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Overview
Through generous
donations by Intel Corporation, the Cornell Nanoscale Facility (CNF) has provided high performance computing capabilities to users since early 2005. This effort is part of the greater
computational initiative in the NNIN to provide nanoscale modeling resources
that accelerate research and innovation.
The Intel cluster consists of 56 dual processor (3.06 GHz) Xeon nodes with a portion linked by Infiniband fabric and the rest linked with Gigabit ethernet. The cluster hosts an ever-expanding
and diverse suite of simulation tools for nanoscale systems including codes for
first principles calculations, photonic devices, molecular dynamics, multiphysics, and
nanoscale transport.
While numerous
standard packages exist for well-known systems in different fields, cutting
edge research often requires developing new algorithms or approaches to address
unique problems. To this end, the CNF is
dedicated to not only providing simulation tools, but also playing a role in
their development. Dr. Derek Stewart
serves as the scientific computation research liaison for the NNIN at
the CNF
and works with users to modify existing codes or need requires,
constructing
new approaches. The cluster also serves as a crucial test-bed
where codes developed in research groups can be tested by users and
develop the
robustness necessary for wide spread distribution.
For more information, please contact Derek Stewart at stewart@cnf.cornell.edu.
Focus Areas
- Electronic Structure of Nanoscale Systems (Tight Binding, Density Functional Theory, Monte Carlo Approaches)
- Nanophotonics Simulation Tools
- Molecular Dynamics
- Modeling Nanoscale Electronic and Thermal Transport
- Quantum Chemistry
- Cyberinfrastructure Tools for Research: (Virtual Vault for Pseudopotentials)
Simulation Workshops hosted at the CNF
Lectures and tutorials on several of the codes available can be found on the CNF Fall Modeling Workshop websites for 2005 "Modeling the Nanoscale World" and 2006 "Building Nanostructures Bit by Bit" and 2007 "Defining the Interface between Nanoscience and Geology"
Publications Resulting from the CNF Cluster
Full List of Publications
Simulation Tools Available
Density Functional Approaches
- Abinit - an open source robust plane wave density functional code
- Wien2k -
Electronic structure calculations using density functional theory based
on a full-potential linearized augmented plane wave approach.
- LM Suite
- Linear Muffin Tin Orbital package that support full potential and
atomic sphere approximation (ASA) calculations. It can also model
electronic transport in nanoscale structures using a non-equilibrium
Green's function approach.
- PARSEC
- (Pseudopotential Algorithms for Real Space Energy Calculations)
solves density functional calculations using a real space approach.
This technique is ideal for modeling small clusters.
- CPMD - Car-Parrinello Molecular Dynamics - This code can be used to perform ab-initio
molecular dynamics calculations. It allows for time-dependent density
functional calculations, wavefunction optimization, and path-integral
molecular dynamics.
- Siesta
- (Spanish Initiative for Electronic Simulations with Thousands of
Atoms). This code using numerically truncated orbitals (single and
double zeta approach) to build an order-N density functional code.
This code is ideal for modeling large scale nanostructures (i.e. nanotubes, nanowires, molecules).
- Plato
- (Package for Linear-combination of ATomic Orbitals) is a suite of
programs designed and written by Andrew Horsfield and Steven Kenny.
Capabilities of the program include a tight-binding algorithm, and a
self-consistent field method using either a local density approximation
or generalized gradent approximation functionals. The program was
specifically developed for application to systems with periodic
boundary conditions (crystals),
however it is also possible to treat isolated molecules. PLATO was
written with speed of calculation as a priority, and uses numerical
basis sets and tables of pre-computed one- and two-centered overlap
integrals.
- Quantum Espresso
- (also known as PWscf) This plane wave density functional code takes
advantage of ultra-soft pseudopotentials to accelerate calculations.
In addition, it has the ability to handle magnetic structures,
calculate phonon dispersions, and perform structural relaxations.
- Fleur - This code
is based on the all-electron full potential linear augmented plane wave
approach. It can provide important check for plane wave calculations
and also has special options for handling surfaces and 1d structures.
- NWChem
- This code is a highly parallel quantum chemistry package capable of
Self Consistent Field, Hartree Fock (RHF, UHF), and Gaussian density
functional calculations as well as several other techniques.
- QuantumWise
(formerly Atomistix) ATK and VNL - This commercial package provides the
ability to calculate I-V curves in nanostructures and molecular
junctions. The code is based on a non-equilibrium Green's function
approach and it also takes advantage of numerically truncated orbitals
to allow for calculations of large systems.
Molecular Dynamics
- LAMMPS -
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 provides an important complement to density functional
techniques.
- DL_POLY - DL_POLY is a parallel molecular dynamics simulation
package developed at Daresbury Laboratory by W. Smith and T.R. Forester under the auspices of the Engineering
and Physical Sciences Research Council (EPSRC) for the EPSRC's Collaborative
Computational Project for the Computer Simulation of Condensed Phases
(CCP5) and the Molecular Simulation
Group (MSG)
at Daresbury Laboratory. You can find a local tutorial on DL_POLY here and this code was also discussed at the 2007 CNF Fall Workshop.
- GROMACS - this
molecular dynamics code was designed primarily to examine biochemical
molecules such as proteins, lipids, and nucleic acids. It can also be
used to simulate proteins. The authors have done considerable work on
optimizing the code.
Nanophotonics
- MPB
- MIT Photonic Bands package. This code can calculate the band
structure and electromagnetic modes of periodic dielectric structures.
- MEEP - This is an open source finite difference time domain (FDTD) simulation code that was developed at MIT.
Nanoscale Electrostatics
- UTQUANT - This is a quasi-static CV simulator for one dimensional silicon MOS structures.
- SEMC-2D -
Schrodinger Equation Monte Carlo 2D simulator for quantum transport and
inelastic scattering effects in nanoscale semiconductor devices such as
nanoscale double gate MOSFETs and tunnel injection lasers. A
dissertation providing more details on the approach is available here.
Multiscale Physics
- Elmer -
This multiphysics packages allows you to model coupled problems. This
could include current induced heating, vibrations in cantilevers, and
fluid flow in microchannels.
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