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 = 4.0612135 4.0612135 4.0612135 Created orthogonal box = (0.0000000 -48.052926 0.0000000) to (58.852575 48.052926 9.9479008) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.7260085 6.1782333 6.6319338 Created 1663 atoms using lattice units in orthogonal box = (0.0000000 -48.052926 0.0000000) to (58.852575 48.052926 9.9479008) create_atoms CPU = 0.002 seconds 1663 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.7260085 6.1782333 6.6319338 Created 1687 atoms using lattice units in orthogonal box = (0.0000000 -48.052926 0.0000000) to (58.852575 48.052926 9.9479008) create_atoms CPU = 0.002 seconds 1687 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 13 20 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 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 31 atoms, new total = 3319 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_411898953661_004#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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 7.888 | 7.888 | 7.888 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8776.2611 0 -8776.2611 3184.6174 130 0 -8912.1866 0 -8912.1866 -5074.5534 Loop time of 6.11882 on 1 procs for 130 steps with 3319 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 = -8776.26108644927 -8912.18001814965 -8912.1866026729 Force two-norm initial, final = 54.847616 0.26313245 Force max component initial, final = 6.2677045 0.094023358 Final line search alpha, max atom move = 0.96996371 0.091199245 Iterations, force evaluations = 130 210 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 5.7781 | 5.7781 | 5.7781 | 0.0 | 94.43 Neigh | 0.27555 | 0.27555 | 0.27555 | 0.0 | 4.50 Comm | 0.02716 | 0.02716 | 0.02716 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03805 | | | 0.62 Nlocal: 3319.00 ave 3319 max 3319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12380.0 ave 12380 max 12380 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: 743510.0 ave 743510 max 743510 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 743510 Ave neighs/atom = 224.01627 Neighbor list builds = 7 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 13 20 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 130 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 7.886 | 7.886 | 7.886 Mbytes Step Temp E_pair E_mol TotEng Press Volume 130 0 -8912.1866 0 -8912.1866 -5074.5534 56266.091 135 0 -8913.0372 0 -8913.0372 -125.35103 55881.655 Loop time of 0.196233 on 1 procs for 5 steps with 3319 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 = -8912.1866026729 -8913.02932719446 -8913.03722611049 Force two-norm initial, final = 334.53470 9.1387263 Force max component initial, final = 252.81121 8.1296081 Final line search alpha, max atom move = 3.6092414e-05 0.00029341718 Iterations, force evaluations = 5 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.19199 | 0.19199 | 0.19199 | 0.0 | 97.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0006341 | 0.0006341 | 0.0006341 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003607 | | | 1.84 Nlocal: 3319.00 ave 3319 max 3319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12349.0 ave 12349 max 12349 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: 743360.0 ave 743360 max 743360 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 743360 Ave neighs/atom = 223.97108 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 8.023 | 8.023 | 8.023 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8913.0372 0 -8913.0372 -125.35103 Loop time of 9.818e-06 on 1 procs for 0 steps with 3319 atoms 122.2% 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 | | 9.818e-06 | | |100.00 Nlocal: 3319.00 ave 3319 max 3319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12348.0 ave 12348 max 12348 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: 745110.0 ave 745110 max 745110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 745110 Ave neighs/atom = 224.49834 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 = 9.80032 ghost atom cutoff = 9.80032 binsize = 4.90016, bins = 12 20 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 9.80032 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) = 8.023 | 8.023 | 8.023 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 -8913.0372 -8913.0372 58.617113 95.792507 9.952067 -125.35103 -125.35103 -115.46553 -232.32311 -28.264435 2.4699704 3251.1012 Loop time of 2.523e-06 on 1 procs for 0 steps with 3319 atoms 317.1% 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 | | 2.523e-06 | | |100.00 Nlocal: 3319.00 ave 3319 max 3319 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12348.0 ave 12348 max 12348 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 372555.0 ave 372555 max 372555 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 745110.0 ave 745110 max 745110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 745110 Ave neighs/atom = 224.49834 Neighbor list builds = 0 Dangerous builds = 0 3319 -8913.03722611049 eV 2.46997042398446 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:06