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 = 3.0829274 3.0829274 3.0829274 Created orthogonal box = (0.0000000 -46.551183 0.0000000) to (32.916657 46.551183 4.3599177) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.1973669 5.3084682 4.3599177 Created 456 atoms using lattice units in orthogonal box = (0.0000000 -46.551183 0.0000000) to (32.916657 46.551183 4.3599177) create_atoms CPU = 0.002 seconds 456 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.1973669 5.3084682 4.3599177 Created 458 atoms using lattice units in orthogonal box = (0.0000000 -46.551183 0.0000000) to (32.916657 46.551183 4.3599177) create_atoms CPU = 0.001 seconds 458 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 10 28 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, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Deleted 0 atoms, new total = 914 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_152208847456_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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 5.706 | 5.706 | 5.706 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4569.4163 0 -4569.4163 266860.73 137 0 -5919.3385 0 -5919.3385 11581.349 Loop time of 70.7215 on 1 procs for 137 steps with 914 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 = -4569.41630228352 -5919.33264178636 -5919.33854338366 Force two-norm initial, final = 3478.7277 0.34755274 Force max component initial, final = 1233.6736 0.071949547 Final line search alpha, max atom move = 0.92428569 0.066501937 Iterations, force evaluations = 137 258 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 70.63 | 70.63 | 70.63 | 0.0 | 99.87 Neigh | 0.062929 | 0.062929 | 0.062929 | 0.0 | 0.09 Comm | 0.014419 | 0.014419 | 0.014419 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.01373 | | | 0.02 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4954.00 ave 4954 max 4954 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: 67388.0 ave 67388 max 67388 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67388 Ave neighs/atom = 73.728665 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 10 28 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 137 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.706 | 5.706 | 5.706 Mbytes Step Temp E_pair E_mol TotEng Press Volume 137 0 -5919.3385 0 -5919.3385 11581.349 13361.485 141 0 -5919.6311 0 -5919.6311 7.6492102 13432.095 Loop time of 1.9108 on 1 procs for 4 steps with 914 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 = -5919.33854338364 -5919.62881007592 -5919.63114090317 Force two-norm initial, final = 173.11608 2.0870318 Force max component initial, final = 123.43929 1.6045909 Final line search alpha, max atom move = 8.0137493e-05 0.00012858789 Iterations, force evaluations = 4 6 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.909 | 1.909 | 1.909 | 0.0 | 99.90 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00031667 | 0.00031667 | 0.00031667 | 0.0 | 0.02 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001529 | | | 0.08 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4966.00 ave 4966 max 4966 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: 68456.0 ave 68456 max 68456 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 68456 Ave neighs/atom = 74.897155 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.844 | 5.844 | 5.844 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -5919.6311 0 -5919.6311 7.6492102 Loop time of 1.853e-06 on 1 procs for 0 steps with 914 atoms 161.9% 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 | | 1.853e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4966.00 ave 4966 max 4966 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: 67400.0 ave 67400 max 67400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67400 Ave neighs/atom = 73.741794 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 = 6.68 ghost atom cutoff = 6.68 binsize = 3.34, bins = 10 28 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, ghost, cut 6.68 pair build: full/bin/ghost stencil: full/ghost/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) = 5.844 | 5.844 | 5.844 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 -5919.6311 -5919.6311 32.928757 93.358637 4.3693206 7.6492102 7.6492102 -20.527717 -148.33258 191.80793 2.4635263 1387.7386 Loop time of 1.9e-06 on 1 procs for 0 steps with 914 atoms 210.5% 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 | | 1.9e-06 | | |100.00 Nlocal: 914.000 ave 914 max 914 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4966.00 ave 4966 max 4966 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 33700.0 ave 33700 max 33700 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 67400.0 ave 67400 max 67400 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 67400 Ave neighs/atom = 73.741794 Neighbor list builds = 0 Dangerous builds = 0 914 -5919.63114090317 eV 2.46352632566692 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:01:14