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 = 3.5200008 3.5200008 3.5200008 Created orthogonal box = (0.0000000 -53.154366 0.0000000) to (37.583324 53.154366 4.9780328) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9342090 6.0610614 4.9780328 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -53.154366 0.0000000) to (37.583324 53.154366 4.9780328) create_atoms CPU = 0.003 seconds 916 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9342090 6.0610614 4.9780328 Created 916 atoms using lattice units in orthogonal box = (0.0000000 -53.154366 0.0000000) to (37.583324 53.154366 4.9780328) create_atoms CPU = 0.003 seconds 916 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 = 10 28 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 7.80375 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 1816 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_657255834688_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 = 10 28 2 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) = 5.977 | 5.977 | 5.977 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8006.5706 0 -8006.5706 4227.1553 46 0 -8059.361 0 -8059.361 -4026.1951 Loop time of 1.41805 on 1 procs for 46 steps with 1816 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 = -8006.57059298489 -8059.35409214838 -8059.36095750248 Force two-norm initial, final = 41.077464 0.42946949 Force max component initial, final = 7.8842636 0.098469676 Final line search alpha, max atom move = 1.0000000 0.098469676 Iterations, force evaluations = 46 83 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3824 | 1.3824 | 1.3824 | 0.0 | 97.49 Neigh | 0.018423 | 0.018423 | 0.018423 | 0.0 | 1.30 Comm | 0.0091572 | 0.0091572 | 0.0091572 | 0.0 | 0.65 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008054 | | | 0.57 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9944.00 ave 9944 max 9944 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: 320600.0 ave 320600 max 320600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320600 Ave neighs/atom = 176.54185 Neighbor list builds = 1 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 = 10 28 2 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 : 46 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.977 | 5.977 | 5.977 Mbytes Step Temp E_pair E_mol TotEng Press Volume 46 0 -8059.361 0 -8059.361 -4026.1951 19889.409 48 0 -8059.3819 0 -8059.3819 -1868.4956 19866.598 Loop time of 0.0853247 on 1 procs for 2 steps with 1816 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 = -8059.36095750249 -8059.38154094825 -8059.38191638364 Force two-norm initial, final = 47.950315 0.44240172 Force max component initial, final = 40.740897 0.099186039 Final line search alpha, max atom move = 0.00027685564 2.7460215e-05 Iterations, force evaluations = 2 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.082954 | 0.082954 | 0.082954 | 0.0 | 97.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00042189 | 0.00042189 | 0.00042189 | 0.0 | 0.49 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001949 | | | 2.28 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9936.00 ave 9936 max 9936 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: 320736.0 ave 320736 max 320736 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320736 Ave neighs/atom = 176.61674 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 = 10 28 2 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) = 6.115 | 6.115 | 6.115 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8059.3819 0 -8059.3819 -1868.4956 Loop time of 2.576e-06 on 1 procs for 0 steps with 1816 atoms 155.3% 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 | | 2.576e-06 | | |100.00 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9952.00 ave 9952 max 9952 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: 320752.0 ave 320752 max 320752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320752 Ave neighs/atom = 176.62555 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 = 10 28 2 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) = 6.115 | 6.115 | 6.115 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 -8059.3819 -8059.3819 37.552207 106.30873 4.9764437 -1868.4956 -1868.4956 -1.471495 -5596.7157 -7.2995056 2.3440445 611.94909 Loop time of 2.749e-06 on 1 procs for 0 steps with 1816 atoms 254.6% 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 | | 2.749e-06 | | |100.00 Nlocal: 1816.00 ave 1816 max 1816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9952.00 ave 9952 max 9952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 160376.0 ave 160376 max 160376 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 320752.0 ave 320752 max 320752 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 320752 Ave neighs/atom = 176.62555 Neighbor list builds = 0 Dangerous builds = 0 1816 -8059.38191638364 eV 2.34404448287293 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01