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 = 3.6149590 3.6149590 3.6149590 Created orthogonal box = (0.0000000 -41.532717 0.0000000) to (29.368066 41.532717 5.1123241) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2295898 5.6635524 5.1123241 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -41.532717 0.0000000) to (29.368066 41.532717 5.1123241) create_atoms CPU = 0.001 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2295898 5.6635524 5.1123241 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -41.532717 0.0000000) to (29.368066 41.532717 5.1123241) 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 = 7.7157521 ghost atom cutoff = 7.7157521 binsize = 3.8578761, bins = 8 22 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 7.715752124786377 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_127245782811_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 = 7.7157521 ghost atom cutoff = 7.7157521 binsize = 3.8578761, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715752124786377 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) = 5.021 | 5.021 | 5.021 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3546.7299 0 -3546.7299 28383.216 88 0 -3701.7458 0 -3701.7458 -547.95848 Loop time of 1.35335 on 1 procs for 88 steps with 1048 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 = -3546.72990266843 -3701.74253793918 -3701.74583214664 Force two-norm initial, final = 250.58295 0.17824712 Force max component initial, final = 60.858791 0.015792176 Final line search alpha, max atom move = 1.0000000 0.015792176 Iterations, force evaluations = 88 152 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3142 | 1.3142 | 1.3142 | 0.0 | 97.10 Neigh | 0.021446 | 0.021446 | 0.021446 | 0.0 | 1.58 Comm | 0.0091564 | 0.0091564 | 0.0091564 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008583 | | | 0.63 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6573.00 ave 6573 max 6573 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: 177632.0 ave 177632 max 177632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 177632 Ave neighs/atom = 169.49618 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 = 7.7157521 ghost atom cutoff = 7.7157521 binsize = 3.8578761, bins = 8 22 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715752124786377 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) = 5.029 | 5.029 | 5.029 Mbytes Step Temp E_pair E_mol TotEng Press Volume 88 0 -3701.7458 0 -3701.7458 -547.95848 12471.367 92 0 -3701.8587 0 -3701.8587 -27.787229 12466.199 Loop time of 0.0540964 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 = -3701.74583214667 -3701.85823767269 -3701.85871628555 Force two-norm initial, final = 51.346807 0.45889972 Force max component initial, final = 36.512731 0.28699696 Final line search alpha, max atom move = 0.00038336887 0.00011002570 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.052234 | 0.052234 | 0.052234 | 0.0 | 96.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00033028 | 0.00033028 | 0.00033028 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001532 | | | 2.83 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7006.00 ave 7006 max 7006 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: 176624.0 ave 176624 max 176624 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176624 Ave neighs/atom = 168.53435 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 = 7.7157521 ghost atom cutoff = 7.7157521 binsize = 3.8578761, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715752124786377 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) = 5.167 | 5.167 | 5.167 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3701.8587 0 -3701.8587 -27.787229 Loop time of 1.821e-06 on 1 procs for 0 steps with 1048 atoms 164.7% 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 | | 1.821e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6988.00 ave 6988 max 6988 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: 176536.0 ave 176536 max 176536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176536 Ave neighs/atom = 168.45038 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 = 7.7157521 ghost atom cutoff = 7.7157521 binsize = 3.8578761, bins = 8 22 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.715752124786377 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) = 5.167 | 5.167 | 5.167 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 -3701.8587 -3701.8587 29.461122 83.014894 5.0971656 -27.787229 -27.787229 -35.541635 -11.044096 -36.775956 2.4032528 642.83145 Loop time of 1.993e-06 on 1 procs for 0 steps with 1048 atoms 200.7% 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 | | 1.993e-06 | | |100.00 Nlocal: 1048.00 ave 1048 max 1048 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6988.00 ave 6988 max 6988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 88268.0 ave 88268 max 88268 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 176536.0 ave 176536 max 176536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 176536 Ave neighs/atom = 168.45038 Neighbor list builds = 0 Dangerous builds = 0 1048 -3701.85871628555 eV 2.40325275950378 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01