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 = 3.4986963 3.4986963 3.4986963 Created orthogonal box = (0.0000000 -61.802798 0.0000000) to (35.679842 61.802798 6.0599198) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4892064 5.5460909 6.0599198 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -61.802798 0.0000000) to (35.679842 61.802798 6.0599198) create_atoms CPU = 0.008 seconds 1250 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4892064 5.5460909 6.0599198 Created 1250 atoms using lattice units in orthogonal box = (0.0000000 -61.802798 0.0000000) to (35.679842 61.802798 6.0599198) create_atoms CPU = 0.011 seconds 1250 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 33 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 28 atoms, new total = 2472 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_715003088863_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.540 | 6.540 | 6.540 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10097.732 0 -10097.732 3507.7647 69 0 -10144.24 0 -10144.24 -7921.4279 Loop time of 5.98746 on 1 procs for 69 steps with 2472 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10097.7321998922 -10144.2299314479 -10144.2395945352 Force two-norm initial, final = 34.885748 0.40694753 Force max component initial, final = 6.3665165 0.10090507 Final line search alpha, max atom move = 0.47221645 0.047649036 Iterations, force evaluations = 69 126 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.8006 | 5.8006 | 5.8006 | 0.0 | 96.88 Neigh | 0.11722 | 0.11722 | 0.11722 | 0.0 | 1.96 Comm | 0.036772 | 0.036772 | 0.036772 | 0.0 | 0.61 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03291 | | | 0.55 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11702.0 ave 11702 max 11702 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: 431100.0 ave 431100 max 431100 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 431100 Ave neighs/atom = 174.39320 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 33 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 69 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.534 | 6.534 | 6.534 Mbytes Step Temp E_pair E_mol TotEng Press Volume 69 0 -10144.24 0 -10144.24 -7921.4279 26725.629 73 0 -10144.487 0 -10144.487 -3095.6144 26612.821 Loop time of 0.281665 on 1 procs for 4 steps with 2472 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -10144.2395945352 -10144.48536126 -10144.4867370225 Force two-norm initial, final = 147.30566 0.56255329 Force max component initial, final = 132.09525 0.11384807 Final line search alpha, max atom move = 0.00012696586 1.4454818e-05 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.27486 | 0.27486 | 0.27486 | 0.0 | 97.58 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0015613 | 0.0015613 | 0.0015613 | 0.0 | 0.55 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005242 | | | 1.86 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11373.0 ave 11373 max 11373 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: 431904.0 ave 431904 max 431904 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 431904 Ave neighs/atom = 174.71845 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.673 | 6.673 | 6.673 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -10144.487 0 -10144.487 -3095.6144 Loop time of 6.144e-06 on 1 procs for 0 steps with 2472 atoms 195.3% 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 | | 6.144e-06 | | |100.00 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11436.0 ave 11436 max 11436 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: 432058.0 ave 432058 max 432058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 432058 Ave neighs/atom = 174.78074 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 6.673 | 6.673 | 6.673 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 -10144.487 -10144.487 35.564622 123.6056 6.0538908 -3095.6144 -3095.6144 2.0596711 -9292.1875 3.2846923 2.2410584 1155.3221 Loop time of 6.745e-06 on 1 procs for 0 steps with 2472 atoms 326.2% 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 | | 6.745e-06 | | |100.00 Nlocal: 2472.00 ave 2472 max 2472 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11436.0 ave 11436 max 11436 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 216029.0 ave 216029 max 216029 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 432058.0 ave 432058 max 432058 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 432058 Ave neighs/atom = 174.78074 Neighbor list builds = 0 Dangerous builds = 0 2472 -10144.4867370225 eV 2.24105836641729 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07