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 = 3.5184747 3.5184747 3.5184747 Created orthogonal box = (0.0000000 -42.513891 0.0000000) to (52.068670 42.513891 8.6184676) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9928862 5.2414386 5.7456450 Created 1751 atoms using lattice units in orthogonal box = (0.0000000 -42.513891 0.0000000) to (52.068670 42.513891 8.6184676) create_atoms CPU = 0.002 seconds 1751 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9928862 5.2414386 5.7456450 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -42.513891 0.0000000) to (52.068670 42.513891 8.6184676) create_atoms CPU = 0.002 seconds 1757 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 14 22 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 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 16 atoms, new total = 3492 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_922363340570_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 7.810 | 7.810 | 7.810 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12454.512 0 -12454.512 177191.61 53 0 -15125.111 0 -15125.111 383.97758 Loop time of 2.95648 on 1 procs for 53 steps with 3492 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12454.5115741452 -15125.0974213525 -15125.1113849034 Force two-norm initial, final = 3087.0321 0.39013365 Force max component initial, final = 452.82338 0.016601013 Final line search alpha, max atom move = 1.0000000 0.016601013 Iterations, force evaluations = 53 89 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.8445 | 2.8445 | 2.8445 | 0.0 | 96.21 Neigh | 0.081482 | 0.081482 | 0.081482 | 0.0 | 2.76 Comm | 0.012747 | 0.012747 | 0.012747 | 0.0 | 0.43 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01776 | | | 0.60 Nlocal: 3492.00 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11885.0 ave 11885 max 11885 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: 692088.0 ave 692088 max 692088 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 692088 Ave neighs/atom = 198.19244 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 14 22 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 53 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.810 | 7.810 | 7.810 Mbytes Step Temp E_pair E_mol TotEng Press Volume 53 0 -15125.111 0 -15125.111 383.97758 38156.399 54 0 -15125.122 0 -15125.122 -544.30957 38174.647 Loop time of 0.0918428 on 1 procs for 1 steps with 3492 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 = -15125.1113849033 -15125.1113849033 -15125.1221557821 Force two-norm initial, final = 35.179456 25.139688 Force max component initial, final = 30.221825 21.404954 Final line search alpha, max atom move = 3.3088670e-05 0.00070826148 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.090116 | 0.090116 | 0.090116 | 0.0 | 98.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029576 | 0.00029576 | 0.00029576 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001431 | | | 1.56 Nlocal: 3492.00 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11873.0 ave 11873 max 11873 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: 692716.0 ave 692716 max 692716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 692716 Ave neighs/atom = 198.37228 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 7.948 | 7.948 | 7.948 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -15125.122 0 -15125.122 -544.30957 Loop time of 2.027e-06 on 1 procs for 0 steps with 3492 atoms 246.7% 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 | | 2.027e-06 | | |100.00 Nlocal: 3492.00 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11873.0 ave 11873 max 11873 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: 692680.0 ave 692680 max 692680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 692680 Ave neighs/atom = 198.36197 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 14 22 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 7.948 | 7.948 | 7.948 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 -15125.122 -15125.122 52.096105 85.006958 8.6201593 -544.30957 -544.30957 -233.01286 -898.1384 -501.77747 2.2752503 1363.6569 Loop time of 2.699e-06 on 1 procs for 0 steps with 3492 atoms 259.4% 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 | | 2.699e-06 | | |100.00 Nlocal: 3492.00 ave 3492 max 3492 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 11873.0 ave 11873 max 11873 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 346340.0 ave 346340 max 346340 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 692680.0 ave 692680 max 692680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 692680 Ave neighs/atom = 198.36197 Neighbor list builds = 0 Dangerous builds = 0 3492 -15125.1221557821 eV 2.27525027382728 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03