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 = 3.8693370 3.8693370 3.8693370 Created orthogonal box = (0.0000000 -41.853279 0.0000000) to (13.951093 41.853279 3.8693370) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3658050 5.3658050 3.8693370 Created 156 atoms using lattice units in orthogonal box = (0.0000000 -41.853279 0.0000000) to (13.951093 41.853279 3.8693370) create_atoms CPU = 0.001 seconds 156 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3658050 5.3658050 3.8693370 Created 158 atoms using lattice units in orthogonal box = (0.0000000 -41.853279 0.0000000) to (13.951093 41.853279 3.8693370) create_atoms CPU = 0.000 seconds 158 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 = 8.1953264 ghost atom cutoff = 8.1953264 binsize = 4.0976632, bins = 4 21 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 8.19532644834285 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 312 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_042691367780_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 = 8.1953264 ghost atom cutoff = 8.1953264 binsize = 4.0976632, bins = 4 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19532644834285 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) = 4.460 | 4.460 | 4.460 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -937.98657 0 -937.98657 48875.172 19 0 -995.52807 0 -995.52807 8381.3269 Loop time of 0.105275 on 1 procs for 19 steps with 312 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 = -937.986568714064 -995.527291169059 -995.528068374904 Force two-norm initial, final = 149.36632 0.088101334 Force max component initial, final = 52.486934 0.019806188 Final line search alpha, max atom move = 1.0000000 0.019806188 Iterations, force evaluations = 19 33 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.10337 | 0.10337 | 0.10337 | 0.0 | 98.19 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0010566 | 0.0010566 | 0.0010566 | 0.0 | 1.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0008482 | | | 0.81 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3788.00 ave 3788 max 3788 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: 44300.0 ave 44300 max 44300 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 44300 Ave neighs/atom = 141.98718 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 = 8.1953264 ghost atom cutoff = 8.1953264 binsize = 4.0976632, bins = 4 21 1 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19532644834285 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 19 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.460 | 4.460 | 4.460 Mbytes Step Temp E_pair E_mol TotEng Press Volume 19 0 -995.52807 0 -995.52807 8381.3269 4518.6039 28 0 -995.67401 0 -995.67401 -52.970414 4543.6836 Loop time of 0.0394988 on 1 procs for 9 steps with 312 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 = -995.528068374904 -995.673972881242 -995.67401231008 Force two-norm initial, final = 46.681322 0.47548661 Force max component initial, final = 41.125544 0.37396093 Final line search alpha, max atom move = 0.0015073149 0.00056367688 Iterations, force evaluations = 9 11 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.037495 | 0.037495 | 0.037495 | 0.0 | 94.93 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00036192 | 0.00036192 | 0.00036192 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001642 | | | 4.16 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3788.00 ave 3788 max 3788 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: 48536.0 ave 48536 max 48536 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 48536 Ave neighs/atom = 155.56410 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 = 8.1953264 ghost atom cutoff = 8.1953264 binsize = 4.0976632, bins = 4 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19532644834285 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) = 4.598 | 4.598 | 4.598 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -995.67401 0 -995.67401 -52.970414 Loop time of 2.153e-06 on 1 procs for 0 steps with 312 atoms 139.3% 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 | | 2.153e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3763.00 ave 3763 max 3763 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: 46600.0 ave 46600 max 46600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46600 Ave neighs/atom = 149.35897 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 = 8.1953264 ghost atom cutoff = 8.1953264 binsize = 4.0976632, bins = 4 21 1 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.19532644834285 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) = 4.598 | 4.598 | 4.598 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 -995.67401 -995.67401 13.917643 84.36081 3.869917 -52.970414 -52.970414 28.306554 -55.333343 -131.88445 2.4753442 180.50989 Loop time of 1.847e-06 on 1 procs for 0 steps with 312 atoms 108.3% 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 | | 1.847e-06 | | |100.00 Nlocal: 312.000 ave 312 max 312 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3763.00 ave 3763 max 3763 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 23300.0 ave 23300 max 23300 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 46600.0 ave 46600 max 46600 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 46600 Ave neighs/atom = 149.35897 Neighbor list builds = 0 Dangerous builds = 0 312 -995.67401231008 eV 2.47534421472569 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00