Corona Virus Information Updated January 4, 2021

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.

New Capabilities

 

Solid State and Quantum Chemistry Codes

JDFTX logo

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.

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Associate Publication - Must cite if code is used
VASP Logo

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 Logo

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) 

Quantum Espresso

Quantum Espresso is an Integrated suite of Open-Source computer codes for electronic-structure calculations and materials modeling at the nanoscale. 

Abinit

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. 

YAMBO

YAMBO is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo relies on the Kohn-Sham wave functions generated by two DFT public codes: ABINIT, and PWscf

NAMD

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. 

DFTB

DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which had been developed for the DFTB framework so far. 

CP2k logo

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

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. 

LAMMPS

Classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. 

Visualization Codes

VESTA logo

VESTA is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies. 

VMD Logo

Molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. 

P4 VASP Logo

Software that can use to visualize Band structures obtain from VASP and plot graphs. 

PARADIM Data Tools and Codes

MARCC

Approved PARADIM Proposals gain access to the JHU-MARCC high-performance computing center

SciServer

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.

PARADIM DATA

PARADIM provides access to curated data sets, public data and private user data. 

Materials Automated

Materials Automated strives to automate repetitive data analysis workflows for anyone working with materials data in materials chemistry, physics, or science

ptychography

e-Ptychography is a computational imaging technique developed at Cornell University by Zhen Chen and David Muller. 

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Associated Publication - Cite if code is used
Rigid Registration

RigidRegistration is an image registration method optimized for low-SNR, cryogenic STEM data.

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Associated Publication - Must cite if code is used
KafkaCrypto

Kafkacrypto is End-to-end message layer encryption for Kafka.

GitHub Logo

vnc2flv is a remote desktop screen recorder.

RSP BldgAdditional 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) 

How to contact us:

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.

>>> Go to the Theory Forum