## NNIN Computational Nanotechnology Software Resources

Software packages hosted by NNIN/C include the following, which are available, installed, and supported by NNIN staff at the NNIN computation sites. Some licensing restrictions may apply to some users.

A list of available codes and a brief description is below. In addition, please note on the left menu, the Code Availability Matrix (by site) and links to the NNIN Virtual Vault For Pseudopotentials.

*Electronic Structure Codes*

- A plane wave pseudopotential first principles code.**ABINIT**computes interatomic forces in covalent solids and liquids which incorporates recent theoretical advances in understanding the environment dependence of (sigma) chemical bonding in condensed phases. [N. A. Marks, Phys. Rev. B 63 035401 (2001), M. Bazant et al., Phys. Rev. B 56, 8542 (1997)].__EDIP (Environment Dependent Interatomic Potential)__calculates electronic structure, in the effective mass approximation, of two dimensional electron gas (2DEG) based heterostructures such as quantum dots and wires. [M. Stopa, Phys. Rev. B 54, 13767 (1996)].__SETE (Single Electron Tunneling Elements)__- Linear Muffin Tin Orbital (LMTO) software package does ASA and full potential calculations and can be used for fully non-equilibrium transport calculations using a Green's function approach.**LM Suite**- A popular electronic structure code using density functional theory based on a full-potential linearized augmented plane wave approach. This code is often used to confirm results from plane wave codes based on pseudopotentials.**WIEN2K**is a computational chemistry package that is designed to run on high-performance parallel supercomputers as well as conventional workstation clusters.**NWChem**is used to perform ab-initio molecular dynamics. It allows for time-dependent DFT, wavefunction optimization, and path integral molecular dynamics.**CPMD (Carr-Parrinello Molecular Dynamics code)**(Pseudopotential Algorithms for Real Space Energy Calculations) solves the atomistic electronic structure problem for using a real space approach. This technique is ideal for modeling small clusters, molecules, and finite nanowires.**PARSEC**This plane wave density functional code takes advantage of ultra-soft pseudopotentials to accelerate calculations. In addition, it has the ability to handle magnetic nanostructures, calculate phonon dispersions, and perform structural relaxations.**Quantum Espresso (also known as PWscf)****VASP**-one of the standard simulation tools based on pseudopotential and plane wave basis set for solid state physics.This code uses numerically truncated orbitals (single, double, and triple zeta approach) to build on order-N density functional code. This code is ideal for modeling large scale nanostructures (i.e.nanotubes, nanowires, and clusters)**Siesta - (Spanish Initiative for Electronic Simulations with Thousands of Atoms)**locates the saddle point in the potential energy surface between an initial and a final state in a physical transition process such as a chemical reaction or diffusion process.**ANEBA (Adaptive Nudged Elastic Band Approach)****GAMESS**- one of the most popular quantum chemistry software packages and is widely used for chemistry and biology applications. It includes density functional theory, and other more sophisticated correlation methods including configuration interaction, perturbation theory, and coupled cluster theory.**Gaussian**- one of the earliest quantum chemistry software packages**ATK/VNL**- designed for electronic transport calculations based on DFT and local basis set.**CHAMP**- for Quantum Monte Carlo calculations.**Molden**and**Ecce**- these can be used to visualize and build structures, plot wavefunction and charge densities, visualize molecular orbitals, and visualize vibrational movements. Ecce also has extensive structure database for typical structures and structure fragments frequently used in chemistry and biology

*Molecular Dynamics*

- general purpose molecular dynamics simulator that has the option to use leonard-jones potentials, embedded atom potentials, and potentials for biomolecules and proteins. This parallel code can easily handle systems with thousands of atoms. The ability to incorporate the effect of temperature is an important complement to density functional techniques.**LAMMPS****GROMACS**- molecular dynamics package primarily designed for biomolecular systems such as proteins and lipids**Desmond**- high-speed molecular dynamics program for bio-molecules**CP2K**- performs atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It uses a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potential.**MOSAICS**- for the conformational/sequence sampling/optimization of biophysical structures (proteins, nucleic acids). Molecular entities/biopolymers can be described at different resolution from one center per monomer (residue/nucleotide) to all atom description with solvent effects.

*Photonics*

Package to compute the band structure and electromagnetic modes of periodic dielectric structures.**MIT Photonic Bands (MPB)**This is an open source finite difference time domain (FDTD) simulation code developed at MIT.**MEEP**

*Nanoscale Electrostatics*

**UT-MARLOWE**is a neutron transport simulator which models scattering, electronic stopping, and damage accumulation. [see: http://homer.mer.utexas.edu/utmarlowe ].(TOpography based Monte CArlo Transport) is a general-purpose Monte Carlo simulator of particle transport in arbitrary 2-D structures. The main application of TOMCAT is in the simulation of ion implantation. For more info see http://homer.mer.utexas.edu/tomcat02/**TOMCAT**is a quasi-static CV simulator for one-dimensional silicon MOS structures.**UT-QUANT**- SEMC-2D (Schrodinger Equation Monte-Carlo) simulation for quantum transport and scattering in nanoscale non-classical CMOS employing non-equilibrium Green function techniques

*Multiphysics and Finite Element Tools*

- This multiphysics package allows you to model coupled problems using finite element techniques. This could include current induced heating, vibrations in cantilevers, and fluid flow in microchannels.**Elmer**

Additionally, subject to licensing restrictions, NNIN will provide a series of commercial packages and mathematics libraries that include: Matlab, Femlab, ATLAS (self-optimizing LAPACK/BLAS), SILVACO, CADENCE (Electronic layout, modeling, synthesis tool), IntelliSuite (Mechanical modeling tool), Gnu scientific library, FFTW and Intel MKL libraries.