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 = 4.0453532 4.0453532 4.0453532 Created orthogonal box = (0.0000000 -63.710332 0.0000000) to (39.011974 63.710332 9.9090513) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2922538 6.1651245 6.6060342 Created 1494 atoms using lattice units in orthogonal box = (0.0000000 -63.710332 0.0000000) to (39.011974 63.710332 9.9090513) create_atoms CPU = 0.002 seconds 1494 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2922538 6.1651245 6.6060342 Created 1494 atoms using lattice units in orthogonal box = (0.0000000 -63.710332 0.0000000) to (39.011974 63.710332 9.9090513) create_atoms CPU = 0.002 seconds 1494 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 13 41 4 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 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 36 atoms, new total = 2952 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_461927113651_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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 13 41 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.184 | 5.184 | 5.184 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9870.5434 0 -9870.5434 -54.131685 22 0 -9894.0921 0 -9894.0921 -3279.7392 Loop time of 2.77447 on 1 procs for 22 steps with 2952 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 = -9870.54344863483 -9894.08289259276 -9894.09213408053 Force two-norm initial, final = 21.887353 0.21905652 Force max component initial, final = 4.1933738 0.0092775109 Final line search alpha, max atom move = 1.0000000 0.0092775109 Iterations, force evaluations = 22 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.7661 | 2.7661 | 2.7661 | 0.0 | 99.70 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026323 | 0.0026323 | 0.0026323 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005693 | | | 0.21 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6635.00 ave 6635 max 6635 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: 158976.0 ave 158976 max 158976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 158976 Ave neighs/atom = 53.853659 Neighbor list builds = 0 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 13 41 4 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 22 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.184 | 5.184 | 5.184 Mbytes Step Temp E_pair E_mol TotEng Press Volume 22 0 -9894.0921 0 -9894.0921 -3279.7392 49257.216 25 0 -9894.2821 0 -9894.2821 -434.38822 49063.675 Loop time of 0.38924 on 1 procs for 3 steps with 2952 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 = -9894.09213408054 -9894.28126831497 -9894.28207702425 Force two-norm initial, final = 136.99392 3.3146227 Force max component initial, final = 102.60061 3.2807646 Final line search alpha, max atom move = 0.00012892377 0.00042296854 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38708 | 0.38708 | 0.38708 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027111 | 0.00027111 | 0.00027111 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00189 | | | 0.49 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6635.00 ave 6635 max 6635 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: 160008.0 ave 160008 max 160008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160008 Ave neighs/atom = 54.203252 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 13 41 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.322 | 5.322 | 5.322 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9894.2821 0 -9894.2821 -434.38822 Loop time of 2.651e-06 on 1 procs for 0 steps with 2952 atoms 150.9% 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 | | 2.651e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6635.00 ave 6635 max 6635 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: 160032.0 ave 160032 max 160032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160032 Ave neighs/atom = 54.211382 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 = 6.25 ghost atom cutoff = 6.25 binsize = 3.125, bins = 13 41 4 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.25 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) = 5.322 | 5.322 | 5.322 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 -9894.2821 -9894.2821 38.944548 127.42066 9.8872051 -434.38822 -434.38822 106.94835 -1396.7958 -13.317233 2.5370524 1205.1585 Loop time of 2.719e-06 on 1 procs for 0 steps with 2952 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 | | 2.719e-06 | | |100.00 Nlocal: 2952.00 ave 2952 max 2952 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6635.00 ave 6635 max 6635 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 80016.0 ave 80016 max 80016 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 160032.0 ave 160032 max 160032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 160032 Ave neighs/atom = 54.211382 Neighbor list builds = 0 Dangerous builds = 0 2952 -9894.28207702425 eV 2.53705237899925 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03