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NanoLab
Virtual NanoLab can be used to study
the eletronic structure and electron
transport in a variety of different
systems, such as molecules, periodic
systems (crystals, carbon nanotubes,
surfaces), and two-probe systems.
The program can use both semi-empirical
(will become available in the upcoming
version) and first principles or ab initio
methods (see below for more details). In
the latter case, the calculations are
performed without any user input except
the geometry of the system, and some
accuracy parameters. This unique
combination of different methods
accessible from the same graphical
interface makes Virtual NanoLab an
extremely versatile tool for all kinds of
calculations of nanoscale systems.
The main unique feature of the
algorithms used in Virtual NanoLab is that
they can treat open systems, in which a
current of electrons flows through the
system. In this way, it is possible to
calculate the transmission spectrum and
the current;voltage characteristics of
nanoscale transport devices.
The numerical engine behind Virtual
NanoLab is the Atomistix Tool Kit (ATK), a
set of state-of-the-art electronic
structure methods integrated into the same
software design. The basis of ATK is the
non-equilibrium Green's function (NEGF)
and density functional theory (DFT)
software provided in the TranSIESTA-C
package. TranSIESTA-C uses localized
numerical orbitals, and is one of the most
accurate and computationally efficient DFT
methods available today.
The main features of ATK which are also
available in Virtual NanoLab are:
- Self-consistent DFT description of
molecules, crystals and two-probe
systems
- NEGF algorithm with complex contour
integration
- Transmission spectrum and density
of states (DOS) for two-probe systems
- Current&endash;voltage
characteristics of two-probe systems
- Molecular orbitals, Bloch states,
electron density and effective
potentials
- k-point sampling of crystal and
two-probe systems
- Database of numerical basis sets
and pseudopotentials
Virtual NanoLab itself can be seen as a
graphical front-end to ATK, and contains
tools which allow the user to interact
with the advanced numerical methods
through an intuitive interface. These
tools, or instruments, are described on a
separate page.
Seascape Scientific Partner:
Atomistix
TranSIESTA:
Leading edge software for modelling the
electrical properties of nanoscale
devices
Nanotechnology is
becoming a pervasive technological
infrastructure, increasingly impacting
large business sectors like electronics,
life sciences, materials technologies and
chemistries.
Designing and
processing products at the nanoscale boost
the requirements for efficient quantum
theory based software tools at all
scientific and technical levels.
Seascape offers
TranSIESTA-C software. This software is
not only capable of performing
calculations on isolated molecules, but
also capable of calculating properties of
periodic systems such as metals, crystals
and carbon nanotubes. Even more
importantly, this product as the only
commercially available product that can
perform calculations on integrated nano
systems such as metal-molecule-metal. In
addition, this product is able to
calculate electron structure and transport
across interfaces and junctions, which is
invaluable in nano electronics and ultra
small-scale semiconductors.
TranSIESTA-C, is
a first principles electronic structure
program capable of modelling electrical
properties of nanostructured systems
coupled to semi-infinite electrodes. The
two electrodes, for instance, could be a
nanotube and a metal, and the
nanostructure could be the interface
region between the two systems. Other
typical systems include molecules between
metal surfaces and interfaces between
materials.
TranSIESTA-C is
based on non-equilibrium Green's function
(NEGF) techniques, and is capable of
treating situations in which the two
electrodes have different electrochemical
potentials, i.e. in which an external bias
voltage is applied across the
nanostructure. It can calculate the
electrical current, voltage drop across
the junction, electron transmission waves,
etc.
TranSIESTA-C is
also capable of performing conventional
electronic structure simulations on
isolated and periodic systems.
TranSIESTA-C is based on very efficient
electronic structure methods and is a very
accurate and efficient method for geometry
optimization.
Platforms:
Currently, TranSIESTA-C
runs on the following platforms:
- Linux on i686
compatible PC
- MS Windows on
I686 compatible PC
- MS Windows on
Athlon compatible PC
- MS Windows on
Opteron
- 64 bit Linux
on Opteron
- Solaris on
Sun Sparc
- Irix on
Silicon Graphics mips
- Apple G5
PowerPC
How Does It
Work?
The unique
feature of TranSIESTA-C is its ability to
treat open systems, in which an applied
bias voltage is driving an electrical
current. This is done by dividing the open
system into three regions in the
z-direction: Left electrode, Scattering
region, Right Electrode. In the electrode
regions the effective potential retains
its bulk value and is obtained from a
seperate bulk calculation. The effective
potential in the scattering region is
calculated self consistently using a Non
Equilibrium Green's Function(NEGF)
technique.
Using a starting
guess for the potential in the scattering
region we can calculate the Hamiltonian
Matrix using a localized basis sets. The
Hamiltonian matrix is used to setup the
NEGF of the system. In the next step the
nonequilibrium density matrix is
calculated from the NEGF. The density
matrix defines the effective potential in
the scattering region, and thereby new
Hamiltonian parameters. The steps are
repeated until a selfconsistent solution
is found.
TheTranSiesta-C
code has historically developed from the
McDCal, Siesta and TranSiesta programs.
The main references for these programs
are:
- Jeremy
Taylor, Hong Guo, and Jian Wang, Ab
initio modeling of quantum transport
properties of molecular electronic
devices, Phys. Rev. B 63, 245407 (2001)
- Mads
Brandbyge, Jose-Luis Mozos, Pablo
Ordejon, Jeremy Taylor and Kurt
Stokbro, Density functional method for
nonequilibrium electron transport,
Phys. Rev. B. 65, 165401 (2002)
- Jose M.
Soler, Emilio Artacho, Julian D. Gale,
Alberto Garcia, Javier Junquera, Pablo
Ordejon and Daniel Sanchez-Portal, The
SIESTA method for ab initio order-N
materials simulation, J. Phys. Cond.
Mat. 14, 2745 (2002)
- Jeremy
Taylor, Mads Brandbyge and Kurt
Stokbro, Theory of rectification in
Tour wires: the role of electrode
coupling, Phys. Rev. Lett. 89, 138301
(2002)
Customer
Statements
Professor Mark
Ratner from Northwestern University,
Evanston, Illinois, USA:
Calculating
coherent transport in molecular junctions
has become an important activity, in the
area of molecular electronics. To my
knowledge, this is certainly the best
available program for doing such
calculations, and it is both user friendly
and broad in its appeal and in its
capabilities.
Ph.D. Student
Peter Klason from Chalmers University of
Technology, Göteborg, Sweden:
Transiesta is a
fantastic program, built on the density
functional theory with the possiblity to
calculate transport properties across a
nanocontact. I think this program will be
used in the frontedge research for a long
time.
Research
Associate Brian Larade from HP Labs, Palo
Alto, California, USA:
An integral part
of my research involves locating target
molecules for molecular electronic devices
based on the way in which they attach to
metal surfaces and the intrinsic
current-carrying efficiency of the
molecule. The TranSiesta-C package is the
leading software for doing these
calculations.
Dr. Jeffrey
Reimers from University of Sydney, Sydney,
Australia:
TranSIESTA marks
a significant advance in making transport
theory calculations accessible to people
other than experts in this area. The power
to perform relatively large calculations
with such ease whilst utilizing the
accuracy of DFT is a real
advantage.
References
TranSIESTA-C is a
further development of the TranSiesta and
McDCal programs, employing localized basis
sets as developed in the Siesta program.
The TranSiesta and McDCal programs have
been used to study the electrical
properties of a wide range of systems,
including metal-nanotube interfaces,
molecular devices, nanotube defects and
atomic wires. References for the
TranSiesta-, McDCal- and SIESTA programs
are available here along with a
non-comprehensive list of references
regarding the applications of the
TranSiesta and McDCal programs.
The TranSiesta
Program:
Mads Brandbyge,
Jose-Luis Mozos, Pablo Ordejon, Jeremy
Taylor and Kurt Stokbro, Density
functional method for nonequilibrium
electron transport, Phys. Rev. B 65,
165401 (2002).
The McDCal
Program:
Jeremy Taylor,
Hong Guo and Jian Wang, Ab initio modeling
of quantum transport properties of
molecular electronic devices, Phys. Rev. B
63, 245407 (2001).
The SIESTA
Program:
Jose M. Soler,
Emilio Artacho, Julian D. Gale, Alberto
Garcia, Javier Junquera, Pablo Ordejon and
Daniel Sanchez-Portal, The SIESTA method
for ab initio order-N materials
simulation, J. Phys. Cond. Mat. 14, 2745
(2002).
Applications
of TranSiesta:
Mads Brandbyge,
Jose-Luis Mozos, Pablo Ordejon, Jeremy
Taylor and Kurt Stokbro, Density
functional method for nonequilibrium
electron transport, Phys. Rev. B. 65,
165401 (2002).
Mads Brandbyge,
Kurt Stokbro, Jeremy Taylor, Jorge L.
Mozos and Pablo Ordejon, New method for
first principles modeling of electron
transport through nanoelectronic devices,
Material Research Society symposium
proceedings volume 636 ,D9.25 (2001).
Jorge L. Mozos,
Pablo Ordejon, Mads Brandbyge, Jeremy
Taylor and Kurt Stokbro, Simulations of
quantum transport in nanoscale systems:
application to atomic gold and silver
wires, Nanotechnology 13, 346 2002).
Jeremy Taylor,
Mads Brandbyge and Kurt Stokbro, Theory of
rectification in Tour wires: the role of
electrode coupling, Phys. Rev. Lett. 89,
138301 (2002).
S. K. Nielsen, M.
Brandbyge, K. Hansen, K. Stokbro, J. M.
van Ruitenbeek and F. Besenbacher,
Current-Voltage Curves of Atomic-Sized
Transition Metal Contacts: Why Au is Ohmic
and Pt is Not, Phys. Rev. Lett. 89, 66804
(2002).
Jorge L. Mozos,
Pablo Ordejon, Mads Brandbyge, Jeremy
Taylor and Kurt Stokbro, Density
functional theory calculations of quantum
electron transport: carbon nanotubes-gold
contacts, Advances in Quantum Chemistry
42, 299 (2003).
Kurt Stokbro,
Jorge L. Mozos, Pablo Ordejon, Mads
Brandbyge and Jeremy Taylor, Theoretical
study of the nonlinear conductance of
Di-thiol benzene coupled to Au(111)
surfaces via thiol and thiolate
bonds,Computational Materials Science 27,
151 (2003).
M. Brandbyge, K.
Stokbro, J. Taylor, J.-L. Mozos and Pablo
Ordejon, First principles Calculation of
Current Induced Forces In An Atomic Gold
Wire, Phys. Rev. B67, 193104 (2003).
Kurt Stokbro,
Jeremy Taylor and Mads Brandbyge, Do
Aviram-Ratner diodes rectify?, Journal of
the American Chemical Society 125, 3674
(2003).
Jeremy Taylor,
Mads Brandbyge and Kurt Stokbro,
Conductance switching in a molecular
device: the role of sidegroups and
intermolecular interactions, Phys. Rev. B
Rapid Comm.
Kurt Stokbro,
Mads Brandbyge, Jeremy Taylor and Pablo
Ordejon, TranSIESTA a SPICE for Molecular
Electronics, Proceedings of Nanotech
Venture Fair, San Francisco, February
2003.
Kurt Stokbro,
Mads Brandbyge,Jeremy Taylor and Pablo
Ordejon, TranSIESTA a SPICE for Molecular
Electronics, Proceedings of UEF molecular
electronics conference, Key West
2002.
Applications
of McDCal:
Jeremy Taylor,
Hong Guo and Jian Wang, Ab initio modeling
of quantum transport properties of
molecular electronic devices, Phys. Rev. B
63, 245407 (2001).
Jeremy Taylor,
Hong Guo and Jian Wang, Ab initio modeling
of open systems: charge transfer, electron
conduction, and molecular switching of a
C60 device, Phys. Rev. B 63, R121104
(2001).
Brian Larade,
Jeremy Taylor, H. Mehrez and Hong Guo,
Conductance, I-V curves, and negative
differential resistance of Carbon atomic
wires, Phys. Rev. B 64, 75420 (2001).
Brian Larade,
Jeremy Taylor, Q.R. Zheng, Hatem Mehrez,
Pawel Pomorski and Hong Guo, Renormalized
molecular levels in a Sc3N@C80 molecular
electronic device, Phys. Rev. B 64, 195402
(2001).
Christopher
Roland, Brian Larade, Jeremy Taylor and
Hong Guo, Ab initio I-V characteristics of
short C20 chains, Phys. Rev. B 65, R041401
(2002).
H. Mehrez, Alex
Wlasenko, Brian Larade, Jeremy Taylor,
Peter Grutter and Hong Guo, I-V
characteristics and differential
conductance fluctuations of Au nanowires,
Phys. Rev. B 65, 195419 (2002).
Chao-Cheng Kaun,
Brian Larade, Hatem Mehrez, Jeremy Taylor
and Hong Guo, Current-voltage
characteristics of carbon nanotubes with
substitutional Nitrogen, Phys. Rev. B 65,
205416 (2002).
Seascape Scientific Partner:
Atomistix
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