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 = 3.5200004 3.5200004 3.5200004 Created orthogonal box = (0.0000000 -46.698082 0.0000000) to (28.596618 46.698082 8.6222048) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1993851 5.3066002 5.7481365 Created 1049 atoms using lattice units in orthogonal box = (0.0000000 -46.698082 0.0000000) to (28.596618 46.698082 8.6222048) create_atoms CPU = 0.002 seconds 1049 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1993851 5.3066002 5.7481365 Created 1073 atoms using lattice units in orthogonal box = (0.0000000 -46.698082 0.0000000) to (28.596618 46.698082 8.6222048) create_atoms CPU = 0.002 seconds 1073 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 8 25 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 10 atoms, new total = 2112 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_418978237058_005#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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 8 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.038 | 6.038 | 6.038 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9312.1054 0 -9312.1054 12173.844 40 0 -9386.4472 0 -9386.4472 6028.2145 Loop time of 1.44401 on 1 procs for 40 steps with 2112 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 = -9312.10542642852 -9386.44291770975 -9386.44724349451 Force two-norm initial, final = 56.867567 0.18898705 Force max component initial, final = 4.6620012 0.011759873 Final line search alpha, max atom move = 1.0000000 0.011759873 Iterations, force evaluations = 40 77 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4284 | 1.4284 | 1.4284 | 0.0 | 98.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0068783 | 0.0068783 | 0.0068783 | 0.0 | 0.48 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008702 | | | 0.60 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8604.00 ave 8604 max 8604 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: 371030.0 ave 371030 max 371030 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 371030 Ave neighs/atom = 175.67708 Neighbor list builds = 0 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 8 25 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 40 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.036 | 6.036 | 6.036 Mbytes Step Temp E_pair E_mol TotEng Press Volume 40 0 -9386.4472 0 -9386.4472 6028.2145 23028.309 45 0 -9386.8172 0 -9386.8172 -76.349659 23107.295 Loop time of 0.130606 on 1 procs for 5 steps with 2112 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 = -9386.44724349453 -9386.80946390704 -9386.81723885636 Force two-norm initial, final = 182.76432 2.0551045 Force max component initial, final = 171.66662 1.6222218 Final line search alpha, max atom move = 6.1757149e-05 0.00010018380 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.12722 | 0.12722 | 0.12722 | 0.0 | 97.41 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00049306 | 0.00049306 | 0.00049306 | 0.0 | 0.38 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002893 | | | 2.22 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8338.00 ave 8338 max 8338 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: 369120.0 ave 369120 max 369120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 369120 Ave neighs/atom = 174.77273 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 8 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.174 | 6.174 | 6.174 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9386.8172 0 -9386.8172 -76.349659 Loop time of 2.088e-06 on 1 procs for 0 steps with 2112 atoms 143.7% 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 | | 2.088e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8338.00 ave 8338 max 8338 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: 369120.0 ave 369120 max 369120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 369120 Ave neighs/atom = 174.77273 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 8 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.174 | 6.174 | 6.174 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 -9386.8172 -9386.8172 28.578225 93.833475 8.6169993 -76.349659 -76.349659 -112.40667 -76.005406 -40.636903 2.3772566 638.5113 Loop time of 2.498e-06 on 1 procs for 0 steps with 2112 atoms 200.2% 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 | | 2.498e-06 | | |100.00 Nlocal: 2112.00 ave 2112 max 2112 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8338.00 ave 8338 max 8338 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 184560.0 ave 184560 max 184560 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 369120.0 ave 369120 max 369120 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 369120 Ave neighs/atom = 174.77273 Neighbor list builds = 0 Dangerous builds = 0 2112 -9386.81723885636 eV 2.37725656422348 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02