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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -35.424349 0.0000000) to (16.697848 35.424349 4.0498230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9111318 4.8617725 4.0498230 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -35.424349 0.0000000) to (16.697848 35.424349 4.0498230) create_atoms CPU = 0.002 seconds 206 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9111318 4.8617725 4.0498230 Created 206 atoms using lattice units in orthogonal box = (0.0000000 -35.424349 0.0000000) to (16.697848 35.424349 4.0498230) create_atoms CPU = 0.002 seconds 206 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 26 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 408 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.439 | 4.439 | 4.439 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1696.4503 0 -1696.4503 33343.177 20 0 -1741.319 0 -1741.319 7704.5269 Loop time of 0.843756 on 1 procs for 20 steps with 408 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 = -1696.45026535822 -1741.31794664508 -1741.31900852508 Force two-norm initial, final = 85.834403 0.090379266 Force max component initial, final = 24.943306 0.013932306 Final line search alpha, max atom move = 1.0000000 0.013932306 Iterations, force evaluations = 20 34 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.83931 | 0.83931 | 0.83931 | 0.0 | 99.47 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0019779 | 0.0019779 | 0.0019779 | 0.0 | 0.23 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002469 | | | 0.29 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2366.00 ave 2366 max 2366 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: 23792.0 ave 23792 max 23792 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23792 Ave neighs/atom = 58.313725 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 20 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.439 | 4.439 | 4.439 Mbytes Step Temp E_pair E_mol TotEng Press Volume 20 0 -1741.319 0 -1741.319 7704.5269 4791.0249 23 0 -1741.3398 0 -1741.3398 4074.8181 4800.9905 Loop time of 0.147663 on 1 procs for 3 steps with 408 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 = -1741.31900852508 -1741.33930256914 -1741.33978712523 Force two-norm initial, final = 21.338386 0.10737351 Force max component initial, final = 20.279896 0.019053946 Final line search alpha, max atom move = 0.00036618790 6.9773243e-06 Iterations, force evaluations = 3 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.14606 | 0.14606 | 0.14606 | 0.0 | 98.92 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00035043 | 0.00035043 | 0.00035043 | 0.0 | 0.24 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00125 | | | 0.85 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2355.00 ave 2355 max 2355 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: 23816.0 ave 23816 max 23816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23816 Ave neighs/atom = 58.372549 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.577 | 4.577 | 4.577 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1741.3398 0 -1741.3398 4074.8181 Loop time of 6.395e-06 on 1 procs for 0 steps with 408 atoms 156.4% 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 | | 6.395e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2351.00 ave 2351 max 2351 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: 23816.0 ave 23816 max 23816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23816 Ave neighs/atom = 58.372549 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 6 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.577 | 4.577 | 4.577 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 -1741.3398 -1741.3398 16.731957 70.848697 4.0499741 4074.8181 4074.8181 -0.098153862 12224.773 -0.22048545 2.2830822 259.09737 Loop time of 6.826e-06 on 1 procs for 0 steps with 408 atoms 278.3% 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 | | 6.826e-06 | | |100.00 Nlocal: 408.000 ave 408 max 408 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2351.00 ave 2351 max 2351 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 11908.0 ave 11908 max 11908 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 23816.0 ave 23816 max 23816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 23816 Ave neighs/atom = 58.372549 Neighbor list builds = 0 Dangerous builds = 0 408 -1741.33978712523 eV 2.28308216371657 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01