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 = 3.1465590 3.1465590 3.1465590 Created orthogonal box = (0.0000000 -58.022827 0.0000000) to (29.009840 58.022827 3.1465590) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.4367991 4.4367991 3.1465590 Created 341 atoms using lattice units in orthogonal box = (0.0000000 -58.022827 0.0000000) to (29.009840 58.022827 3.1465590) create_atoms CPU = 0.002 seconds 341 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.4367991 4.4367991 3.1465590 Created 341 atoms using lattice units in orthogonal box = (0.0000000 -58.022827 0.0000000) to (29.009840 58.022827 3.1465590) create_atoms CPU = 0.001 seconds 341 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 41 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 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 4 atoms, new total = 678 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_805823015127_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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.501 | 4.501 | 4.501 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4579.4694 0 -4579.4694 6558.3035 37 0 -4604.6666 0 -4604.6666 -4002.273 Loop time of 3.12831 on 1 procs for 37 steps with 678 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4579.46941442297 -4604.66380711724 -4604.66661790209 Force two-norm initial, final = 25.017609 0.21586961 Force max component initial, final = 6.2632167 0.055494444 Final line search alpha, max atom move = 0.95212950 0.052837897 Iterations, force evaluations = 37 73 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 3.1145 | 3.1145 | 3.1145 | 0.0 | 99.56 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0069007 | 0.0069007 | 0.0069007 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006879 | | | 0.22 Nlocal: 678.000 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3988.00 ave 3988 max 3988 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: 39016.0 ave 39016 max 39016 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39016 Ave neighs/atom = 57.545723 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 41 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 37 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.502 | 4.502 | 4.502 Mbytes Step Temp E_pair E_mol TotEng Press Volume 37 0 -4604.6666 0 -4604.6666 -4002.273 10592.783 39 0 -4604.6964 0 -4604.6964 -97.089869 10577.081 Loop time of 0.171007 on 1 procs for 2 steps with 678 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4604.66661790209 -4604.69368805603 -4604.69643223199 Force two-norm initial, final = 45.003823 2.7246297 Force max component initial, final = 42.529423 2.2444894 Final line search alpha, max atom move = 0.00011782541 0.00026445789 Iterations, force evaluations = 2 3 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.16945 | 0.16945 | 0.16945 | 0.0 | 99.09 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00034141 | 0.00034141 | 0.00034141 | 0.0 | 0.20 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001219 | | | 0.71 Nlocal: 678.000 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4078.00 ave 4078 max 4078 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: 39202.0 ave 39202 max 39202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39202 Ave neighs/atom = 57.820059 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.640 | 4.640 | 4.640 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4604.6964 0 -4604.6964 -97.089869 Loop time of 6.525e-06 on 1 procs for 0 steps with 678 atoms 183.9% 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 | | 6.525e-06 | | |100.00 Nlocal: 678.000 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4081.00 ave 4081 max 4081 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: 39202.0 ave 39202 max 39202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39202 Ave neighs/atom = 57.820059 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 = 5.8 ghost atom cutoff = 5.8 binsize = 2.9, bins = 11 41 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.8 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) = 4.640 | 4.640 | 4.640 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 -4604.6964 -4604.6964 29.00854 116.04565 3.1420355 -97.089869 -97.089869 339.97157 -862.42702 231.18584 2.4645118 164.14448 Loop time of 6.515e-06 on 1 procs for 0 steps with 678 atoms 276.3% 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 | | 6.515e-06 | | |100.00 Nlocal: 678.000 ave 678 max 678 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4081.00 ave 4081 max 4081 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 19601.0 ave 19601 max 19601 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 39202.0 ave 39202 max 39202 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 39202 Ave neighs/atom = 57.820059 Neighbor list builds = 0 Dangerous builds = 0 678 -4604.69643223199 eV 2.46451180385335 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03