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 = 4.0515263 4.0515263 4.0515263 Created orthogonal box = (0.0000000 -58.991113 0.0000000) to (29.495557 58.991113 4.0515263) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.0086794 5.0086794 4.0515263 Created 424 atoms using lattice units in orthogonal box = (0.0000000 -58.991113 0.0000000) to (29.495557 58.991113 4.0515263) create_atoms CPU = 0.002 seconds 424 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.0086794 5.0086794 4.0515263 Created 426 atoms using lattice units in orthogonal box = (0.0000000 -58.991113 0.0000000) to (29.495557 58.991113 4.0515263) create_atoms CPU = 0.001 seconds 426 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 8 30 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 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 848 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_109933561507_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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 8 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 4.960 | 4.960 | 4.960 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2540.5201 0 -2540.5201 79519.038 70 0 -2838.5629 0 -2838.5629 9003.5069 Loop time of 1.78846 on 1 procs for 70 steps with 848 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 = -2540.52008479409 -2838.56083711333 -2838.56285529199 Force two-norm initial, final = 802.07022 0.14867463 Force max component initial, final = 270.89105 0.032943169 Final line search alpha, max atom move = 1.0000000 0.032943169 Iterations, force evaluations = 70 133 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.7375 | 1.7375 | 1.7375 | 0.0 | 97.15 Neigh | 0.015077 | 0.015077 | 0.015077 | 0.0 | 0.84 Comm | 0.019953 | 0.019953 | 0.019953 | 0.0 | 1.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01591 | | | 0.89 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6517.00 ave 6517 max 6517 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: 112364.0 ave 112364 max 112364 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112364 Ave neighs/atom = 132.50472 Neighbor list builds = 1 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 8 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 70 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.960 | 4.960 | 4.960 Mbytes Step Temp E_pair E_mol TotEng Press Volume 70 0 -2838.5629 0 -2838.5629 9003.5069 14099.115 80 0 -2839.0958 0 -2839.0958 22.950905 14226.566 Loop time of 0.190599 on 1 procs for 10 steps with 848 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 = -2838.562855292 -2839.09559316111 -2839.0957845097 Force two-norm initial, final = 146.46882 0.94653724 Force max component initial, final = 121.02402 0.84170121 Final line search alpha, max atom move = 0.00034118880 0.00028717903 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16792 | 0.16792 | 0.16792 | 0.0 | 88.10 Neigh | 0.01443 | 0.01443 | 0.01443 | 0.0 | 7.57 Comm | 0.0020625 | 0.0020625 | 0.0020625 | 0.0 | 1.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006184 | | | 3.24 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6527.00 ave 6527 max 6527 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: 112264.0 ave 112264 max 112264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112264 Ave neighs/atom = 132.38679 Neighbor list builds = 1 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 8 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.098 | 5.098 | 5.098 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2839.0958 0 -2839.0958 22.950905 Loop time of 6.826e-06 on 1 procs for 0 steps with 848 atoms 161.1% 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 | | 6.826e-06 | | |100.00 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6527.00 ave 6527 max 6527 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: 112264.0 ave 112264 max 112264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112264 Ave neighs/atom = 132.38679 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 = 7.954144 ghost atom cutoff = 7.954144 binsize = 3.977072, bins = 8 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.954144000238657 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) = 5.098 | 5.098 | 5.098 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 -2839.0958 -2839.0958 29.520017 119.02139 4.0490998 22.950905 22.950905 94.86985 -14.294426 -11.722708 2.6571235 477.83087 Loop time of 7.187e-06 on 1 procs for 0 steps with 848 atoms 250.5% 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 | | 7.187e-06 | | |100.00 Nlocal: 848.000 ave 848 max 848 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6527.00 ave 6527 max 6527 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 56132.0 ave 56132 max 56132 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 112264.0 ave 112264 max 112264 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 112264 Ave neighs/atom = 132.38679 Neighbor list builds = 0 Dangerous builds = 0 848 -2839.09578450187 eV 2.6571235153211 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02