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 = 3.6110985 3.6110985 3.6110985 Created orthogonal box = (0.0000000 -47.906636 0.0000000) to (29.336703 47.906636 8.8453488) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.3339460 5.4439359 5.8968992 Created 1050 atoms using lattice units in orthogonal box = (0.0000000 -47.906636 0.0000000) to (29.336703 47.906636 8.8453488) create_atoms CPU = 0.002 seconds 1050 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.3339460 5.4439359 5.8968992 Created 1074 atoms using lattice units in orthogonal box = (0.0000000 -47.906636 0.0000000) to (29.336703 47.906636 8.8453488) create_atoms CPU = 0.001 seconds 1074 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 = 9 29 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 0 atoms, new total = 2124 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_110119204723_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 = 9 29 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) = 5.522 | 5.522 | 5.522 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8289.4124 0 -8289.4124 90587.892 230 0 -9002.7825 0 -9002.7825 14314.38 Loop time of 56.7598 on 1 procs for 230 steps with 2124 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8289.4123723583 -9002.77485739737 -9002.78247396868 Force two-norm initial, final = 404.40534 0.29914940 Force max component initial, final = 41.271936 0.085081404 Final line search alpha, max atom move = 1.0000000 0.085081404 Iterations, force evaluations = 230 432 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 56.506 | 56.506 | 56.506 | 0.0 | 99.55 Neigh | 0.16472 | 0.16472 | 0.16472 | 0.0 | 0.29 Comm | 0.038825 | 0.038825 | 0.038825 | 0.0 | 0.07 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.04982 | | | 0.09 Nlocal: 2124.00 ave 2124 max 2124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6985.00 ave 6985 max 6985 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: 264258.0 ave 264258 max 264258 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 264258 Ave neighs/atom = 124.41525 Neighbor list builds = 9 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 = 9 29 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 : 230 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.523 | 5.523 | 5.523 Mbytes Step Temp E_pair E_mol TotEng Press Volume 230 0 -9002.7825 0 -9002.7825 14314.38 24862.909 234 0 -9003.6891 0 -9003.6891 -4.6386932 25067.382 Loop time of 0.971463 on 1 procs for 4 steps with 2124 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 = -9002.78247396869 -9003.68862131111 -9003.68907665655 Force two-norm initial, final = 384.78040 0.67587075 Force max component initial, final = 224.26828 0.48195832 Final line search alpha, max atom move = 0.00030369778 0.00014636967 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.96832 | 0.96832 | 0.96832 | 0.0 | 99.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00043398 | 0.00043398 | 0.00043398 | 0.0 | 0.04 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002712 | | | 0.28 Nlocal: 2124.00 ave 2124 max 2124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6973.00 ave 6973 max 6973 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: 264710.0 ave 264710 max 264710 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 264710 Ave neighs/atom = 124.62806 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 = 9 29 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) = 5.661 | 5.661 | 5.661 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9003.6891 0 -9003.6891 -4.6386932 Loop time of 2.381e-06 on 1 procs for 0 steps with 2124 atoms 168.0% 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 | | 2.381e-06 | | |100.00 Nlocal: 2124.00 ave 2124 max 2124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6957.00 ave 6957 max 6957 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: 261030.0 ave 261030 max 261030 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261030 Ave neighs/atom = 122.89548 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 = 9 29 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) = 5.661 | 5.661 | 5.661 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 -9003.6891 -9003.6891 29.408705 96.087361 8.8708824 -4.6386932 -4.6386932 -5.9213217 22.898429 -30.893187 2.3194221 5809.6953 Loop time of 2.227e-06 on 1 procs for 0 steps with 2124 atoms 269.4% 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 | | 2.227e-06 | | |100.00 Nlocal: 2124.00 ave 2124 max 2124 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6957.00 ave 6957 max 6957 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 130515.0 ave 130515 max 130515 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 261030.0 ave 261030 max 261030 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 261030 Ave neighs/atom = 122.89548 Neighbor list builds = 0 Dangerous builds = 0 2124 -9003.68907665655 eV 2.31942207133397 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:58