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 = 4.0500001 4.0500001 4.0500001 Created orthogonal box = (0.0000000 -63.779465 0.0000000) to (39.056786 63.779465 9.9204336) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2994817 6.1722063 6.6136224 Created 1485 atoms using lattice units in orthogonal box = (0.0000000 -63.779465 0.0000000) to (39.056786 63.779465 9.9204336) create_atoms CPU = 0.007 seconds 1485 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2994817 6.1722063 6.6136224 Created 1491 atoms using lattice units in orthogonal box = (0.0000000 -63.779465 0.0000000) to (39.056786 63.779465 9.9204336) create_atoms CPU = 0.006 seconds 1491 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 11 34 3 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 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2976 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_418978237058_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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 11 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.433 | 6.433 | 6.433 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9834.9818 0 -9834.9818 12699.846 61 0 -9988.3368 0 -9988.3368 4679.124 Loop time of 3.7895 on 1 procs for 61 steps with 2976 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 = -9834.98175362136 -9988.32718649339 -9988.33680041254 Force two-norm initial, final = 106.96235 0.21379562 Force max component initial, final = 20.143812 0.040209642 Final line search alpha, max atom move = 1.0000000 0.040209642 Iterations, force evaluations = 61 110 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.6261 | 3.6261 | 3.6261 | 0.0 | 95.69 Neigh | 0.10665 | 0.10665 | 0.10665 | 0.0 | 2.81 Comm | 0.023599 | 0.023599 | 0.023599 | 0.0 | 0.62 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03316 | | | 0.87 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8684.00 ave 8684 max 8684 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: 389198.0 ave 389198 max 389198 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 389198 Ave neighs/atom = 130.77890 Neighbor list builds = 2 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 11 34 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 61 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.055 | 6.055 | 6.055 Mbytes Step Temp E_pair E_mol TotEng Press Volume 61 0 -9988.3368 0 -9988.3368 4679.124 49424.016 69 0 -9989.1604 0 -9989.1604 97.53058 49712.297 Loop time of 0.391319 on 1 procs for 8 steps with 2976 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9988.33680041254 -9989.15670793174 -9989.16041103877 Force two-norm initial, final = 276.57050 5.2849830 Force max component initial, final = 240.34691 3.5927356 Final line search alpha, max atom move = 0.00011831247 0.00042506543 Iterations, force evaluations = 8 9 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.32554 | 0.32554 | 0.32554 | 0.0 | 83.19 Neigh | 0.053399 | 0.053399 | 0.053399 | 0.0 | 13.65 Comm | 0.0026692 | 0.0026692 | 0.0026692 | 0.0 | 0.68 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.009714 | | | 2.48 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8951.00 ave 8951 max 8951 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: 388430.0 ave 388430 max 388430 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 388430 Ave neighs/atom = 130.52083 Neighbor list builds = 1 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 11 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.192 | 6.192 | 6.192 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9989.1604 0 -9989.1604 97.53058 Loop time of 6.525e-06 on 1 procs for 0 steps with 2976 atoms 229.9% 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 | | 6.525e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8951.00 ave 8951 max 8951 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: 388452.0 ave 388452 max 388452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 388452 Ave neighs/atom = 130.52823 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 = 7.65 ghost atom cutoff = 7.65 binsize = 3.825, bins = 11 34 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.65 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) = 6.192 | 6.192 | 6.192 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 -9989.1604 -9989.1604 39.043165 128.51141 9.9077973 97.53058 97.53058 86.763035 116.6548 89.173903 2.6083782 1548.5777 Loop time of 6.896e-06 on 1 procs for 0 steps with 2976 atoms 290.0% 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 | | 6.896e-06 | | |100.00 Nlocal: 2976.00 ave 2976 max 2976 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8951.00 ave 8951 max 8951 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 194226.0 ave 194226 max 194226 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 388452.0 ave 388452 max 388452 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 388452 Ave neighs/atom = 130.52823 Neighbor list builds = 0 Dangerous builds = 0 2976 -9989.16041103877 eV 2.6083781922135 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05