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 = 3.6584048 3.6584048 3.6584048 Created orthogonal box = (0.0000000 -64.620313 0.0000000) to (37.308555 64.620313 6.3365430) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.7397777 5.7992589 6.3365430 Created 1245 atoms using lattice units in orthogonal box = (0.0000000 -64.620313 0.0000000) to (37.308555 64.620313 6.3365430) create_atoms CPU = 0.003 seconds 1245 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.7397777 5.7992589 6.3365430 Created 1249 atoms using lattice units in orthogonal box = (0.0000000 -64.620313 0.0000000) to (37.308555 64.620313 6.3365430) create_atoms CPU = 0.002 seconds 1249 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 36 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 5 atoms, new total = 2489 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_249706810527_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.122 | 6.122 | 6.122 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9385.3438 0 -9385.3438 31021.033 734 0 -9792.6602 0 -9792.6602 -55992.074 Loop time of 26.7751 on 1 procs for 734 steps with 2489 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 = -9385.34377760531 -9792.652393693 -9792.66020949804 Force two-norm initial, final = 566.91938 0.35468500 Force max component initial, final = 307.54236 0.12708399 Final line search alpha, max atom move = 0.59214010 0.075251524 Iterations, force evaluations = 734 1439 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 26.094 | 26.094 | 26.094 | 0.0 | 97.46 Neigh | 0.28572 | 0.28572 | 0.28572 | 0.0 | 1.07 Comm | 0.20204 | 0.20204 | 0.20204 | 0.0 | 0.75 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1929 | | | 0.72 Nlocal: 2489.00 ave 2489 max 2489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10285.0 ave 10285 max 10285 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: 337772.0 ave 337772 max 337772 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 337772 Ave neighs/atom = 135.70591 Neighbor list builds = 13 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 11 36 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 734 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.121 | 6.121 | 6.121 Mbytes Step Temp E_pair E_mol TotEng Press Volume 734 0 -9792.6602 0 -9792.6602 -55992.074 30553.423 767 0 -9821.3149 0 -9821.3149 4.0811721 29344.341 Loop time of 0.736579 on 1 procs for 33 steps with 2489 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 = -9792.66020949807 -9821.31185248019 -9821.31488660998 Force two-norm initial, final = 1929.6601 4.8637567 Force max component initial, final = 1398.9790 1.3145936 Final line search alpha, max atom move = 0.00011468564 0.00015076500 Iterations, force evaluations = 33 35 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.66753 | 0.66753 | 0.66753 | 0.0 | 90.63 Neigh | 0.045043 | 0.045043 | 0.045043 | 0.0 | 6.12 Comm | 0.0037991 | 0.0037991 | 0.0037991 | 0.0 | 0.52 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0202 | | | 2.74 Nlocal: 2489.00 ave 2489 max 2489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10367.0 ave 10367 max 10367 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: 351682.0 ave 351682 max 351682 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 351682 Ave neighs/atom = 141.29450 Neighbor list builds = 2 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.258 | 6.258 | 6.258 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9821.3149 0 -9821.3149 4.0811721 Loop time of 2.291e-06 on 1 procs for 0 steps with 2489 atoms 174.6% 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 | | 2.291e-06 | | |100.00 Nlocal: 2489.00 ave 2489 max 2489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10334.0 ave 10334 max 10334 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: 351802.0 ave 351802 max 351802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 351802 Ave neighs/atom = 141.34271 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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 35 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.3 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) = 6.258 | 6.258 | 6.258 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 -9821.3149 -9821.3149 36.292916 126.98823 6.3670614 4.0811721 4.0811721 63.716402 -70.524807 19.051922 2.2005089 6216.0103 Loop time of 2.759e-06 on 1 procs for 0 steps with 2489 atoms 326.2% 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 | | 2.759e-06 | | |100.00 Nlocal: 2489.00 ave 2489 max 2489 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10334.0 ave 10334 max 10334 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 175901.0 ave 175901 max 175901 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 351802.0 ave 351802 max 351802 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 351802 Ave neighs/atom = 141.34271 Neighbor list builds = 0 Dangerous builds = 0 2489 -9821.31488660998 eV 2.20050889129133 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:28