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 = 3.5184747 3.5184747 3.5184747 Created orthogonal box = (0.0000000 -41.032113 0.0000000) to (14.507043 41.032113 4.9758746) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.9734881 6.0341342 4.9758746 Created 272 atoms using lattice units in orthogonal box = (0.0000000 -41.032113 0.0000000) to (14.507043 41.032113 4.9758746) create_atoms CPU = 0.001 seconds 272 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.9734881 6.0341342 4.9758746 Created 274 atoms using lattice units in orthogonal box = (0.0000000 -41.032113 0.0000000) to (14.507043 41.032113 4.9758746) create_atoms CPU = 0.001 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 21 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 8 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_922363340570_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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 4.921 | 4.921 | 4.921 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1927.4672 0 -1927.4672 185878.8 58 0 -2356.2685 0 -2356.2685 4879.8442 Loop time of 0.616092 on 1 procs for 58 steps with 544 atoms 96.5% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1927.46723627584 -2356.26631748957 -2356.26849320044 Force two-norm initial, final = 1199.6016 0.15920498 Force max component initial, final = 362.85417 0.020011514 Final line search alpha, max atom move = 1.0000000 0.020011514 Iterations, force evaluations = 58 104 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.6005 | 0.6005 | 0.6005 | 0.0 | 97.47 Neigh | 0.0069518 | 0.0069518 | 0.0069518 | 0.0 | 1.13 Comm | 0.0051691 | 0.0051691 | 0.0051691 | 0.0 | 0.84 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003474 | | | 0.56 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5197.00 ave 5197 max 5197 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: 107716.0 ave 107716 max 107716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 107716 Ave neighs/atom = 198.00735 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 = 8 ghost atom cutoff = 8 binsize = 4, bins = 4 21 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 58 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.918 | 4.918 | 4.918 Mbytes Step Temp E_pair E_mol TotEng Press Volume 58 0 -2356.2685 0 -2356.2685 4879.8442 5923.8246 63 0 -2356.3415 0 -2356.3415 -9.1229545 5939.2819 Loop time of 0.044299 on 1 procs for 5 steps with 544 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 = -2356.26849320044 -2356.34134635255 -2356.3414538074 Force two-norm initial, final = 42.462067 0.31317758 Force max component initial, final = 41.322989 0.18699029 Final line search alpha, max atom move = 0.00054701144 0.00010228583 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.042517 | 0.042517 | 0.042517 | 0.0 | 95.98 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031207 | 0.00031207 | 0.00031207 | 0.0 | 0.70 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.00147 | | | 3.32 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4880.00 ave 4880 max 4880 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: 108208.0 ave 108208 max 108208 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108208 Ave neighs/atom = 198.91176 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 ghost atom cutoff = 8 binsize = 4, bins = 4 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.056 | 5.056 | 5.056 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -2356.3415 0 -2356.3415 -9.1229545 Loop time of 1.665e-06 on 1 procs for 0 steps with 544 atoms 120.1% 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 | | 1.665e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4880.00 ave 4880 max 4880 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: 108084.0 ave 108084 max 108084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108084 Ave neighs/atom = 198.68382 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 ghost atom cutoff = 8 binsize = 4, bins = 4 21 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 8 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) = 5.056 | 5.056 | 5.056 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 -2356.3415 -2356.3415 14.495954 82.366767 4.974336 -9.1229545 -9.1229545 31.705019 -8.6471089 -50.426773 2.3213815 264.25913 Loop time of 1.458e-06 on 1 procs for 0 steps with 544 atoms 137.2% 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 | | 1.458e-06 | | |100.00 Nlocal: 544.000 ave 544 max 544 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4880.00 ave 4880 max 4880 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 54042.0 ave 54042 max 54042 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 108084.0 ave 108084 max 108084 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 108084 Ave neighs/atom = 198.68382 Neighbor list builds = 0 Dangerous builds = 0 544 -2356.3414538074 eV 2.32138149890919 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01