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 = 3.1472000 3.1472000 3.1472000 Created orthogonal box = (0.0000000 -40.057316 0.0000000) to (28.324800 40.057316 4.4508129) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.2453333 5.4398824 4.4508129 Created 323 atoms using lattice units in orthogonal box = (0.0000000 -40.057316 0.0000000) to (28.324800 40.057316 4.4508129) create_atoms CPU = 0.001 seconds 323 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.2453333 5.4398824 4.4508129 Created 325 atoms using lattice units in orthogonal box = (0.0000000 -40.057316 0.0000000) to (28.324800 40.057316 4.4508129) create_atoms CPU = 0.001 seconds 325 atoms in group lower Displacing atoms ... WARNING: KIM Model does not provide 'partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1161) 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 10 26 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 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 0 atoms, new total = 648 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_424746498193_002#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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 10 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.492 | 4.492 | 4.492 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4224.3033 0 -4224.3033 81581.901 87 0 -4384.7883 0 -4384.7883 9731.3501 Loop time of 0.49621 on 1 procs for 87 steps with 648 atoms 98.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -4224.30325070936 -4384.78472272808 -4384.78830244876 Force two-norm initial, final = 262.77239 0.20590064 Force max component initial, final = 81.550000 0.043991992 Final line search alpha, max atom move = 1.0000000 0.043991992 Iterations, force evaluations = 87 168 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.48726 | 0.48726 | 0.48726 | 0.0 | 98.20 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0043466 | 0.0043466 | 0.0043466 | 0.0 | 0.88 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.004605 | | | 0.93 Nlocal: 648.000 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3132.00 ave 3132 max 3132 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: 37932.0 ave 37932 max 37932 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37932 Ave neighs/atom = 58.537037 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 10 26 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 87 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 4.492 | 4.492 | 4.492 Mbytes Step Temp E_pair E_mol TotEng Press Volume 87 0 -4384.7883 0 -4384.7883 9731.3501 10099.922 92 0 -4385.0075 0 -4385.0075 -4.2629764 10131.94 Loop time of 0.0239714 on 1 procs for 5 steps with 648 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 = -4384.78830244876 -4385.00663109634 -4385.00754443553 Force two-norm initial, final = 124.98592 0.62199389 Force max component initial, final = 114.98011 0.11876423 Final line search alpha, max atom move = 0.00010344770 1.2285886e-05 Iterations, force evaluations = 5 7 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.022712 | 0.022712 | 0.022712 | 0.0 | 94.75 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.00022005 | 0.00022005 | 0.00022005 | 0.0 | 0.92 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.001039 | | | 4.34 Nlocal: 648.000 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3110.00 ave 3110 max 3110 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: 37900.0 ave 37900 max 37900 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37900 Ave neighs/atom = 58.487654 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 10 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.630 | 4.630 | 4.630 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -4385.0075 0 -4385.0075 -4.2629764 Loop time of 1.719e-06 on 1 procs for 0 steps with 648 atoms 174.5% 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 | | 1.719e-06 | | |100.00 Nlocal: 648.000 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3110.00 ave 3110 max 3110 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: 37866.0 ave 37866 max 37866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37866 Ave neighs/atom = 58.435185 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 = 6.2447 ghost atom cutoff = 6.2447 binsize = 3.12235, bins = 10 26 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 6.2447 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) = 4.630 | 4.630 | 4.630 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 -4385.0075 -4385.0075 28.306413 80.442679 4.4496026 -4.2629764 -4.2629764 -12.764698 -9.0640351 9.0398043 2.4358214 508.88948 Loop time of 1.401e-06 on 1 procs for 0 steps with 648 atoms 214.1% 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 | | 1.401e-06 | | |100.00 Nlocal: 648.000 ave 648 max 648 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 3110.00 ave 3110 max 3110 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 18933.0 ave 18933 max 18933 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 37866.0 ave 37866 max 37866 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 37866 Ave neighs/atom = 58.435185 Neighbor list builds = 0 Dangerous builds = 0 648 -4385.00754443553 eV 2.4358214281007 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:00 Potential info: Mo potential Atomic number: 42 Potential info: Mo potential Atomic number: 42