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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -39.840000 0.0000000) to (17.251226 39.840000 6.0992294) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7504086 4.9800000 6.0992294 Created 384 atoms using lattice units in orthogonal box = (0.0000000 -39.840000 0.0000000) to (17.251226 39.840000 6.0992294) create_atoms CPU = 0.001 seconds 384 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7504086 4.9800000 6.0992294 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -39.840000 0.0000000) to (17.251226 39.840000 6.0992294) create_atoms CPU = 0.001 seconds 396 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 ghost atom cutoff = 6 binsize = 3, bins = 6 27 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 772 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_912636107108_001#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 ghost atom cutoff = 6 binsize = 3, bins = 6 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.542 | 4.542 | 4.542 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3067.3079 0 -3067.3079 119529.04 57 0 -3412.4993 0 -3412.4993 26865.946 Loop time of 2.64494 on 1 procs for 57 steps with 772 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 = -3067.30792893798 -3412.49681468749 -3412.49932981746 Force two-norm initial, final = 459.25244 0.19914950 Force max component initial, final = 95.628476 0.038670587 Final line search alpha, max atom move = 1.0000000 0.038670587 Iterations, force evaluations = 57 108 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6332 | 2.6332 | 2.6332 | 0.0 | 99.56 Neigh | 0.0047746 | 0.0047746 | 0.0047746 | 0.0 | 0.18 Comm | 0.003248 | 0.003248 | 0.003248 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00367 | | | 0.14 Nlocal: 772.000 ave 772 max 772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3627.00 ave 3627 max 3627 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: 60176.0 ave 60176 max 60176 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 60176 Ave neighs/atom = 77.948187 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 6 27 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 57 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.542 | 4.542 | 4.542 Mbytes Step Temp E_pair E_mol TotEng Press Volume 57 0 -3412.4993 0 -3412.4993 26865.946 8383.8646 72 0 -3414.2788 0 -3414.2788 -93.035278 8501.762 Loop time of 0.418289 on 1 procs for 15 steps with 772 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 = -3412.49932981747 -3414.27847089898 -3414.27884770036 Force two-norm initial, final = 282.95647 1.2312068 Force max component initial, final = 258.25043 0.56298639 Final line search alpha, max atom move = 0.00047274270 0.00026614771 Iterations, force evaluations = 15 16 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.41025 | 0.41025 | 0.41025 | 0.0 | 98.08 Neigh | 0.00473 | 0.00473 | 0.00473 | 0.0 | 1.13 Comm | 0.00058187 | 0.00058187 | 0.00058187 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00273 | | | 0.65 Nlocal: 772.000 ave 772 max 772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3627.00 ave 3627 max 3627 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: 59880.0 ave 59880 max 59880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59880 Ave neighs/atom = 77.564767 Neighbor list builds = 1 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 ghost atom cutoff = 6 binsize = 3, bins = 6 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.680 | 4.680 | 4.680 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3414.2788 0 -3414.2788 -93.035278 Loop time of 1.737e-06 on 1 procs for 0 steps with 772 atoms 172.7% 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 | | 1.737e-06 | | |100.00 Nlocal: 772.000 ave 772 max 772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3627.00 ave 3627 max 3627 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: 59880.0 ave 59880 max 59880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59880 Ave neighs/atom = 77.564767 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 ghost atom cutoff = 6 binsize = 3, bins = 6 27 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.680 | 4.680 | 4.680 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 -3414.2788 -3414.2788 17.236133 80.811903 6.1037084 -93.035278 -93.035278 -69.157968 -107.60323 -102.34463 2.2172242 472.20533 Loop time of 1.669e-06 on 1 procs for 0 steps with 772 atoms 179.7% 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 | | 1.669e-06 | | |100.00 Nlocal: 772.000 ave 772 max 772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3627.00 ave 3627 max 3627 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 29940.0 ave 29940 max 29940 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 59880.0 ave 59880 max 59880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 59880 Ave neighs/atom = 77.564767 Neighbor list builds = 0 Dangerous builds = 0 772 -3414.27884770036 eV 2.21722418292373 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03