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 = 4.0709491 4.0709491 4.0709491 Created orthogonal box = (0.0000000 -54.011314 0.0000000) to (33.072547 54.011314 9.9717481) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0131904 6.1371867 6.6478321 Created 1069 atoms using lattice units in orthogonal box = (0.0000000 -54.011314 0.0000000) to (33.072547 54.011314 9.9717481) create_atoms CPU = 0.002 seconds 1069 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0131904 6.1371867 6.6478321 Created 1069 atoms using lattice units in orthogonal box = (0.0000000 -54.011314 0.0000000) to (33.072547 54.011314 9.9717481) create_atoms CPU = 0.001 seconds 1069 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 = 11 36 4 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 30 atoms, new total = 2108 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 = 11 36 4 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) = 5.039 | 5.039 | 5.039 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7084.1615 0 -7084.1615 1293.5166 12 0 -7087.9589 0 -7087.9589 1090.9475 Loop time of 1.30789 on 1 procs for 12 steps with 2108 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7084.16147671474 -7087.9564116465 -7087.95890107976 Force two-norm initial, final = 7.7892698 0.10949284 Force max component initial, final = 0.85478009 0.022446338 Final line search alpha, max atom move = 1.0000000 0.022446338 Iterations, force evaluations = 12 24 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.3047 | 1.3047 | 1.3047 | 0.0 | 99.76 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0011544 | 0.0011544 | 0.0011544 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001991 | | | 0.15 Nlocal: 2108.00 ave 2108 max 2108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5062.00 ave 5062 max 5062 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: 113716.0 ave 113716 max 113716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113716 Ave neighs/atom = 53.944972 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 11 36 4 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 : 12 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.039 | 5.039 | 5.039 Mbytes Step Temp E_pair E_mol TotEng Press Volume 12 0 -7087.9589 0 -7087.9589 1090.9475 35624.902 13 0 -7087.9649 0 -7087.9649 1670.0779 35604.174 Loop time of 0.158106 on 1 procs for 1 steps with 2108 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 = -7087.95890107978 -7087.95890107978 -7087.96488633453 Force two-norm initial, final = 21.819391 9.2136343 Force max component initial, final = 21.786635 9.2051059 Final line search alpha, max atom move = 4.5899699e-05 0.00042251159 Iterations, force evaluations = 1 2 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.15739 | 0.15739 | 0.15739 | 0.0 | 99.55 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00011464 | 0.00011464 | 0.00011464 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0006011 | | | 0.38 Nlocal: 2108.00 ave 2108 max 2108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5062.00 ave 5062 max 5062 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: 113332.0 ave 113332 max 113332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113332 Ave neighs/atom = 53.762808 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 = 11 36 4 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) = 5.177 | 5.177 | 5.177 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7087.9649 0 -7087.9649 1670.0779 Loop time of 1.618e-06 on 1 procs for 0 steps with 2108 atoms 185.4% 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 | | 1.618e-06 | | |100.00 Nlocal: 2108.00 ave 2108 max 2108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5062.00 ave 5062 max 5062 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: 113332.0 ave 113332 max 113332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113332 Ave neighs/atom = 53.762808 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 = 11 36 4 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) = 5.177 | 5.177 | 5.177 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 -7087.9649 -7087.9649 33.0543 108.02263 9.9714476 1670.0779 1670.0779 -16.860369 4612.8798 414.21435 2.6390222 995.67263 Loop time of 1.757e-06 on 1 procs for 0 steps with 2108 atoms 113.8% 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 | | 1.757e-06 | | |100.00 Nlocal: 2108.00 ave 2108 max 2108 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5062.00 ave 5062 max 5062 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56666.0 ave 56666 max 56666 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 113332.0 ave 113332 max 113332 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 113332 Ave neighs/atom = 53.762808 Neighbor list builds = 0 Dangerous builds = 0 2108 -7087.96488633453 eV 2.63902221187032 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01