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 = 3.6135806 3.6135806 3.6135806 Created orthogonal box = (0.0000000 -47.939564 0.0000000) to (29.356868 47.939564 8.8514286) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3376123 5.4476777 5.9009524 Created 1056 atoms using lattice units in orthogonal box = (0.0000000 -47.939564 0.0000000) to (29.356868 47.939564 8.8514286) create_atoms CPU = 0.004 seconds 1056 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3376123 5.4476777 5.9009524 Created 1080 atoms using lattice units in orthogonal box = (0.0000000 -47.939564 0.0000000) to (29.356868 47.939564 8.8514286) create_atoms CPU = 0.004 seconds 1080 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 8 26 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 7.50679 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 24 atoms, new total = 2112 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_426403318662_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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 8 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 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) = 6.001 | 6.001 | 6.001 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7458.9889 0 -7458.9889 3716.046 13 0 -7467.7986 0 -7467.7986 2322.0544 Loop time of 0.75811 on 1 procs for 13 steps with 2112 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 = -7458.98891231039 -7467.79667039729 -7467.79855582424 Force two-norm initial, final = 18.870260 0.082344051 Force max component initial, final = 1.9179906 0.0040061573 Final line search alpha, max atom move = 1.0000000 0.0040061573 Iterations, force evaluations = 13 26 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.74758 | 0.74758 | 0.74758 | 0.0 | 98.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0048035 | 0.0048035 | 0.0048035 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00573 | | | 0.76 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7941.00 ave 7941 max 7941 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: 296160.0 ave 296160 max 296160 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 296160 Ave neighs/atom = 140.22727 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 8 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 13 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.001 | 6.001 | 6.001 Mbytes Step Temp E_pair E_mol TotEng Press Volume 13 0 -7467.7986 0 -7467.7986 2322.0544 24914.212 18 0 -7467.9974 0 -7467.9974 198.03057 24951.642 Loop time of 0.208802 on 1 procs for 5 steps with 2112 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 = -7467.79855582424 -7467.99582378717 -7467.9973687991 Force two-norm initial, final = 95.615356 5.5971748 Force max component initial, final = 95.053541 4.3898542 Final line search alpha, max atom move = 0.00017738789 0.00077870697 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.20215 | 0.20215 | 0.20215 | 0.0 | 96.82 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012441 | 0.0012441 | 0.0012441 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005405 | | | 2.59 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7941.00 ave 7941 max 7941 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: 295776.0 ave 295776 max 295776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 295776 Ave neighs/atom = 140.04545 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 8 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 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) = 6.139 | 6.139 | 6.139 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7467.9974 0 -7467.9974 198.03057 Loop time of 6.254e-06 on 1 procs for 0 steps with 2112 atoms 175.9% 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 | | 6.254e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7941.00 ave 7941 max 7941 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: 295776.0 ave 295776 max 295776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 295776 Ave neighs/atom = 140.04545 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 = 7.50679 ghost atom cutoff = 7.50679 binsize = 3.753395, bins = 8 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.50679 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) = 6.139 | 6.139 | 6.139 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 -7467.9974 -7467.9974 29.305905 96.284698 8.8427372 198.03057 198.03057 133.05582 283.07044 177.96546 2.4112238 663.87263 Loop time of 6.836e-06 on 1 procs for 0 steps with 2112 atoms 234.1% 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 | | 6.836e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7941.00 ave 7941 max 7941 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 147888.0 ave 147888 max 147888 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 295776.0 ave 295776 max 295776 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 295776 Ave neighs/atom = 140.04545 Neighbor list builds = 0 Dangerous builds = 0 2112 -7468.0079287991 eV 2.41122382253873 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01