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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -43.809124 0.0000000) to (35.770000 43.809124 8.8507796) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1100000 5.0663613 5.9005197 Created 1176 atoms using lattice units in orthogonal box = (0.0000000 -43.809124 0.0000000) to (35.770000 43.809124 8.8507796) create_atoms CPU = 0.002 seconds 1176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1100000 5.0663613 5.9005197 Created 1184 atoms using lattice units in orthogonal box = (0.0000000 -43.809124 0.0000000) to (35.770000 43.809124 8.8507796) create_atoms CPU = 0.001 seconds 1184 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 ghost atom cutoff = 7 binsize = 3.5, 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 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 2352 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_407917731909_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 = 7 ghost atom cutoff = 7 binsize = 3.5, bins = 11 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 5.958 | 5.958 | 5.958 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -7711.5341 0 -7711.5341 58741.89 43 0 -8286.2245 0 -8286.2245 9836.32 Loop time of 6.06422 on 1 procs for 43 steps with 2352 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -7711.53413480372 -8286.21801200038 -8286.22448150363 Force two-norm initial, final = 517.31871 0.31070160 Force max component initial, final = 88.968162 0.034813882 Final line search alpha, max atom move = 1.0000000 0.034813882 Iterations, force evaluations = 43 79 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 6.0446 | 6.0446 | 6.0446 | 0.0 | 99.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0081642 | 0.0081642 | 0.0081642 | 0.0 | 0.13 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01141 | | | 0.19 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7465.00 ave 7465 max 7465 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: 312480.0 ave 312480 max 312480 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 312480 Ave neighs/atom = 132.85714 Neighbor list builds = 0 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 26 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 43 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.958 | 5.958 | 5.958 Mbytes Step Temp E_pair E_mol TotEng Press Volume 43 0 -8286.2245 0 -8286.2245 9836.32 27739.27 53 0 -8287.4176 0 -8287.4176 57.677135 27929.328 Loop time of 0.929147 on 1 procs for 10 steps with 2352 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 = -8286.22448150363 -8287.41746992035 -8287.41760762174 Force two-norm initial, final = 333.71486 2.0329461 Force max component initial, final = 294.12676 1.4864034 Final line search alpha, max atom move = 0.00042825364 0.00063655769 Iterations, force evaluations = 10 12 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.92343 | 0.92343 | 0.92343 | 0.0 | 99.39 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00078793 | 0.00078793 | 0.00078793 | 0.0 | 0.08 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004926 | | | 0.53 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7467.00 ave 7467 max 7467 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: 310560.0 ave 310560 max 310560 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 310560 Ave neighs/atom = 132.04082 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.096 | 6.096 | 6.096 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8287.4176 0 -8287.4176 57.677135 Loop time of 1.924e-06 on 1 procs for 0 steps with 2352 atoms 155.9% 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 | | 1.924e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7415.00 ave 7415 max 7415 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: 310272.0 ave 310272 max 310272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 310272 Ave neighs/atom = 131.91837 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 ghost atom cutoff = 7 binsize = 3.5, bins = 11 26 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7 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) = 6.096 | 6.096 | 6.096 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 -8287.4176 -8287.4176 35.743062 88.400808 8.8391906 57.677135 57.677135 41.186355 46.688602 85.156449 2.2696264 1462.5182 Loop time of 2.123e-06 on 1 procs for 0 steps with 2352 atoms 235.5% 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 | | 2.123e-06 | | |100.00 Nlocal: 2352.00 ave 2352 max 2352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 7415.00 ave 7415 max 7415 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 155136.0 ave 155136 max 155136 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 310272.0 ave 310272 max 310272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 310272 Ave neighs/atom = 131.91837 Neighbor list builds = 0 Dangerous builds = 0 2352 -8287.41760762174 eV 2.26962642800228 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:07