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 = 4.0469996 4.0469996 4.0469996 Created orthogonal box = (0.0000000 -77.427707 0.0000000) to (44.700571 77.427707 7.0096089) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.5951662 5.9231216 7.0096089 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -77.427707 0.0000000) to (44.700571 77.427707 7.0096089) create_atoms CPU = 0.003 seconds 1465 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.5951662 5.9231216 7.0096089 Created 1465 atoms using lattice units in orthogonal box = (0.0000000 -77.427707 0.0000000) to (44.700571 77.427707 7.0096089) 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 13 44 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 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 31 atoms, new total = 2899 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_958395190627_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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 13 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.805 | 5.805 | 5.805 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9675.501 0 -9675.501 962.47436 82 0 -9717.3838 0 -9717.3838 -4969.7748 Loop time of 17.8228 on 1 procs for 82 steps with 2899 atoms 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -9675.50102231631 -9717.37705918273 -9717.38375169105 Force two-norm initial, final = 30.146389 0.22414589 Force max component initial, final = 6.4595221 0.039052530 Final line search alpha, max atom move = 1.0000000 0.039052530 Iterations, force evaluations = 82 148 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.745 | 17.745 | 17.745 | 0.0 | 99.56 Neigh | 0.03702 | 0.03702 | 0.03702 | 0.0 | 0.21 Comm | 0.019884 | 0.019884 | 0.019884 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.02071 | | | 0.12 Nlocal: 2899.00 ave 2899 max 2899 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10739.0 ave 10739 max 10739 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: 248024.0 ave 248024 max 248024 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 248024 Ave neighs/atom = 85.555019 Neighbor list builds = 2 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 13 44 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 82 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.801 | 5.801 | 5.801 Mbytes Step Temp E_pair E_mol TotEng Press Volume 82 0 -9717.3838 0 -9717.3838 -4969.7748 48521.392 86 0 -9717.6917 0 -9717.6917 -1233.6224 48287.823 Loop time of 0.823217 on 1 procs for 4 steps with 2899 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 = -9717.38375169104 -9717.69165835454 -9717.69174876423 Force two-norm initial, final = 179.86771 0.26416138 Force max component initial, final = 128.83342 0.083804591 Final line search alpha, max atom move = 0.00082728775 6.9330511e-05 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.81968 | 0.81968 | 0.81968 | 0.0 | 99.57 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00053264 | 0.00053264 | 0.00053264 | 0.0 | 0.06 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.003007 | | | 0.37 Nlocal: 2899.00 ave 2899 max 2899 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10545.0 ave 10545 max 10545 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: 248122.0 ave 248122 max 248122 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 248122 Ave neighs/atom = 85.588824 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 13 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.940 | 5.940 | 5.940 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -9717.6917 0 -9717.6917 -1233.6224 Loop time of 3.357e-06 on 1 procs for 0 steps with 2899 atoms 238.3% 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 | | 3.357e-06 | | |100.00 Nlocal: 2899.00 ave 2899 max 2899 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10640.0 ave 10640 max 10640 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: 248220.0 ave 248220 max 248220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 248220 Ave neighs/atom = 85.622628 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 = 7.1 ghost atom cutoff = 7.1 binsize = 3.55, bins = 13 44 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.1 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) = 5.940 | 5.940 | 5.940 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 -9717.6917 -9717.6917 44.59905 154.85541 6.9917457 -1233.6224 -1233.6224 -2.7742978 -3697.2308 -0.86216648 2.506938 1396.4363 Loop time of 2.156e-06 on 1 procs for 0 steps with 2899 atoms 185.5% 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 | | 2.156e-06 | | |100.00 Nlocal: 2899.00 ave 2899 max 2899 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 10640.0 ave 10640 max 10640 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 124110.0 ave 124110 max 124110 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 248220.0 ave 248220 max 248220 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 248220 Ave neighs/atom = 85.622628 Neighbor list builds = 0 Dangerous builds = 0 2899 -9717.69174876423 eV 2.50693796281589 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19