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 = 2.8548760 2.8548760 2.8548760 Created orthogonal box = (0.0000000 -34.498453 0.0000000) to (42.248307 34.498453 6.9929895) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.0512075 4.2528819 4.6619930 Created 879 atoms using lattice units in orthogonal box = (0.0000000 -34.498453 0.0000000) to (42.248307 34.498453 6.9929895) create_atoms CPU = 0.004 seconds 879 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.0512075 4.2528819 4.6619930 Created 879 atoms using lattice units in orthogonal box = (0.0000000 -34.498453 0.0000000) to (42.248307 34.498453 6.9929895) create_atoms CPU = 0.003 seconds 879 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 19 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 21 atoms, new total = 1737 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_634187028437_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.553 | 5.553 | 5.553 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6753.1634 0 -6753.1634 30698.952 137 0 -6929.9848 0 -6929.9848 -3850.1221 Loop time of 6.85921 on 1 procs for 137 steps with 1737 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 = -6753.16335938126 -6929.97884552755 -6929.98480406696 Force two-norm initial, final = 299.70510 0.30333045 Force max component initial, final = 59.247762 0.049701333 Final line search alpha, max atom move = 0.62762856 0.031193976 Iterations, force evaluations = 137 263 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.7263 | 6.7263 | 6.7263 | 0.0 | 98.06 Neigh | 0.035575 | 0.035575 | 0.035575 | 0.0 | 0.52 Comm | 0.047906 | 0.047906 | 0.047906 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04941 | | | 0.72 Nlocal: 1737.00 ave 1737 max 1737 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7172.00 ave 7172 max 7172 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: 236376.0 ave 236376 max 236376 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 236376 Ave neighs/atom = 136.08290 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 19 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 137 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.549 | 5.549 | 5.549 Mbytes Step Temp E_pair E_mol TotEng Press Volume 137 0 -6929.9848 0 -6929.9848 -3850.1221 20384.581 140 0 -6930.0888 0 -6930.0888 613.65762 20332.001 Loop time of 0.131993 on 1 procs for 3 steps with 1737 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 = -6929.98480406697 -6930.08580377589 -6930.08875147959 Force two-norm initial, final = 96.118404 0.55120679 Force max component initial, final = 85.749361 0.35601693 Final line search alpha, max atom move = 8.6621989e-05 3.0838894e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12841 | 0.12841 | 0.12841 | 0.0 | 97.28 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0006761 | 0.0006761 | 0.0006761 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002911 | | | 2.21 Nlocal: 1737.00 ave 1737 max 1737 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6720.00 ave 6720 max 6720 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: 235796.0 ave 235796 max 235796 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235796 Ave neighs/atom = 135.74899 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.687 | 5.687 | 5.687 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -6930.0888 0 -6930.0888 613.65762 Loop time of 6.164e-06 on 1 procs for 0 steps with 1737 atoms 178.5% 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 | | 6.164e-06 | | |100.00 Nlocal: 1737.00 ave 1737 max 1737 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6729.00 ave 6729 max 6729 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: 235954.0 ave 235954 max 235954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235954 Ave neighs/atom = 135.83995 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 12 19 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 5.687 | 5.687 | 5.687 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 -6930.0888 -6930.0888 42.153747 68.996906 6.9905979 613.65762 613.65762 -27.991603 1887.4142 -18.449748 2.2302987 1513.4455 Loop time of 7.407e-06 on 1 procs for 0 steps with 1737 atoms 283.5% 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 | | 7.407e-06 | | |100.00 Nlocal: 1737.00 ave 1737 max 1737 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6729.00 ave 6729 max 6729 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 117977.0 ave 117977 max 117977 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 235954.0 ave 235954 max 235954 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 235954 Ave neighs/atom = 135.83995 Neighbor list builds = 0 Dangerous builds = 0 1737 -6684.43939074229 eV 2.23029867270127 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07