Theory and Simulation Facility (at Clark Atlanta University)
Theory and Simulation are a critical part of the Materials by Design process employed by PARADIM. PARADIM’s user resources for theory and simulation are under the direction of Prof. Xiao-Qian (Larry) Wang and located primarily at Clark Atlanta University. They are accessible remotely. All successful PARADIM projects should employ Theory and Simulation as an integral part of the research plan.
Solid State and Quantum Chemistry Codes
JDFTx is a plane-wave density-functional theory (DFT) code designed to be as easy to develop with as it is easy to use. It is distributed under the GPL license (version 3 or higher) and publications resulting from its use must cite originating publication.
VASP is a computer program for atomic scale materials modeling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. (Available through PARADIM Collaboration only)
Materials Studio is a complete modeling and simulation environment designed to allow researchers in materials science and chemistry to predict and understand the relationships of a material’s atomic and molecular structure with its properties and behavior . (Licensed to CAU and available only via collaboration with Prof. Wang)
ABINIT is a program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a plane wave or wavelet basis.
NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
CP2K is a quantum chemistry and solid state physics software package that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems.
SIESTA is both a method and its computer program implementation to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids.
Classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator.
VESTA is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies.
Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
Software that can use to visualize Band structures obtain from VASP and plot graphs.
PARADIM Data Tools and Codes
Approved PARADIM Proposals gain access to the JHU-MARCC high-performance computing center
The SciServer PARADIM Data Collective (PDC) Cloud is a collaborative research platform for large-scale data-driven science. PARADIM users can run density functional theory (DFT) computational simulations and analyze microscopy data via inbuilt Jupyter notebook recipes.
Materials Automated strives to automate repetitive data analysis workflows for anyone working with materials data in materials chemistry, physics, or science
vnc2flv is a remote desktop screen recorder.
Additional information on the use of these codes is available in the Materials by Design Toolbox.
Computer cycles are available via clusters at Clark Atlanta and Cornell. In addition, PARADIM has received an allocation from XSEDE (an NSF supported supercomputer facility) and MARCC (through Johns Hopkins)
Theory user facility staff include Dr. Xiao-Qian Wang , Dr. Duminda Samarakoon (Research Associate) and Gabriel Anyanwu (Graduate Student) at Clark Atlanta and Prof. Craig J. Fennie and Dr. Betül Pamuk at Cornell. Dr. Samarakoon is available for general theory support; Dr. Pamuk is available for collaborative projects. Please contact Dr. Samarakoon for questions regarding the use of simulation resources for PARADIM proposals.