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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -56.761258 0.0000000) to (34.759030 56.761258 8.8288024) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6062952 5.4930250 5.8858683 Created 1487 atoms using lattice units in orthogonal box = (0.0000000 -56.761258 0.0000000) to (34.759030 56.761258 8.8288024) create_atoms CPU = 0.002 seconds 1487 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6062952 5.4930250 5.8858683 Created 1493 atoms using lattice units in orthogonal box = (0.0000000 -56.761258 0.0000000) to (34.759030 56.761258 8.8288024) create_atoms CPU = 0.002 seconds 1493 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 38 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 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2980 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_304347095149_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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 38 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.581 | 5.581 | 5.581 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12085.189 0 -12085.189 58065.048 283 0 -12632.894 0 -12632.894 4150.8558 Loop time of 57.5239 on 1 procs for 283 steps with 2980 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -12085.1889697104 -12632.8810576559 -12632.8935610245 Force two-norm initial, final = 1192.8447 0.36850360 Force max component initial, final = 277.85878 0.13143288 Final line search alpha, max atom move = 0.99399622 0.13064379 Iterations, force evaluations = 283 526 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 57.242 | 57.242 | 57.242 | 0.0 | 99.51 Neigh | 0.13779 | 0.13779 | 0.13779 | 0.0 | 0.24 Comm | 0.058887 | 0.058887 | 0.058887 | 0.0 | 0.10 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.08501 | | | 0.15 Nlocal: 2980.00 ave 2980 max 2980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7653.00 ave 7653 max 7653 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: 231824.0 ave 231824 max 231824 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231824 Ave neighs/atom = 77.793289 Neighbor list builds = 7 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 38 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 283 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.583 | 5.583 | 5.583 Mbytes Step Temp E_pair E_mol TotEng Press Volume 283 0 -12632.894 0 -12632.894 4150.8558 34837.859 288 0 -12633.36 0 -12633.36 -386.37563 34934.892 Loop time of 0.766144 on 1 procs for 5 steps with 2980 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 = -12632.8935610244 -12633.3495178703 -12633.3598352038 Force two-norm initial, final = 205.88844 15.104383 Force max component initial, final = 182.62289 11.397002 Final line search alpha, max atom move = 6.3730709e-05 0.00072633903 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.76247 | 0.76247 | 0.76247 | 0.0 | 99.52 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00047967 | 0.00047967 | 0.00047967 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003193 | | | 0.42 Nlocal: 2980.00 ave 2980 max 2980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7642.00 ave 7642 max 7642 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: 231844.0 ave 231844 max 231844 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231844 Ave neighs/atom = 77.800000 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.721 | 5.721 | 5.721 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12633.36 0 -12633.36 -386.37563 Loop time of 2.428e-06 on 1 procs for 0 steps with 2980 atoms 164.7% 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 | | 2.428e-06 | | |100.00 Nlocal: 2980.00 ave 2980 max 2980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7632.00 ave 7632 max 7632 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: 231770.0 ave 231770 max 231770 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231770 Ave neighs/atom = 77.775168 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 12 38 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.1 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) = 5.721 | 5.721 | 5.721 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 -12633.36 -12633.36 34.812312 113.18227 8.8664166 -386.37563 -386.37563 -274.92988 -521.12029 -363.0767 2.2363605 3333.3935 Loop time of 3.089e-06 on 1 procs for 0 steps with 2980 atoms 259.0% 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 | | 3.089e-06 | | |100.00 Nlocal: 2980.00 ave 2980 max 2980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7632.00 ave 7632 max 7632 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115885.0 ave 115885 max 115885 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 231770.0 ave 231770 max 231770 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 231770 Ave neighs/atom = 77.775168 Neighbor list builds = 0 Dangerous builds = 0 2980 -12633.3598352038 eV 2.23636047355565 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:59