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 = 3.6583664 3.6583664 3.6583664 Created orthogonal box = (0.0000000 -57.612011 0.0000000) to (35.280008 57.612011 8.9611309) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.6903238 5.5753559 5.9740873 Created 1488 atoms using lattice units in orthogonal box = (0.0000000 -57.612011 0.0000000) to (35.280008 57.612011 8.9611309) create_atoms CPU = 0.002 seconds 1488 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.6903238 5.5753559 5.9740873 Created 1494 atoms using lattice units in orthogonal box = (0.0000000 -57.612011 0.0000000) to (35.280008 57.612011 8.9611309) create_atoms CPU = 0.002 seconds 1494 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 = 10 32 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 7.3 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 2982 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_807997826449_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 = 7.3 ghost atom cutoff = 7.3 binsize = 3.65, bins = 10 32 3 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) = 6.476 | 6.476 | 6.476 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -11492.808 0 -11492.808 45436.409 548 0 -12079.001 0 -12079.001 -55108.923 Loop time of 22.9462 on 1 procs for 548 steps with 2982 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 = -11492.8079816559 -12078.9897562589 -12079.0014477303 Force two-norm initial, final = 544.39575 0.34691072 Force max component initial, final = 76.582452 0.031857676 Final line search alpha, max atom move = 0.86055956 0.027415428 Iterations, force evaluations = 548 1083 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 22.337 | 22.337 | 22.337 | 0.0 | 97.35 Neigh | 0.35069 | 0.35069 | 0.35069 | 0.0 | 1.53 Comm | 0.10868 | 0.10868 | 0.10868 | 0.0 | 0.47 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.1496 | | | 0.65 Nlocal: 2982.00 ave 2982 max 2982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9474.00 ave 9474 max 9474 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: 411216.0 ave 411216 max 411216 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 411216 Ave neighs/atom = 137.89940 Neighbor list builds = 12 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 = 10 32 3 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 : 548 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 6.477 | 6.477 | 6.477 Mbytes Step Temp E_pair E_mol TotEng Press Volume 548 0 -12079.001 0 -12079.001 -55108.923 36427.933 599 0 -12148.937 0 -12148.937 -5.3356755 35211.898 Loop time of 1.27056 on 1 procs for 51 steps with 2982 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 = -12079.0014477304 -12148.9302939912 -12148.9371639618 Force two-norm initial, final = 2762.0546 20.790680 Force max component initial, final = 2320.2365 15.143206 Final line search alpha, max atom move = 0.00077017469 0.011662914 Iterations, force evaluations = 51 53 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1178 | 1.1178 | 1.1178 | 0.0 | 87.98 Neigh | 0.11513 | 0.11513 | 0.11513 | 0.0 | 9.06 Comm | 0.005599 | 0.005599 | 0.005599 | 0.0 | 0.44 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03202 | | | 2.52 Nlocal: 2982.00 ave 2982 max 2982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9450.00 ave 9450 max 9450 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: 424268.0 ave 424268 max 424268 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 424268 Ave neighs/atom = 142.27632 Neighbor list builds = 4 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 31 3 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) = 6.614 | 6.614 | 6.614 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -12148.937 0 -12148.937 -5.3356755 Loop time of 1.997e-06 on 1 procs for 0 steps with 2982 atoms 200.3% 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 | | 1.997e-06 | | |100.00 Nlocal: 2982.00 ave 2982 max 2982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9364.00 ave 9364 max 9364 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: 424980.0 ave 424980 max 424980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 424980 Ave neighs/atom = 142.51509 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 31 3 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) = 6.614 | 6.614 | 6.614 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 -12148.937 -12148.937 34.589929 110.11227 9.2449393 -5.3356755 -5.3356755 675.5535 -552.04957 -139.51096 2.2901013 4889.2704 Loop time of 2.416e-06 on 1 procs for 0 steps with 2982 atoms 289.7% 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 | | 2.416e-06 | | |100.00 Nlocal: 2982.00 ave 2982 max 2982 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9364.00 ave 9364 max 9364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 212490.0 ave 212490 max 212490 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 424980.0 ave 424980 max 424980 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 424980 Ave neighs/atom = 142.51509 Neighbor list builds = 0 Dangerous builds = 0 2982 -12148.9371639618 eV 2.29010131972593 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:24