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 = 4.0499994 4.0499994 4.0499994 Created orthogonal box = (0.0000000 -81.202236 0.0000000) to (46.882133 81.202236 7.0148048) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2976000 6.4638596 7.0148048 Created 1607 atoms using lattice units in orthogonal box = (0.0000000 -81.202236 0.0000000) to (46.882133 81.202236 7.0148048) create_atoms CPU = 0.003 seconds 1607 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2976000 6.4638596 7.0148048 Created 1609 atoms using lattice units in orthogonal box = (0.0000000 -81.202236 0.0000000) to (46.882133 81.202236 7.0148048) create_atoms CPU = 0.003 seconds 1609 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 11 38 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 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 3 atoms, new total = 3213 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_117656786760_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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 7.054 | 7.054 | 7.054 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10690.234 0 -10690.234 3105.6835 116 0 -10775.34 0 -10775.34 2309.2828 Loop time of 6.56158 on 1 procs for 116 steps with 3213 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 = -10690.2343136398 -10775.3294609444 -10775.3401192973 Force two-norm initial, final = 48.749609 0.23825061 Force max component initial, final = 9.8450368 0.038915949 Final line search alpha, max atom move = 0.73014747 0.028414381 Iterations, force evaluations = 116 209 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.3181 | 6.3181 | 6.3181 | 0.0 | 96.29 Neigh | 0.17029 | 0.17029 | 0.17029 | 0.0 | 2.60 Comm | 0.036746 | 0.036746 | 0.036746 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03642 | | | 0.56 Nlocal: 3213.00 ave 3213 max 3213 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13036.0 ave 13036 max 13036 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: 560572.0 ave 560572 max 560572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 560572 Ave neighs/atom = 174.46997 Neighbor list builds = 5 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 11 38 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 116 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.054 | 7.054 | 7.054 Mbytes Step Temp E_pair E_mol TotEng Press Volume 116 0 -10775.34 0 -10775.34 2309.2828 53409.799 121 0 -10775.673 0 -10775.673 -197.97751 53578.636 Loop time of 0.221713 on 1 procs for 5 steps with 3213 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 = -10775.3401192972 -10775.6672588966 -10775.6725257983 Force two-norm initial, final = 164.47591 12.388282 Force max component initial, final = 153.48412 8.9989581 Final line search alpha, max atom move = 6.0004378e-05 0.00053997689 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.21603 | 0.21603 | 0.21603 | 0.0 | 97.43 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00082698 | 0.00082698 | 0.00082698 | 0.0 | 0.37 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004861 | | | 2.19 Nlocal: 3213.00 ave 3213 max 3213 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13043.0 ave 13043 max 13043 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: 560698.0 ave 560698 max 560698 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 560698 Ave neighs/atom = 174.50918 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 7.192 | 7.192 | 7.192 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10775.673 0 -10775.673 -197.97751 Loop time of 2.176e-06 on 1 procs for 0 steps with 3213 atoms 183.8% 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 | | 2.176e-06 | | |100.00 Nlocal: 3213.00 ave 3213 max 3213 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13034.0 ave 13034 max 13034 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: 560424.0 ave 560424 max 560424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 560424 Ave neighs/atom = 174.42390 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 = 8.724884 ghost atom cutoff = 8.724884 binsize = 4.362442, bins = 11 38 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.724884 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) = 7.192 | 7.192 | 7.192 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 -10775.673 -10775.673 46.88121 163.14928 7.0049928 -197.97751 -197.97751 -239.83878 -85.371866 -268.72188 2.5273865 1383.7997 Loop time of 2.662e-06 on 1 procs for 0 steps with 3213 atoms 263.0% 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 | | 2.662e-06 | | |100.00 Nlocal: 3213.00 ave 3213 max 3213 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 13034.0 ave 13034 max 13034 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 280212.0 ave 280212 max 280212 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 560424.0 ave 560424 max 560424 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 560424 Ave neighs/atom = 174.42390 Neighbor list builds = 0 Dangerous builds = 0 3213 -10578.9285895044 eV 2.52738647011476 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07