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 = 3.6043435 3.6043435 3.6043435 Created orthogonal box = (0.0000000 -58.118293 0.0000000) to (29.059146 58.118293 3.6043435) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.9177017 4.9177017 3.6043435 Created 520 atoms using lattice units in orthogonal box = (0.0000000 -58.118293 0.0000000) to (29.059146 58.118293 3.6043435) create_atoms CPU = 0.003 seconds 520 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.9177017 4.9177017 3.6043435 Created 522 atoms using lattice units in orthogonal box = (0.0000000 -58.118293 0.0000000) to (29.059146 58.118293 3.6043435) create_atoms CPU = 0.002 seconds 522 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 = 10 39 2 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 0 atoms, new total = 1042 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 = 10 39 2 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) = 4.611 | 4.611 | 4.611 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3880.2423 0 -3880.2423 129289.26 81 0 -4411.1636 0 -4411.1636 7228.738 Loop time of 12.955 on 1 procs for 81 steps with 1042 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 = -3880.2422841941 -4411.15967003584 -4411.16363953235 Force two-norm initial, final = 1367.7887 0.21069615 Force max component initial, final = 482.60929 0.047381640 Final line search alpha, max atom move = 1.0000000 0.047381640 Iterations, force evaluations = 81 142 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 12.888 | 12.888 | 12.888 | 0.0 | 99.48 Neigh | 0.025834 | 0.025834 | 0.025834 | 0.0 | 0.20 Comm | 0.021307 | 0.021307 | 0.021307 | 0.0 | 0.16 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02 | | | 0.15 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6107.00 ave 6107 max 6107 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: 81232.0 ave 81232 max 81232 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81232 Ave neighs/atom = 77.957774 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 = 6.1 ghost atom cutoff = 6.1 binsize = 3.05, bins = 10 39 2 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 : 81 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.605 | 4.605 | 4.605 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -4411.1636 0 -4411.1636 7228.738 12174.521 93 0 -4411.5154 0 -4411.5154 -101.28145 12228.889 Loop time of 1.46635 on 1 procs for 12 steps with 1042 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 = -4411.16363953235 -4411.51396352472 -4411.51536849369 Force two-norm initial, final = 102.61164 3.5573986 Force max component initial, final = 80.895370 2.1251882 Final line search alpha, max atom move = 0.00012599536 0.00026776385 Iterations, force evaluations = 12 14 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.4566 | 1.4566 | 1.4566 | 0.0 | 99.34 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0020363 | 0.0020363 | 0.0020363 | 0.0 | 0.14 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007676 | | | 0.52 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5490.00 ave 5490 max 5490 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: 81168.0 ave 81168 max 81168 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81168 Ave neighs/atom = 77.896353 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 = 10 39 2 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) = 4.743 | 4.743 | 4.743 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4411.5154 0 -4411.5154 -101.28145 Loop time of 6.455e-06 on 1 procs for 0 steps with 1042 atoms 170.4% 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 | | 6.455e-06 | | |100.00 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5498.00 ave 5498 max 5498 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: 81172.0 ave 81172 max 81172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81172 Ave neighs/atom = 77.900192 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 = 10 39 2 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) = 4.743 | 4.743 | 4.743 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 -4411.5154 -4411.5154 28.92419 116.04121 3.6434563 -101.28145 -101.28145 -273.02423 -277.96502 247.14488 2.2756459 368.41702 Loop time of 9.472e-06 on 1 procs for 0 steps with 1042 atoms 221.7% 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 | | 9.472e-06 | | |100.00 Nlocal: 1042.00 ave 1042 max 1042 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5498.00 ave 5498 max 5498 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 40586.0 ave 40586 max 40586 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 81172.0 ave 81172 max 81172 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 81172 Ave neighs/atom = 77.900192 Neighbor list builds = 0 Dangerous builds = 0 1042 -4411.51536849369 eV 2.27564590062802 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:15