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 = 3.5213917 3.5213917 3.5213917 Created orthogonal box = (0.0000000 -43.557210 0.0000000) to (20.533066 43.557210 4.9800000) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.0391370 5.9784406 4.9800000 Created 407 atoms using lattice units in orthogonal box = (0.0000000 -43.557210 0.0000000) to (20.533066 43.557210 4.9800000) create_atoms CPU = 0.001 seconds 407 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.0391370 5.9784406 4.9800000 Created 411 atoms using lattice units in orthogonal box = (0.0000000 -43.557210 0.0000000) to (20.533066 43.557210 4.9800000) create_atoms CPU = 0.001 seconds 411 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 ghost atom cutoff = 6 binsize = 3, bins = 7 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 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 816 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_000553624872_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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 7 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.552 | 4.552 | 4.552 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3108.1348 0 -3108.1348 117913.32 39 0 -3616.5628 0 -3616.5628 9973.3742 Loop time of 1.92991 on 1 procs for 39 steps with 816 atoms 98.4% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -3108.13480273513 -3616.55976129972 -3616.56283977075 Force two-norm initial, final = 667.45708 0.18265297 Force max component initial, final = 137.48964 0.019083727 Final line search alpha, max atom move = 1.0000000 0.019083727 Iterations, force evaluations = 39 63 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.9165 | 1.9165 | 1.9165 | 0.0 | 99.31 Neigh | 0.0053072 | 0.0053072 | 0.0053072 | 0.0 | 0.27 Comm | 0.0037623 | 0.0037623 | 0.0037623 | 0.0 | 0.19 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004335 | | | 0.22 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3905.00 ave 3905 max 3905 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: 63652.0 ave 63652 max 63652 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63652 Ave neighs/atom = 78.004902 Neighbor list builds = 1 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 ghost atom cutoff = 6 binsize = 3, bins = 7 30 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 39 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.552 | 4.552 | 4.552 Mbytes Step Temp E_pair E_mol TotEng Press Volume 39 0 -3616.5628 0 -3616.5628 9973.3742 8907.8561 45 0 -3616.823 0 -3616.823 117.60408 8954.5458 Loop time of 0.233903 on 1 procs for 6 steps with 816 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 = -3616.56283977075 -3616.82278692858 -3616.82302385416 Force two-norm initial, final = 111.17652 1.3158080 Force max component initial, final = 101.15409 1.0233599 Final line search alpha, max atom move = 0.00039235504 0.00040152043 Iterations, force evaluations = 6 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.23208 | 0.23208 | 0.23208 | 0.0 | 99.22 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00028219 | 0.00028219 | 0.00028219 | 0.0 | 0.12 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001544 | | | 0.66 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3940.00 ave 3940 max 3940 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: 63572.0 ave 63572 max 63572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63572 Ave neighs/atom = 77.906863 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 ghost atom cutoff = 6 binsize = 3, bins = 7 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.690 | 4.690 | 4.690 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -3616.823 0 -3616.823 117.60408 Loop time of 2.5e-06 on 1 procs for 0 steps with 816 atoms 160.0% 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 | | 2.5e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3933.00 ave 3933 max 3933 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: 63504.0 ave 63504 max 63504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63504 Ave neighs/atom = 77.823529 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 ghost atom cutoff = 6 binsize = 3, bins = 7 30 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 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) = 4.690 | 4.690 | 4.690 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 -3616.823 -3616.823 20.540529 87.554869 4.9791091 117.60408 117.60408 133.6188 184.02866 35.1648 2.3762106 446.95407 Loop time of 2.565e-06 on 1 procs for 0 steps with 816 atoms 194.9% 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 | | 2.565e-06 | | |100.00 Nlocal: 816.000 ave 816 max 816 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3933.00 ave 3933 max 3933 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 31752.0 ave 31752 max 31752 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 63504.0 ave 63504 max 63504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 63504 Ave neighs/atom = 77.823529 Neighbor list builds = 0 Dangerous builds = 0 816 -3616.82302385416 eV 2.37621059852137 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:02