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 = 3.6133156 3.6133156 3.6133156 Created orthogonal box = (0.0000000 -62.588076 0.0000000) to (25.550000 62.588076 8.8507796) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 6.1320000 5.4239868 5.9005197 Created 1202 atoms using lattice units in orthogonal box = (0.0000000 -62.588076 0.0000000) to (25.550000 62.588076 8.8507796) create_atoms CPU = 0.002 seconds 1202 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 6.1320000 5.4239868 5.9005197 Created 1202 atoms using lattice units in orthogonal box = (0.0000000 -62.588076 0.0000000) to (25.550000 62.588076 8.8507796) create_atoms CPU = 0.002 seconds 1202 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 = 9 42 3 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 20 atoms, new total = 2384 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_087820130586_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 = 9 42 3 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) = 5.159 | 5.159 | 5.159 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8384.1206 0 -8384.1206 3209.5033 31 0 -8417.409 0 -8417.409 -6011.5425 Loop time of 2.64409 on 1 procs for 31 steps with 2384 atoms 98.2% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8384.12059277113 -8417.40206894171 -8417.40901839571 Force two-norm initial, final = 36.594044 0.22303264 Force max component initial, final = 5.5925886 0.038127142 Final line search alpha, max atom move = 1.0000000 0.038127142 Iterations, force evaluations = 31 55 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 2.6293 | 2.6293 | 2.6293 | 0.0 | 99.44 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0057993 | 0.0057993 | 0.0057993 | 0.0 | 0.22 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.008968 | | | 0.34 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6881.00 ave 6881 max 6881 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: 184352.0 ave 184352 max 184352 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184352 Ave neighs/atom = 77.328859 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 = 6 ghost atom cutoff = 6 binsize = 3, bins = 9 42 3 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 : 31 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 5.159 | 5.159 | 5.159 Mbytes Step Temp E_pair E_mol TotEng Press Volume 31 0 -8417.409 0 -8417.409 -6011.5425 28307.012 34 0 -8417.5745 0 -8417.5745 -1396.5179 28213.526 Loop time of 0.178497 on 1 procs for 3 steps with 2384 atoms 98.9% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -8417.40901839569 -8417.57262468531 -8417.5745410527 Force two-norm initial, final = 134.53382 1.0014543 Force max component initial, final = 108.06105 0.72384504 Final line search alpha, max atom move = 0.00013306074 9.6315354e-05 Iterations, force evaluations = 3 4 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.17645 | 0.17645 | 0.17645 | 0.0 | 98.85 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00029988 | 0.00029988 | 0.00029988 | 0.0 | 0.17 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001751 | | | 0.98 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6891.00 ave 6891 max 6891 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: 184272.0 ave 184272 max 184272 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184272 Ave neighs/atom = 77.295302 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 = 9 42 3 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) = 5.297 | 5.297 | 5.297 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -8417.5745 0 -8417.5745 -1396.5179 Loop time of 1.915e-06 on 1 procs for 0 steps with 2384 atoms 208.9% 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 | | 1.915e-06 | | |100.00 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6891.00 ave 6891 max 6891 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: 184368.0 ave 184368 max 184368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184368 Ave neighs/atom = 77.335570 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 = 9 42 3 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) = 5.297 | 5.297 | 5.297 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 -8417.5745 -8417.5745 25.523137 125.17615 8.8308342 -1396.5179 -1396.5179 -36.967136 -4111.5738 -41.012741 2.3700539 789.31579 Loop time of 2.083e-06 on 1 procs for 0 steps with 2384 atoms 192.0% 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 | | 2.083e-06 | | |100.00 Nlocal: 2384.00 ave 2384 max 2384 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 6891.00 ave 6891 max 6891 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 92184.0 ave 92184 max 92184 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 184368.0 ave 184368 max 184368 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 184368 Ave neighs/atom = 77.335570 Neighbor list builds = 0 Dangerous builds = 0 2384 -8417.5745410527 eV 2.37005394664551 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:03