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 = 3.5673230 3.5673230 3.5673230 Created orthogonal box = (0.0000000 -40.985421 0.0000000) to (28.981069 40.985421 5.0449565) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1474994 5.5889210 5.0449565 Created 528 atoms using lattice units in orthogonal box = (0.0000000 -40.985421 0.0000000) to (28.981069 40.985421 5.0449565) create_atoms CPU = 0.002 seconds 528 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1474994 5.5889210 5.0449565 Created 532 atoms using lattice units in orthogonal box = (0.0000000 -40.985421 0.0000000) to (28.981069 40.985421 5.0449565) create_atoms CPU = 0.001 seconds 532 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 30 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 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 1060 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_196726067688_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.595 | 4.595 | 4.595 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4121.4871 0 -4121.4871 87746.37 284 0 -4474.3842 0 -4474.3842 66968.271 Loop time of 18.0657 on 1 procs for 284 steps with 1060 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 = -4121.48706119534 -4474.3814005536 -4474.3842050305 Force two-norm initial, final = 357.68039 0.39713591 Force max component initial, final = 72.922727 0.087285001 Final line search alpha, max atom move = 1.0000000 0.087285001 Iterations, force evaluations = 284 553 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 17.984 | 17.984 | 17.984 | 0.0 | 99.55 Neigh | 0.017298 | 0.017298 | 0.017298 | 0.0 | 0.10 Comm | 0.030029 | 0.030029 | 0.030029 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.03388 | | | 0.19 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4313.00 ave 4313 max 4313 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: 65768.0 ave 65768 max 65768 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 65768 Ave neighs/atom = 62.045283 Neighbor list builds = 3 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 284 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.594 | 4.594 | 4.594 Mbytes Step Temp E_pair E_mol TotEng Press Volume 284 0 -4474.3842 0 -4474.3842 66968.271 11984.812 311 0 -4481.9979 0 -4481.9979 -108.67776 12346.481 Loop time of 0.914097 on 1 procs for 27 steps with 1060 atoms 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4474.3842050305 -4481.99519659754 -4481.99787005467 Force two-norm initial, final = 881.47816 5.8347247 Force max component initial, final = 604.72817 4.1498781 Final line search alpha, max atom move = 0.00030642055 0.0012716079 Iterations, force evaluations = 27 28 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.89446 | 0.89446 | 0.89446 | 0.0 | 97.85 Neigh | 0.010915 | 0.010915 | 0.010915 | 0.0 | 1.19 Comm | 0.00137 | 0.00137 | 0.00137 | 0.0 | 0.15 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.007348 | | | 0.80 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4296.00 ave 4296 max 4296 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: 61128.0 ave 61128 max 61128 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61128 Ave neighs/atom = 57.667925 Neighbor list builds = 2 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.733 | 4.733 | 4.733 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4481.9979 0 -4481.9979 -108.67776 Loop time of 1.89e-06 on 1 procs for 0 steps with 1060 atoms 211.6% 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 | | 1.89e-06 | | |100.00 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4296.00 ave 4296 max 4296 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: 61200.0 ave 61200 max 61200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61200 Ave neighs/atom = 57.735849 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 11 31 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 5.6 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) = 4.733 | 4.733 | 4.733 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 -4481.9979 -4481.9979 29.324846 84.048627 5.0092977 -108.67776 -108.67776 148.68001 -552.17116 77.457873 2.3779353 2050.9272 Loop time of 2.282e-06 on 1 procs for 0 steps with 1060 atoms 175.3% 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 | | 2.282e-06 | | |100.00 Nlocal: 1060.00 ave 1060 max 1060 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 4296.00 ave 4296 max 4296 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 30600.0 ave 30600 max 30600 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 61200.0 ave 61200 max 61200 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 61200 Ave neighs/atom = 57.735849 Neighbor list builds = 0 Dangerous builds = 0 1060 -4481.99787005468 eV 2.37793529467312 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:19