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 = 4.0310361 4.0310361 4.0310361 Created orthogonal box = (0.0000000 -61.398913 0.0000000) to (30.699456 61.398913 4.0310361) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2930097 5.2930097 4.0310361 Created 464 atoms using lattice units in orthogonal box = (0.0000000 -61.398913 0.0000000) to (30.699456 61.398913 4.0310361) create_atoms CPU = 0.001 seconds 464 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2930097 5.2930097 4.0310361 Created 466 atoms using lattice units in orthogonal box = (0.0000000 -61.398913 0.0000000) to (30.699456 61.398913 4.0310361) create_atoms CPU = 0.001 seconds 466 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 8 32 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 928 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_699137396381_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 8 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 4.988 | 4.988 | 4.988 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3067.0303 0 -3067.0303 6378.4867 34 0 -3109.5613 0 -3109.5613 4060.9791 Loop time of 0.368615 on 1 procs for 34 steps with 928 atoms 97.3% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3067.03034959189 -3109.55863166853 -3109.56132804139 Force two-norm initial, final = 31.864609 0.15588752 Force max component initial, final = 6.4603435 0.047233029 Final line search alpha, max atom move = 1.0000000 0.047233029 Iterations, force evaluations = 34 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.36159 | 0.36159 | 0.36159 | 0.0 | 98.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0038011 | 0.0038011 | 0.0038011 | 0.0 | 1.03 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003223 | | | 0.87 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6917.00 ave 6917 max 6917 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: 123168.0 ave 123168 max 123168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 123168 Ave neighs/atom = 132.72414 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 8 32 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 34 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.988 | 4.988 | 4.988 Mbytes Step Temp E_pair E_mol TotEng Press Volume 34 0 -3109.5613 0 -3109.5613 4060.9791 15196.307 42 0 -3109.8049 0 -3109.8049 -4.9565691 15278.937 Loop time of 0.0603834 on 1 procs for 8 steps with 928 atoms 99.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3109.56132804139 -3109.80336331445 -3109.80486247017 Force two-norm initial, final = 77.297513 0.49472034 Force max component initial, final = 69.767266 0.25003525 Final line search alpha, max atom move = 0.00030562153 7.6416156e-05 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.057285 | 0.057285 | 0.057285 | 0.0 | 94.87 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00052412 | 0.00052412 | 0.00052412 | 0.0 | 0.87 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002574 | | | 4.26 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6887.00 ave 6887 max 6887 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: 122280.0 ave 122280 max 122280 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122280 Ave neighs/atom = 131.76724 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 8 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.126 | 5.126 | 5.126 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3109.8049 0 -3109.8049 -4.9565691 Loop time of 1.581e-06 on 1 procs for 0 steps with 928 atoms 126.5% 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 | | 1.581e-06 | | |100.00 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6897.00 ave 6897 max 6897 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: 122032.0 ave 122032 max 122032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122032 Ave neighs/atom = 131.50000 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 8 33 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 5.126 | 5.126 | 5.126 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 -3109.8049 -3109.8049 30.645531 123.73324 4.0293926 -4.9565691 -4.9565691 19.67806 -8.3393157 -26.208452 2.5766083 606.63576 Loop time of 2.189e-06 on 1 procs for 0 steps with 928 atoms 182.7% 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 | | 2.189e-06 | | |100.00 Nlocal: 928.000 ave 928 max 928 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6897.00 ave 6897 max 6897 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 61016.0 ave 61016 max 61016 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 122032.0 ave 122032 max 122032 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 122032 Ave neighs/atom = 131.50000 Neighbor list builds = 0 Dangerous builds = 0 928 -3109.80486247017 eV 2.57660826145485 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01