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 = 4.2107003 4.2107003 4.2107003 Created orthogonal box = (0.0000000 -52.083486 0.0000000) to (24.552391 52.083486 5.9548295) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 7.2212914 7.1487138 5.9548295 Created 408 atoms using lattice units in orthogonal box = (0.0000000 -52.083486 0.0000000) to (24.552391 52.083486 5.9548295) create_atoms CPU = 0.001 seconds 408 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 7.2212914 7.1487138 5.9548295 Created 412 atoms using lattice units in orthogonal box = (0.0000000 -52.083486 0.0000000) to (24.552391 52.083486 5.9548295) create_atoms CPU = 0.001 seconds 412 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 6 24 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 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 816 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_878712978062_003#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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 4.975 | 4.975 | 4.975 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2709.7131 0 -2709.7131 92052.178 77 0 -3039.0863 0 -3039.0863 1389.6384 Loop time of 1.65697 on 1 procs for 77 steps with 816 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 = -2709.71310369394 -3039.08396691897 -3039.08634368547 Force two-norm initial, final = 866.72070 0.085865105 Force max component initial, final = 159.06016 0.015209395 Final line search alpha, max atom move = 1.0000000 0.015209395 Iterations, force evaluations = 77 141 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6325 | 1.6325 | 1.6325 | 0.0 | 98.52 Neigh | 0.0083966 | 0.0083966 | 0.0083966 | 0.0 | 0.51 Comm | 0.0086208 | 0.0086208 | 0.0086208 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0075 | | | 0.45 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5760.00 ave 5760 max 5760 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: 140264.0 ave 140264 max 140264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 140264 Ave neighs/atom = 171.89216 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 6 24 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 77 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.975 | 4.975 | 4.975 Mbytes Step Temp E_pair E_mol TotEng Press Volume 77 0 -3039.0863 0 -3039.0863 1389.6384 15229.764 80 0 -3039.1144 0 -3039.1144 -13.572783 15280.879 Loop time of 0.0583328 on 1 procs for 3 steps with 816 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 = -3039.08634368548 -3039.11165242585 -3039.1143788299 Force two-norm initial, final = 23.493169 0.49197995 Force max component initial, final = 17.489515 0.37718291 Final line search alpha, max atom move = 0.00034148670 0.00012880295 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.05694 | 0.05694 | 0.05694 | 0.0 | 97.61 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00024771 | 0.00024771 | 0.00024771 | 0.0 | 0.42 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001145 | | | 1.96 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5792.00 ave 5792 max 5792 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: 139680.0 ave 139680 max 139680 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139680 Ave neighs/atom = 171.17647 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 5.113 | 5.113 | 5.113 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3039.1144 0 -3039.1144 -13.572783 Loop time of 2.366e-06 on 1 procs for 0 steps with 816 atoms 169.1% 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 | | 2.366e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5792.00 ave 5792 max 5792 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: 139584.0 ave 139584 max 139584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139584 Ave neighs/atom = 171.05882 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 6 24 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9 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) = 5.113 | 5.113 | 5.113 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 -3039.1144 -3039.1144 24.549993 104.46187 5.9585306 -13.572783 -13.572783 -39.543181 21.706377 -22.881544 2.8151017 1609.3992 Loop time of 2.806e-06 on 1 procs for 0 steps with 816 atoms 285.1% 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 | | 2.806e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5792.00 ave 5792 max 5792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 69792.0 ave 69792 max 69792 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 139584.0 ave 139584 max 139584 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 139584 Ave neighs/atom = 171.05882 Neighbor list builds = 0 Dangerous builds = 0 816 -3039.1143788299 eV 2.81510168511289 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02