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 = 3.6200001 3.6200001 3.6200001 Created orthogonal box = (0.0000000 -37.966881 0.0000000) to (46.499743 37.966881 8.8671530) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9181491 5.5224554 5.9114353 Created 1317 atoms using lattice units in orthogonal box = (0.0000000 -37.966881 0.0000000) to (46.499743 37.966881 8.8671530) create_atoms CPU = 0.002 seconds 1317 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9181491 5.5224554 5.9114353 Created 1323 atoms using lattice units in orthogonal box = (0.0000000 -37.966881 0.0000000) to (46.499743 37.966881 8.8671530) create_atoms CPU = 0.002 seconds 1323 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 20 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2640 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_803527979660_000#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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.462 | 6.462 | 6.462 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8871.8147 0 -8871.8147 35510.313 87 0 -9306.9038 0 -9306.9038 8738.3897 Loop time of 3.48573 on 1 procs for 87 steps with 2640 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 = -8871.81471628158 -9306.89568671764 -9306.90380874878 Force two-norm initial, final = 425.86779 0.29937578 Force max component initial, final = 73.595014 0.10074840 Final line search alpha, max atom move = 0.56100785 0.056520646 Iterations, force evaluations = 87 146 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.351 | 3.351 | 3.351 | 0.0 | 96.13 Neigh | 0.092495 | 0.092495 | 0.092495 | 0.0 | 2.65 Comm | 0.017603 | 0.017603 | 0.017603 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02467 | | | 0.71 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9042.00 ave 9042 max 9042 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: 458330.0 ave 458330 max 458330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 458330 Ave neighs/atom = 173.60985 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 87 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.462 | 6.462 | 6.462 Mbytes Step Temp E_pair E_mol TotEng Press Volume 87 0 -9306.9038 0 -9306.9038 8738.3897 31309.034 97 0 -9308.355 0 -9308.355 11.963614 31514.182 Loop time of 0.282113 on 1 procs for 10 steps with 2640 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 = -9306.90380874874 -9308.35312047667 -9308.35497398785 Force two-norm initial, final = 357.75024 0.85060971 Force max component initial, final = 331.05185 0.26900901 Final line search alpha, max atom move = 0.00014135690 3.8026280e-05 Iterations, force evaluations = 10 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27475 | 0.27475 | 0.27475 | 0.0 | 97.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00092889 | 0.00092889 | 0.00092889 | 0.0 | 0.33 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006439 | | | 2.28 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9042.00 ave 9042 max 9042 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: 458408.0 ave 458408 max 458408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 458408 Ave neighs/atom = 173.63939 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.600 | 6.600 | 6.600 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9308.355 0 -9308.355 11.963614 Loop time of 2.386e-06 on 1 procs for 0 steps with 2640 atoms 167.6% 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 | | 2.386e-06 | | |100.00 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9042.00 ave 9042 max 9042 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: 457330.0 ave 457330 max 457330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 457330 Ave neighs/atom = 173.23106 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 = 7.80375 ghost atom cutoff = 7.80375 binsize = 3.901875, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.80375 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) = 6.600 | 6.600 | 6.600 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 -9308.355 -9308.355 46.497302 76.641947 8.8432469 11.963614 11.963614 12.982144 9.2691901 13.639508 2.3631058 1378.9345 Loop time of 2.681e-06 on 1 procs for 0 steps with 2640 atoms 335.7% 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 | | 2.681e-06 | | |100.00 Nlocal: 2640.00 ave 2640 max 2640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9042.00 ave 9042 max 9042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 228665.0 ave 228665 max 228665 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 457330.0 ave 457330 max 457330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 457330 Ave neighs/atom = 173.23106 Neighbor list builds = 0 Dangerous builds = 0 2640 -9308.35497398785 eV 2.36310575159754 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04