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 = 3.6584030 3.6584030 3.6584030 Created orthogonal box = (0.0000000 -54.139421 0.0000000) to (44.204652 54.139421 8.9612207) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4498886 5.1914513 5.9741471 Created 1749 atoms using lattice units in orthogonal box = (0.0000000 -54.139421 0.0000000) to (44.204652 54.139421 8.9612207) create_atoms CPU = 0.002 seconds 1749 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4498886 5.1914513 5.9741471 Created 1757 atoms using lattice units in orthogonal box = (0.0000000 -54.139421 0.0000000) to (44.204652 54.139421 8.9612207) create_atoms CPU = 0.002 seconds 1757 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 26 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 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 3506 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_577453891941_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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 11.77 | 11.77 | 11.77 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13023.468 0 -13023.468 52872.289 1205 0 -13783.463 0 -13783.463 -48713.461 Loop time of 85.5173 on 1 procs for 1205 steps with 3506 atoms 99.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13023.4683836566 -13783.4497987945 -13783.4633588098 Force two-norm initial, final = 667.47625 0.33741106 Force max component initial, final = 106.25921 0.041417767 Final line search alpha, max atom move = 0.77518598 0.032106472 Iterations, force evaluations = 1205 2380 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 84.06 | 84.06 | 84.06 | 0.0 | 98.30 Neigh | 0.83241 | 0.83241 | 0.83241 | 0.0 | 0.97 Comm | 0.27582 | 0.27582 | 0.27582 | 0.0 | 0.32 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.349 | | | 0.41 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12809.0 ave 12809 max 12809 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: 718450.0 ave 718450 max 718450 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 718450 Ave neighs/atom = 204.92014 Neighbor list builds = 20 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 1205 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 11.77 | 11.77 | 11.77 Mbytes Step Temp E_pair E_mol TotEng Press Volume 1205 0 -13783.463 0 -13783.463 -48713.461 42892.243 1249 0 -13842.689 0 -13842.689 -36.639602 41629.721 Loop time of 1.83448 on 1 procs for 44 steps with 3506 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 = -13783.4633588096 -13842.6846752727 -13842.6888642334 Force two-norm initial, final = 2824.1053 14.087608 Force max component initial, final = 2433.6817 9.8563998 Final line search alpha, max atom move = 0.00024130129 0.0023783620 Iterations, force evaluations = 44 45 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.6355 | 1.6355 | 1.6355 | 0.0 | 89.15 Neigh | 0.16495 | 0.16495 | 0.16495 | 0.0 | 8.99 Comm | 0.005323 | 0.005323 | 0.005323 | 0.0 | 0.29 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02874 | | | 1.57 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12668.0 ave 12668 max 12668 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: 763922.0 ave 763922 max 763922 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 763922 Ave neighs/atom = 217.88990 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 11.28 | 11.28 | 11.28 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13842.689 0 -13842.689 -36.639602 Loop time of 1.865e-06 on 1 procs for 0 steps with 3506 atoms 160.9% 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 | | 1.865e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12661.0 ave 12661 max 12661 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: 762988.0 ave 762988 max 762988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 762988 Ave neighs/atom = 217.62350 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 = 8.5 ghost atom cutoff = 8.5 binsize = 4.25, bins = 11 25 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8.5 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) = 11.28 | 11.28 | 11.28 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 -13842.689 -13842.689 43.612122 103.88832 9.1881814 -36.639602 -36.639602 42.97478 236.05085 -388.94443 2.1939178 7183.3455 Loop time of 2.101e-06 on 1 procs for 0 steps with 3506 atoms 333.2% 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 | | 2.101e-06 | | |100.00 Nlocal: 3506.00 ave 3506 max 3506 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 12661.0 ave 12661 max 12661 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 381494.0 ave 381494 max 381494 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 762988.0 ave 762988 max 762988 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 762988 Ave neighs/atom = 217.62350 Neighbor list builds = 0 Dangerous builds = 0 3506 -13842.6888642334 eV 2.19391776541369 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:28