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 -66.256529 0.0000000) to (23.425221 66.256529 5.1737657) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.2848153 5.6560452 5.1737657 Created 656 atoms using lattice units in orthogonal box = (0.0000000 -66.256529 0.0000000) to (23.425221 66.256529 5.1737657) create_atoms CPU = 0.002 seconds 656 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.2848153 5.6560452 5.1737657 Created 658 atoms using lattice units in orthogonal box = (0.0000000 -66.256529 0.0000000) to (23.425221 66.256529 5.1737657) create_atoms CPU = 0.002 seconds 658 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 = 7 37 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 4 atoms, new total = 1310 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 = 7 37 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) = 5.105 | 5.105 | 5.105 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4714.3014 0 -4714.3014 63506.307 263 0 -5144.9309 0 -5144.9309 -68321 Loop time of 5.1421 on 1 procs for 263 steps with 1310 atoms 99.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4714.30143210993 -5144.92623385912 -5144.93088887807 Force two-norm initial, final = 987.19237 0.22789830 Force max component initial, final = 321.12874 0.032845040 Final line search alpha, max atom move = 1.0000000 0.032845040 Iterations, force evaluations = 263 500 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 4.9843 | 4.9843 | 4.9843 | 0.0 | 96.93 Neigh | 0.072903 | 0.072903 | 0.072903 | 0.0 | 1.42 Comm | 0.04655 | 0.04655 | 0.04655 | 0.0 | 0.91 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03831 | | | 0.75 Nlocal: 1310.00 ave 1310 max 1310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7719.00 ave 7719 max 7719 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: 179236.0 ave 179236 max 179236 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179236 Ave neighs/atom = 136.82137 Neighbor list builds = 6 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 = 7 37 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 : 263 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.106 | 5.106 | 5.106 Mbytes Step Temp E_pair E_mol TotEng Press Volume 263 0 -5144.9309 0 -5144.9309 -68321 16060.133 299 0 -5167.815 0 -5167.815 -1952.5615 15291.221 Loop time of 0.424841 on 1 procs for 36 steps with 1310 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 = -5144.9308888781 -5167.81271411132 -5167.81501709153 Force two-norm initial, final = 1237.0889 33.150917 Force max component initial, final = 857.62907 21.213315 Final line search alpha, max atom move = 4.4925645e-05 0.00095302188 Iterations, force evaluations = 36 39 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.40719 | 0.40719 | 0.40719 | 0.0 | 95.84 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0026654 | 0.0026654 | 0.0026654 | 0.0 | 0.63 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01499 | | | 3.53 Nlocal: 1310.00 ave 1310 max 1310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7677.00 ave 7677 max 7677 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: 179000.0 ave 179000 max 179000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 179000 Ave neighs/atom = 136.64122 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 = 7 37 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) = 5.250 | 5.250 | 5.250 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5167.815 0 -5167.815 -1952.5615 Loop time of 1.92e-06 on 1 procs for 0 steps with 1310 atoms 104.2% 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 | | 1.92e-06 | | |100.00 Nlocal: 1310.00 ave 1310 max 1310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7967.00 ave 7967 max 7967 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: 187444.0 ave 187444 max 187444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187444 Ave neighs/atom = 143.08702 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 = 7 37 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) = 5.250 | 5.250 | 5.250 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 -5167.815 -5167.815 22.911745 133.03932 5.0165364 -1952.5615 -1952.5615 -1848.093 -1854.4592 -2155.1323 2.2790626 3724.3555 Loop time of 2.187e-06 on 1 procs for 0 steps with 1310 atoms 182.9% 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 | | 2.187e-06 | | |100.00 Nlocal: 1310.00 ave 1310 max 1310 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7967.00 ave 7967 max 7967 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 93722.0 ave 93722 max 93722 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 187444.0 ave 187444 max 187444 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 187444 Ave neighs/atom = 143.08702 Neighbor list builds = 0 Dangerous builds = 0 1310 -5167.81501709153 eV 2.27906263886583 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:05