Data Visualization for Atomistic/Molecular Simulations. Douglas E. Spearot University of Arkansas

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1 Data Visualization for Atomistic/Molecular Simulations Douglas E. Spearot University of Arkansas

2 What is Atomistic Simulation? Molecular dynamics (MD) involves the explicit simulation of atomic scale particles atoms and molecules Example: DNA Molecular mechanics (statics) Athermal calculation used to find minimum energy configuration Uses numerical algorithm such as steepest decent or conjugate gradients Molecular dynamics Simulate motion of atoms in time at desired temperature / pressure Uses numerical integration to solve equations of motion for each atom Monte Carlo methods Sample equilibrium configurations of atoms via random displacements Uses random numbers to perturb system from current state Rokadia et al. (2010)

3 How Does Molecular Dynamics Work? In the molecular dynamics method, each atom is treated as a point mass in space U ( r ) Simplify F i = r N i Once the force on each atom is computed, atomic motion is determined through application of Newton s Laws i F i F i r i i i = m a = m i Second-order ordinary differential equation which can be numerically integrated to find new atomic positions!

4 Need for Advanced Cyberinfrastructure Problem 1: Materials are made up of a lot of atoms Forces and atom positions have to be updated at each time step in molecular dynamics or at each iteration in molecular statics and Monte Carlo Example: Small sample cube of Cu 1 µm 3 10 nm 1 µ m 1unit cell nm 3 1µ m atoms 1unit cell = 84.7 billion Cu atoms

5 Need for Advanced Cyberinfrastructure Solution 1: Parallel decomposition techniques Core 1 Core 2 Core 3 Core 4 Core 5 Core 6 Core 7 Core 8 Current world record: 320 billion atoms with EAM potential (T. Germann et al., using 131,072 cores on IBM BlueGene/L at LLNL)

6 Need for Advanced Cyberinfrastructure Problem 2: What do I do with all of this data?

7 Need for Advanced Cyberinfrastructure Solution 2: Data visualization and Analysis Paul Navratil, TACC For atomistic/molecular simulations, geometric primitives are spheres meant to represent each atom in the system

8 Types of Input Data Paul Navratil, TACC Atomistic/molecular simulation data

9 Open-Source General Visualization Apps ParaView:

10 Open-Source General Visualization Apps VisIt:

11 Open-Source Atomistic Visualization Apps VMD:

12 Open-Source Atomistic Visualization Apps Ovito:

13 Ovito Case Studies Case Study 1: Polycrystalline Material Example provided with Ovito download Illustrates both visualization and analysis features Case Study 2: Polymer Nanocomposite Spearot dataset from research Illustrates visualization and flexibility of Ovito

14 Ovito imports data from data file LAMMPS VASP IMD XYZ text

15 Can load the first snapshot of atoms or all snapshots For 2010 version of LAMMPS, Ovito will recognize data structure

16 Identifies data source and provides links to analysis tools Visualization tools

17 Under modifier list select Color Coding Select Potential Energy and Adjust Range

18 Under modifier list select Coordination Analysis To compute coordination must select a cut-off distance Analysis command creates a new data variable no changes to current display

19 Under modifier list select Select By Expression Mathematical expressions can be evaluated using data variables

20 Under modifier list select Delete Selected Atoms Data is not actually deleted, just not shown on the screen

21 Under modifier list select Slice For a 45 o slice set normal vector to [110] Define a slice width

22 Ovito Case Studies Case Study 1: Polycrystalline Material Example provided with Ovito download Illustrates both visualization and analysis features Case Study 2: Polymer Nanocomposite Spearot dataset from research Illustrates visualization and flexibility of Ovito

23 Ovito imports data from data file LAMMPS VASP IMD XYZ text

24 Load all snapshots so that animation can be displayed Auto-assign columns recognizes the unknown variable mol

25 Change atom rendering quality Change radius of atom types

26 Under modifier list select Coordination Analysis Set cut-off distance and bond variables Set bond display width

27 Under modifier list select Select By Expression Mathematical expressions can be evaluated using data variables

28 Under modifier list select Delete Selected Atoms Under modifier list select Invert Selection

29 Under modifier list select Slice For a 45 o slice set normal vector to [-110] Define a slice width

30 Future Needs for Atomistic Visualization Creating contour renderings from atomistic data Challenging because of atomic vibrations atoms do not necessarily have the same scalar value for a given variable! Albe et al. (2010)