Comparison to LAMMPS-REAX

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Presentation transcript:

Comparison to LAMMPS-REAX PuReMD: Purdue Reactive Molecular Dynamics Program H. Aktulga§, J.Fogarty¶, S. Pandit¶, A. Grama§ § Purdue University, West Lafayette, IN 47907, USA ¶University of South Florida, Tampa, FL 33620, USA 1. ReaxFF Overview Reax Force Field Works at the atomistic level Dynamic bonding in ReaxFF vs Static bonding in other classical methods At the heart of dynamic bonding lies a classical bond order interaction Bond strength is determined by atom types and distance Dynamic bonding makes the simulation of reactive systems possible Dynamic bonding also introduces many challenges: Updating bond, valence angle, and dihedral angle lists at each step Updating the partial charge on each atom at each step  QEq Shorter time-steps need to be used due to chemical reactions 2. Implementation System Geometry Control Parameters Force Field Trajectory Snapshots System Status Update Program Log File PurdueReax Initialization Read input data Initialize data-structs Compute Bonds Corrections are applied after all uncorrected bonds are computed Bonded Interactions Bonds Lone pairs Over/UnderCoord Valence Angles Hydrogen Bonds Torsion Angles 3-body & 4-body intrs are Built from lower order intrs QEq Huge sparse linear system PGMRES(50) or PCG ILUT-based preconditioners give excellent performance vd Waals & electrostatics Single pass over the far nbr-list after charges are updated Interpolation with cubic splines for nice speed-up Evolve the System Ftotal = Fnonbonded + Fbonded Update x & v with velocity Verlet NVE, NVT and NPT ensembles Reallocate Fully dynamic and adaptive memory management: excellent use of resources can handle very large systems on a single processor Neighbor Generation 3D-grid based O(n) neighbor generation Several optimizations for best performance Init Forces Initialize the QEq coef matrix Compute uncorrected bond orders Generate H-bond lists 3. Performance Weak Scaling: Bulk Water – 6540 atoms in 40x40x40A3 box / core Strong Scaling: Bulk Water – 52320 atoms in 80x80x80A3 box 4. Applications Y. Park, H. Aktulga, A. Grama, A. Strachan “Strain relaxation in Si/Ge/Si nanoscale bars from MD simulations” J Appl Phys 106, 034304 (2009) J. Fogarty, H. Aktulga, A. van Duin, A. Grama, S. Pandit “A Reactive Simulation of the Silica-Water Interface” J Chem Phys (2010) Comparison to LAMMPS-REAX weak scaling strong scaling J. Fogarty, H. Aktulga, A. Grama, S. Pandit “Oxidative Damage in Lipid Bilayers: A Reactive Molecular Dynamics Study” Biophysical Society Meeting (2010) 5. Status Code (PuReMD) fully validated and released to a number of applications groups -- Goddard (CalTech), van Duin (PSU), Pandit (USF), Buehler (MIT), Thompson (Sandia), Germann (LANL), Kent (ORNL), Andzelm (ARL), Quenneville (Spectral Sc. Inc). Code fully integrated into LAMMPS (currently being fully validated). Optimizations for various platforms and improvement of algorithms ongoing.