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 | | 2.388e-06 | | |100.00 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8393.00 ave 8393 max 8393 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: 366372.0 ave 366372 max 366372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 366372 Ave neighs/atom = 139.41096 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 = 8.28721 ghost atom cutoff = 8.28721 binsize = 4.143605, bins = 13 21 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.28721 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) = 6.180 | 6.180 | 6.180 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 -8799.6006 -8799.6006 52.006367 85.325624 9.8896946 56.675925 56.675925 50.857445 65.948725 53.221606 2.5925344 1927.3061 Loop time of 2.75e-06 on 1 procs for 0 steps with 2628 atoms 254.5% 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 | | 2.75e-06 | | |100.00 Nlocal: 2628.00 ave 2628 max 2628 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8393.00 ave 8393 max 8393 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 183186.0 ave 183186 max 183186 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 366372.0 ave 366372 max 366372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 366372 Ave neighs/atom = 139.41096 Neighbor list builds = 0 Dangerous builds = 0 2628 -8799.60061069774 eV 2.59253436343114 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03