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 = 2.8636573 2.8636573 2.8636573 Created orthogonal box = (0.0000000 -37.990708 0.0000000) to (13.431744 37.990708 4.0498230) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 4.8842704 4.3171259 4.0498230 Created 176 atoms using lattice units in orthogonal box = (0.0000000 -37.990708 0.0000000) to (13.431744 37.990708 4.0498230) create_atoms CPU = 0.001 seconds 176 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 4.8842704 4.3171259 4.0498230 Created 178 atoms using lattice units in orthogonal box = (0.0000000 -37.990708 0.0000000) to (13.431744 37.990708 4.0498230) create_atoms CPU = 0.000 seconds 178 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 = 5 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, cut 5.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 2 atoms, new total = 352 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_856956178669_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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 5 28 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) = 4.433 | 4.433 | 4.433 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1269.0389 0 -1269.0389 108945.3 63 0 -1502.1999 0 -1502.1999 9375.2242 Loop time of 0.958389 on 1 procs for 63 steps with 352 atoms 99.6% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -1269.0388550377 -1502.19866945674 -1502.19987163654 Force two-norm initial, final = 528.86421 0.11160983 Force max component initial, final = 165.44280 0.021745086 Final line search alpha, max atom move = 1.0000000 0.021745086 Iterations, force evaluations = 63 109 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.9484 | 0.9484 | 0.9484 | 0.0 | 98.96 Neigh | 0.0040065 | 0.0040065 | 0.0040065 | 0.0 | 0.42 Comm | 0.0032958 | 0.0032958 | 0.0032958 | 0.0 | 0.34 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.002689 | | | 0.28 Nlocal: 352.000 ave 352 max 352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2604.00 ave 2604 max 2604 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: 20504.0 ave 20504 max 20504 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20504 Ave neighs/atom = 58.250000 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 = 5.6 ghost atom cutoff = 5.6 binsize = 2.8, bins = 5 28 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 : 63 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.433 | 4.433 | 4.433 Mbytes Step Temp E_pair E_mol TotEng Press Volume 63 0 -1502.1999 0 -1502.1999 9375.2242 4133.0991 72 0 -1502.4114 0 -1502.4114 -62.952513 4155.1974 Loop time of 0.0905403 on 1 procs for 9 steps with 352 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 = -1502.19987163655 -1502.41047128905 -1502.41143314794 Force two-norm initial, final = 55.202374 0.40813425 Force max component initial, final = 53.531254 0.17877263 Final line search alpha, max atom move = 0.00042699883 7.6335706e-05 Iterations, force evaluations = 9 10 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.089343 | 0.089343 | 0.089343 | 0.0 | 98.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022377 | 0.00022377 | 0.00022377 | 0.0 | 0.25 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009735 | | | 1.08 Nlocal: 352.000 ave 352 max 352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2572.00 ave 2572 max 2572 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: 20468.0 ave 20468 max 20468 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20468 Ave neighs/atom = 58.147727 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 = 5 28 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) = 4.571 | 4.571 | 4.571 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -1502.4114 0 -1502.4114 -62.952513 Loop time of 1.509e-06 on 1 procs for 0 steps with 352 atoms 198.8% 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 | | 1.509e-06 | | |100.00 Nlocal: 352.000 ave 352 max 352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2572.00 ave 2572 max 2572 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: 20448.0 ave 20448 max 20448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20448 Ave neighs/atom = 58.090909 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 = 5 28 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) = 4.571 | 4.571 | 4.571 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 -1502.4114 -1502.4114 13.41338 76.631906 4.0424421 -62.952513 -62.952513 -56.267877 -69.521957 -63.067706 2.2908774 274.89564 Loop time of 1.526e-06 on 1 procs for 0 steps with 352 atoms 131.1% 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 | | 1.526e-06 | | |100.00 Nlocal: 352.000 ave 352 max 352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 2572.00 ave 2572 max 2572 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 10224.0 ave 10224 max 10224 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 20448.0 ave 20448 max 20448 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 20448 Ave neighs/atom = 58.090909 Neighbor list builds = 0 Dangerous builds = 0 352 -1502.41143314794 eV 2.29087743842468 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:01