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 = 4.0446508 4.0446508 4.0446508 Created orthogonal box = (0.0000000 -77.378726 0.0000000) to (44.674628 77.378726 7.0055406) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5913386 5.9196839 7.0055406 Created 1463 atoms using lattice units in orthogonal box = (0.0000000 -77.378726 0.0000000) to (44.674628 77.378726 7.0055406) create_atoms CPU = 0.003 seconds 1463 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5913386 5.9196839 7.0055406 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -77.378726 0.0000000) to (44.674628 77.378726 7.0055406) create_atoms CPU = 0.003 seconds 1465 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 14 46 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 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 2924 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_618133763375_001#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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 14 46 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.726 | 5.726 | 5.726 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9558.5219 0 -9558.5219 13233.483 99 0 -9799.2996 0 -9799.2996 2058.904 Loop time of 16.834 on 1 procs for 99 steps with 2924 atoms 98.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9558.52188016722 -9799.29083016632 -9799.29962387772 Force two-norm initial, final = 287.67347 0.24212597 Force max component initial, final = 86.531635 0.063888559 Final line search alpha, max atom move = 1.0000000 0.063888559 Iterations, force evaluations = 99 165 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 16.699 | 16.699 | 16.699 | 0.0 | 99.20 Neigh | 0.089419 | 0.089419 | 0.089419 | 0.0 | 0.53 Comm | 0.017917 | 0.017917 | 0.017917 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02777 | | | 0.16 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8356.00 ave 8356 max 8356 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: 227064.0 ave 227064 max 227064 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227064 Ave neighs/atom = 77.655267 Neighbor list builds = 5 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 14 46 3 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 99 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.735 | 5.735 | 5.735 Mbytes Step Temp E_pair E_mol TotEng Press Volume 99 0 -9799.2996 0 -9799.2996 2058.904 48434.427 103 0 -9799.4709 0 -9799.4709 -36.30839 48562.62 Loop time of 0.629468 on 1 procs for 4 steps with 2924 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 = -9799.29962387774 -9799.46795886623 -9799.4708745176 Force two-norm initial, final = 122.26648 2.8892462 Force max component initial, final = 108.64809 2.4998875 Final line search alpha, max atom move = 5.1719816e-05 0.00012929372 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.62596 | 0.62596 | 0.62596 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00045342 | 0.00045342 | 0.00045342 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003053 | | | 0.49 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8463.00 ave 8463 max 8463 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: 227018.0 ave 227018 max 227018 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 227018 Ave neighs/atom = 77.639535 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 14 46 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.873 | 5.873 | 5.873 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9799.4709 0 -9799.4709 -36.30839 Loop time of 2.348e-06 on 1 procs for 0 steps with 2924 atoms 170.4% 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 | | 2.348e-06 | | |100.00 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8462.00 ave 8462 max 8462 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: 226960.0 ave 226960 max 226960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226960 Ave neighs/atom = 77.619699 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 = 6.8 ghost atom cutoff = 6.8 binsize = 3.4, bins = 14 46 3 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.8 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) = 5.873 | 5.873 | 5.873 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 -9799.4709 -9799.4709 44.641678 155.27339 7.00591 -36.30839 -36.30839 -82.415381 17.218602 -43.728391 2.5115317 1248.5669 Loop time of 2.531e-06 on 1 procs for 0 steps with 2924 atoms 276.6% 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 | | 2.531e-06 | | |100.00 Nlocal: 2924.00 ave 2924 max 2924 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 8462.00 ave 8462 max 8462 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 113480.0 ave 113480 max 113480 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 226960.0 ave 226960 max 226960 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 226960 Ave neighs/atom = 77.619699 Neighbor list builds = 0 Dangerous builds = 0 2924 -9799.4708745176 eV 2.51153169924111 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:18