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 = 4.0310361 4.0310361 4.0310361 Created orthogonal box = (0.0000000 -47.009555 0.0000000) to (16.620388 47.009555 5.7007459) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.8436890 6.9131699 5.7007459 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -47.009555 0.0000000) to (16.620388 47.009555 5.7007459) create_atoms CPU = 0.003 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.8436890 6.9131699 5.7007459 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -47.009555 0.0000000) to (16.620388 47.009555 5.7007459) create_atoms CPU = 0.002 seconds 274 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 5 25 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 7.687316 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 544 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_699137396381_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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 4.510 | 4.510 | 4.510 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1779.1613 0 -1779.1613 7949.4717 81 0 -1823.785 0 -1823.785 2506.6617 Loop time of 1.07624 on 1 procs for 81 steps with 544 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 = -1779.16134482976 -1823.78323022737 -1823.78502081875 Force two-norm initial, final = 27.345628 0.10230982 Force max component initial, final = 6.1685260 0.020368983 Final line search alpha, max atom move = 1.0000000 0.020368983 Iterations, force evaluations = 81 141 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.0212 | 1.0212 | 1.0212 | 0.0 | 94.89 Neigh | 0.028701 | 0.028701 | 0.028701 | 0.0 | 2.67 Comm | 0.014097 | 0.014097 | 0.014097 | 0.0 | 1.31 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01221 | | | 1.13 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3830.00 ave 3830 max 3830 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: 71440.0 ave 71440 max 71440 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71440 Ave neighs/atom = 131.32353 Neighbor list builds = 3 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 5 25 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 4.510 | 4.510 | 4.510 Mbytes Step Temp E_pair E_mol TotEng Press Volume 81 0 -1823.785 0 -1823.785 2506.6617 8908.1798 88 0 -1823.907 0 -1823.907 -32.003633 8937.7757 Loop time of 0.0659763 on 1 procs for 7 steps with 544 atoms 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1823.78502081875 -1823.90542102183 -1823.90704046318 Force two-norm initial, final = 36.604470 0.36845653 Force max component initial, final = 35.174104 0.23157201 Final line search alpha, max atom move = 0.00035759156 8.2808194e-05 Iterations, force evaluations = 7 8 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.062756 | 0.062756 | 0.062756 | 0.0 | 95.12 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00067408 | 0.00067408 | 0.00067408 | 0.0 | 1.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002546 | | | 3.86 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3691.00 ave 3691 max 3691 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: 71652.0 ave 71652 max 71652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71652 Ave neighs/atom = 131.71324 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 4.648 | 4.648 | 4.648 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1823.907 0 -1823.907 -32.003633 Loop time of 6.094e-06 on 1 procs for 0 steps with 544 atoms 164.1% 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 | | 6.094e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3677.00 ave 3677 max 3677 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: 71620.0 ave 71620 max 71620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71620 Ave neighs/atom = 131.65441 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 = 7.687316 ghost atom cutoff = 7.687316 binsize = 3.843658, bins = 5 25 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.687316 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) = 4.648 | 4.648 | 4.648 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 -1823.907 -1823.907 16.565017 94.654058 5.7003082 -32.003633 -32.003633 -25.626902 -28.875825 -41.508173 2.6991429 344.06335 Loop time of 6.525e-06 on 1 procs for 0 steps with 544 atoms 245.2% 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 | | 6.525e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3677.00 ave 3677 max 3677 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 35810.0 ave 35810 max 35810 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 71620.0 ave 71620 max 71620 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 71620 Ave neighs/atom = 131.65441 Neighbor list builds = 0 Dangerous builds = 0 544 -1823.90704046318 eV 2.69914294652187 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01