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 -47.638636 0.0000000) to (20.628134 47.638636 7.2931469) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8760448 5.9548295 7.2931469 Created 384 atoms using lattice units in orthogonal box = (0.0000000 -47.638636 0.0000000) to (20.628134 47.638636 7.2931469) create_atoms CPU = 0.003 seconds 384 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8760448 5.9548295 7.2931469 Created 396 atoms using lattice units in orthogonal box = (0.0000000 -47.638636 0.0000000) to (20.628134 47.638636 7.2931469) create_atoms CPU = 0.002 seconds 396 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 = 5 22 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 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_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 = 5 22 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) = 4.976 | 4.976 | 4.976 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2622.0531 0 -2622.0531 77846.496 60 0 -2872.8902 0 -2872.8902 5050.6322 Loop time of 2.49573 on 1 procs for 60 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 = -2622.05312433302 -2872.88779061329 -2872.89018146036 Force two-norm initial, final = 507.80617 0.097034341 Force max component initial, final = 100.36824 0.011893758 Final line search alpha, max atom move = 1.0000000 0.011893758 Iterations, force evaluations = 60 112 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.4525 | 2.4525 | 2.4525 | 0.0 | 98.27 Neigh | 0.017399 | 0.017399 | 0.017399 | 0.0 | 0.70 Comm | 0.013944 | 0.013944 | 0.013944 | 0.0 | 0.56 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01189 | | | 0.48 Nlocal: 772.000 ave 772 max 772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4778.00 ave 4778 max 4778 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: 133096.0 ave 133096 max 133096 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133096 Ave neighs/atom = 172.40415 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 = 5 22 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 : 60 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 60 0 -2872.8902 0 -2872.8902 5050.6322 14333.895 75 0 -2873.3764 0 -2873.3764 -0.8021548 14509.057 Loop time of 0.412853 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 = -2872.89018146036 -2873.37446392054 -2873.37643285479 Force two-norm initial, final = 84.560744 0.45410963 Force max component initial, final = 70.083072 0.22712716 Final line search alpha, max atom move = 0.00046727770 0.00010613146 Iterations, force evaluations = 15 15 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.38422 | 0.38422 | 0.38422 | 0.0 | 93.06 Neigh | 0.018871 | 0.018871 | 0.018871 | 0.0 | 4.57 Comm | 0.0022487 | 0.0022487 | 0.0022487 | 0.0 | 0.54 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007516 | | | 1.82 Nlocal: 772.000 ave 772 max 772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4857.00 ave 4857 max 4857 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: 133368.0 ave 133368 max 133368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133368 Ave neighs/atom = 172.75648 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 = 9 ghost atom cutoff = 9 binsize = 4.5, bins = 5 22 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) = 5.114 | 5.114 | 5.114 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2873.3764 0 -2873.3764 -0.8021548 Loop time of 7.457e-06 on 1 procs for 0 steps with 772 atoms 174.3% 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 | | 7.457e-06 | | |100.00 Nlocal: 772.000 ave 772 max 772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4909.00 ave 4909 max 4909 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: 133248.0 ave 133248 max 133248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133248 Ave neighs/atom = 172.60104 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 = 5 22 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) = 5.114 | 5.114 | 5.114 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 -2873.3764 -2873.3764 20.535085 96.706431 7.3061292 -0.8021548 -0.8021548 -16.268148 25.456945 -11.595261 2.7131051 750.37208 Loop time of 8.339e-06 on 1 procs for 0 steps with 772 atoms 239.8% 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 | | 8.339e-06 | | |100.00 Nlocal: 772.000 ave 772 max 772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4909.00 ave 4909 max 4909 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 66624.0 ave 66624 max 66624 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 133248.0 ave 133248 max 133248 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 133248 Ave neighs/atom = 172.60104 Neighbor list builds = 0 Dangerous builds = 0 772 -2873.37643285479 eV 2.71310507509978 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:04