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 = 3.5213918 3.5213918 3.5213918 Created orthogonal box = (0.0000000 -46.716541 0.0000000) to (16.516791 46.716541 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0061060 5.3086978 4.9800000 Created 352 atoms using lattice units in orthogonal box = (0.0000000 -46.716541 0.0000000) to (16.516791 46.716541 4.9800000) create_atoms CPU = 0.001 seconds 352 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0061060 5.3086978 4.9800000 Created 360 atoms using lattice units in orthogonal box = (0.0000000 -46.716541 0.0000000) to (16.516791 46.716541 4.9800000) create_atoms CPU = 0.001 seconds 360 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 = 5 27 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 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 8 atoms, new total = 704 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_050461957184_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 ghost atom cutoff = 7 binsize = 3.5, bins = 5 27 2 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) = 4.559 | 4.559 | 4.559 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3125.267 0 -3125.267 4594.3564 12 0 -3128.8437 0 -3128.8437 3606.6858 Loop time of 1.19533 on 1 procs for 12 steps with 704 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 = -3125.26696544371 -3128.84183611238 -3128.84371478352 Force two-norm initial, final = 12.899425 0.071184485 Force max component initial, final = 2.2765185 0.0044692946 Final line search alpha, max atom move = 1.0000000 0.0044692946 Iterations, force evaluations = 12 24 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.1927 | 1.1927 | 1.1927 | 0.0 | 99.78 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0012873 | 0.0012873 | 0.0012873 | 0.0 | 0.11 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001376 | | | 0.12 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4863.00 ave 4863 max 4863 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: 94080.0 ave 94080 max 94080 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94080 Ave neighs/atom = 133.63636 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 = 5 27 2 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 : 12 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.559 | 4.559 | 4.559 Mbytes Step Temp E_pair E_mol TotEng Press Volume 12 0 -3128.8437 0 -3128.8437 3606.6858 7685.2093 16 0 -3128.9068 0 -3128.9068 -128.03202 7700.564 Loop time of 0.303994 on 1 procs for 4 steps with 704 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 = -3128.84371478353 -3128.90643702416 -3128.90682335596 Force two-norm initial, final = 41.288076 1.7643404 Force max component initial, final = 39.111462 1.5247477 Final line search alpha, max atom move = 0.00028277170 0.00043115548 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.30249 | 0.30249 | 0.30249 | 0.0 | 99.51 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00027463 | 0.00027463 | 0.00027463 | 0.0 | 0.09 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001225 | | | 0.40 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4863.00 ave 4863 max 4863 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: 94016.0 ave 94016 max 94016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94016 Ave neighs/atom = 133.54545 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 = 5 27 2 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) = 4.697 | 4.697 | 4.697 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3128.9068 0 -3128.9068 -128.03202 Loop time of 2e-06 on 1 procs for 0 steps with 704 atoms 200.0% 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 | | 2e-06 | | |100.00 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4863.00 ave 4863 max 4863 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: 94016.0 ave 94016 max 94016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94016 Ave neighs/atom = 133.54545 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 = 5 27 2 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) = 4.697 | 4.697 | 4.697 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 -3128.9068 -3128.9068 16.497791 93.729987 4.9798721 -128.03202 -128.03202 -158.7848 91.919011 -317.23029 2.358773 222.10067 Loop time of 2.035e-06 on 1 procs for 0 steps with 704 atoms 196.6% 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 | | 2.035e-06 | | |100.00 Nlocal: 704.000 ave 704 max 704 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4863.00 ave 4863 max 4863 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 47008.0 ave 47008 max 47008 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 94016.0 ave 94016 max 94016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 94016 Ave neighs/atom = 133.54545 Neighbor list builds = 0 Dangerous builds = 0 704 -3128.90682335596 eV 2.3587729560894 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01