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 = 3.6583649 3.6583649 3.6583649 Created orthogonal box = (0.0000000 -69.025890 0.0000000) to (34.512945 69.025890 3.6583649) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0412167 5.0412167 3.6583649 Created 712 atoms using lattice units in orthogonal box = (0.0000000 -69.025890 0.0000000) to (34.512945 69.025890 3.6583649) create_atoms CPU = 0.003 seconds 712 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0412167 5.0412167 3.6583649 Created 714 atoms using lattice units in orthogonal box = (0.0000000 -69.025890 0.0000000) to (34.512945 69.025890 3.6583649) create_atoms CPU = 0.002 seconds 714 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 37 1 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 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1426 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_469343973171_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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 37 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.511 | 5.511 | 5.511 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5555.1347 0 -5555.1347 29906.251 190 0 -5705.3701 0 -5705.3701 2204.1972 Loop time of 8.53995 on 1 procs for 190 steps with 1426 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 = -5555.13465693489 -5705.36491286774 -5705.37005477071 Force two-norm initial, final = 417.15871 0.26338932 Force max component initial, final = 191.93664 0.052776405 Final line search alpha, max atom move = 1.0000000 0.052776405 Iterations, force evaluations = 190 367 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 8.315 | 8.315 | 8.315 | 0.0 | 97.37 Neigh | 0.080844 | 0.080844 | 0.080844 | 0.0 | 0.95 Comm | 0.083213 | 0.083213 | 0.083213 | 0.0 | 0.97 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.06093 | | | 0.71 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10029.0 ave 10029 max 10029 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: 209356.0 ave 209356 max 209356 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 209356 Ave neighs/atom = 146.81346 Neighbor list builds = 3 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 37 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 190 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.512 | 5.512 | 5.512 Mbytes Step Temp E_pair E_mol TotEng Press Volume 190 0 -5705.3701 0 -5705.3701 2204.1972 17430.548 249 0 -5728.0838 0 -5728.0838 -202.31349 17499.309 Loop time of 1.70068 on 1 procs for 59 steps with 1426 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 = -5705.37005477071 -5728.08090953035 -5728.08375729259 Force two-norm initial, final = 607.52174 6.7618632 Force max component initial, final = 464.36428 5.2324403 Final line search alpha, max atom move = 0.00013745497 0.00071922493 Iterations, force evaluations = 59 61 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.463 | 1.463 | 1.463 | 0.0 | 86.02 Neigh | 0.17012 | 0.17012 | 0.17012 | 0.0 | 10.00 Comm | 0.016661 | 0.016661 | 0.016661 | 0.0 | 0.98 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05089 | | | 2.99 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10074.0 ave 10074 max 10074 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: 208592.0 ave 208592 max 208592 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208592 Ave neighs/atom = 146.27770 Neighbor list builds = 6 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.635 | 5.635 | 5.635 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5728.0838 0 -5728.0838 -202.31349 Loop time of 6.425e-06 on 1 procs for 0 steps with 1426 atoms 186.8% 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 | | 6.425e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10074.0 ave 10074 max 10074 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: 208876.0 ave 208876 max 208876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208876 Ave neighs/atom = 146.47686 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 = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 10 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 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) = 5.635 | 5.635 | 5.635 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 -5728.0838 -5728.0838 34.691579 131.22171 3.8440688 -202.31349 -202.31349 -50.876467 -455.36265 -100.70135 2.1916992 499.02958 Loop time of 6.755e-06 on 1 procs for 0 steps with 1426 atoms 281.3% 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 | | 6.755e-06 | | |100.00 Nlocal: 1426.00 ave 1426 max 1426 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10074.0 ave 10074 max 10074 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 104438.0 ave 104438 max 104438 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 208876.0 ave 208876 max 208876 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 208876 Ave neighs/atom = 146.47686 Neighbor list builds = 0 Dangerous builds = 0 1426 -5728.08375729258 eV 2.19169922245513 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:10