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 = 4.0329885 4.0329885 4.0329885 Created orthogonal box = (0.0000000 -48.395862 0.0000000) to (17.110521 48.395862 5.7035070) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7035070 6.7216475 5.7035070 Created 288 atoms using lattice units in orthogonal box = (0.0000000 -48.395862 0.0000000) to (17.110521 48.395862 5.7035070) create_atoms CPU = 0.001 seconds 288 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7035070 6.7216475 5.7035070 Created 292 atoms using lattice units in orthogonal box = (0.0000000 -48.395862 0.0000000) to (17.110521 48.395862 5.7035070) create_atoms CPU = 0.001 seconds 292 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 3 15 1 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 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 572 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_140175748626_004#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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 3 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 5.827 | 5.827 | 5.827 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1637.3228 0 -1637.3228 6156.7607 63 0 -1661.0494 0 -1661.0494 -1997.604 Loop time of 2.12044 on 1 procs for 63 steps with 572 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 = -1637.32281216045 -1661.04790649357 -1661.04939896654 Force two-norm initial, final = 31.576803 0.10989729 Force max component initial, final = 6.8367766 0.0088647118 Final line search alpha, max atom move = 1.0000000 0.0088647118 Iterations, force evaluations = 63 122 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.0865 | 2.0865 | 2.0865 | 0.0 | 98.40 Neigh | 0.017127 | 0.017127 | 0.017127 | 0.0 | 0.81 Comm | 0.01139 | 0.01139 | 0.01139 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.005389 | | | 0.25 Nlocal: 572.000 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10418.0 ave 10418 max 10418 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: 379192.0 ave 379192 max 379192 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 379192 Ave neighs/atom = 662.92308 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 3 15 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.827 | 5.827 | 5.827 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -1661.0494 0 -1661.0494 -1997.604 9445.9022 69 0 -1661.1182 0 -1661.1182 9.4191686 9420.1609 Loop time of 0.141914 on 1 procs for 6 steps with 572 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 = -1661.04939896653 -1661.11778695109 -1661.11823327963 Force two-norm initial, final = 27.810815 0.22702013 Force max component initial, final = 26.966910 0.074013915 Final line search alpha, max atom move = 0.00070933342 5.2500544e-05 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.13909 | 0.13909 | 0.13909 | 0.0 | 98.01 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0005989 | 0.0005989 | 0.0005989 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002224 | | | 1.57 Nlocal: 572.000 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10413.0 ave 10413 max 10413 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: 380208.0 ave 380208 max 380208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 380208 Ave neighs/atom = 664.69930 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 3 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 5.965 | 5.965 | 5.965 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1661.1182 0 -1661.1182 9.4191686 Loop time of 1.955e-06 on 1 procs for 0 steps with 572 atoms 153.5% 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 | | 1.955e-06 | | |100.00 Nlocal: 572.000 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10413.0 ave 10413 max 10413 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: 380504.0 ave 380504 max 380504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 380504 Ave neighs/atom = 665.21678 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 = 13.7567 ghost atom cutoff = 13.7567 binsize = 6.87835, bins = 3 15 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 13.7567 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) = 5.965 | 5.965 | 5.965 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 -1661.1182 -1661.1182 17.017783 96.875574 5.7140108 9.4191686 9.4191686 12.520024 6.6643969 9.0730852 2.6149129 478.73661 Loop time of 2.393e-06 on 1 procs for 0 steps with 572 atoms 250.7% 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 | | 2.393e-06 | | |100.00 Nlocal: 572.000 ave 572 max 572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10413.0 ave 10413 max 10413 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 190252.0 ave 190252 max 190252 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 380504.0 ave 380504 max 380504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 380504 Ave neighs/atom = 665.21678 Neighbor list builds = 0 Dangerous builds = 0 572 -1661.11823327963 eV 2.6149129111364 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02