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 -60.971722 0.0000000) to (24.890164 60.971722 8.6222058) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9736394 5.2839108 5.7481372 Created 1204 atoms using lattice units in orthogonal box = (0.0000000 -60.971722 0.0000000) to (24.890164 60.971722 8.6222058) create_atoms CPU = 0.006 seconds 1204 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9736394 5.2839108 5.7481372 Created 1204 atoms using lattice units in orthogonal box = (0.0000000 -60.971722 0.0000000) to (24.890164 60.971722 8.6222058) create_atoms CPU = 0.005 seconds 1204 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 = 7 32 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 24 atoms, new total = 2384 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_820335782779_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 = 7 32 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) = 6.509 | 6.509 | 6.509 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10537.906 0 -10537.906 1377.5592 26 0 -10577.507 0 -10577.507 -8332.5035 Loop time of 2.16743 on 1 procs for 26 steps with 2384 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10537.9062351084 -10577.4991956462 -10577.5072559783 Force two-norm initial, final = 37.219254 0.38235241 Force max component initial, final = 5.1610396 0.091319111 Final line search alpha, max atom move = 1.0000000 0.091319111 Iterations, force evaluations = 26 47 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.086 | 2.086 | 2.086 | 0.0 | 96.24 Neigh | 0.058456 | 0.058456 | 0.058456 | 0.0 | 2.70 Comm | 0.01097 | 0.01097 | 0.01097 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01204 | | | 0.56 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9673.00 ave 9673 max 9673 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: 419866.0 ave 419866 max 419866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 419866 Ave neighs/atom = 176.11829 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 = 7 32 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 : 26 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.509 | 6.509 | 6.509 Mbytes Step Temp E_pair E_mol TotEng Press Volume 26 0 -10577.507 0 -10577.507 -8332.5035 26170.053 29 0 -10577.743 0 -10577.743 -1669.5635 26075.45 Loop time of 0.264756 on 1 procs for 3 steps with 2384 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 = -10577.5072559783 -10577.742041076 -10577.7428217848 Force two-norm initial, final = 182.32179 0.42771354 Force max component initial, final = 136.19822 0.098858677 Final line search alpha, max atom move = 0.00017279361 1.7082147e-05 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.25886 | 0.25886 | 0.25886 | 0.0 | 97.77 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012317 | 0.0012317 | 0.0012317 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004664 | | | 1.76 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9689.00 ave 9689 max 9689 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: 420554.0 ave 420554 max 420554 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 420554 Ave neighs/atom = 176.40688 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 = 7 32 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) = 6.647 | 6.647 | 6.647 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10577.743 0 -10577.743 -1669.5635 Loop time of 6.525e-06 on 1 procs for 0 steps with 2384 atoms 183.9% 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 | | 6.525e-06 | | |100.00 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9701.00 ave 9701 max 9701 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: 420972.0 ave 420972 max 420972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 420972 Ave neighs/atom = 176.58221 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 = 7 32 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) = 6.647 | 6.647 | 6.647 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 -10577.743 -10577.743 24.852652 121.94344 8.6040043 -1669.5635 -1669.5635 -0.54744436 -5008.735 0.59205535 2.3302558 690.29091 Loop time of 6.635e-06 on 1 procs for 0 steps with 2384 atoms 256.2% 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 | | 6.635e-06 | | |100.00 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9701.00 ave 9701 max 9701 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 210486.0 ave 210486 max 210486 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 420972.0 ave 420972 max 420972 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 420972 Ave neighs/atom = 176.58221 Neighbor list builds = 0 Dangerous builds = 0 2384 -10577.7428217848 eV 2.33025583611134 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03