Atomistix ToolKit Atomistix ToolKit (ATK)是一个能模拟纳米结构体系和纳米器件的电学性质和量子输运性 质的第一性原理电子结构计算程序。对于所模拟的纳米器件的电极，它可以是纳米管或金 属。对于所模拟的纳米结构体系，它可以是两种不同材料形成的界面区，或界于两个金属表 面之间的分子。ATK 是由 Atomistix 公司在 McDCal、 SIES
TA 和 TranSIESTA 等电子结构 计算程序包的基础上根据现代软件工程原理开发出来的第一个商用的模拟电子输运性质的 大型计算软件，它的前身 是 TranSIESTA-C。目前版本(2.0.4)的 ATK 采用 C 和 C++高级语 言来编写核心的库代码，即将在 2006 年 12 月发布的 ATK2.1 版本 并在此基础上提供了 Python 脚本语言编写的各种函数接口，用户可以利用所提供的函数接口采用 Python 脚本语 言来编写和实现特定的计算功能和数据处 理。 基于密度泛函理论，ATK 实现了赝势法和原子轨道线性组合方法等现代电子结构计算方法。 在此基础上，它利用非平衡格林函数方法来处理纳米器件在外置偏压下 的电子输运性质。 因此它能处理纳米器件中的两个电极具有不同化学势时的情况， 能计算纳米器件在外置偏压 下的电流、穿过接触结的电压降、电子透射波和电子的 透射系数等等。ATK 也实现了自旋 极化的电子结构计算方法， 因此它也可以处理纳米器件中相关的磁性和自旋输运问题。 除此 之外，ATK 也能进行传统的电子结 构计算，处理孤立的分子体系和具有周期性的体系。另 外 ATK 也采用非常有效和稳定的算法来精确地计算原子所受的力并优化体系的几何结构。 ATK 软件的特点： 1、 基于密度泛函理论，采用第一性原理电子结构计算方法自洽计算分子、周期结构和双电 极体系的电子结构 2、 采用非平衡格林函数方法并结合复平面积分手段来计算纳米器件在外置偏压下的电流 3、 实现了局域密度近似(LDA)和广义梯度近似(GGA)的交换关联函数，以及相关的自旋极 化计算 4、 能计算自旋极化情况下的电流-电压(I-V)曲线和透射谱(T-Energy 或 G-Energy)等 5、 实现了 Hoffmann-Muller 发展的扩展 Huckel 方法 6、 实现了从 SIESTA 程序包中发展出来的局域数值轨道 7、 利用 MPICH 实现了并行计算的功能，特别是在输运性质计算、k 点取样、能量积分和 矩阵元计算中进行了优化处理 8、 能计算分子体系的分子能级（包括 HOMO 和 LUMO 能级） 、分子轨道和 HOMO-LUMO 能隙 9、 能计算周期性体系的能带、布络赫(Bloch)波函数和费米能级等 10、 能计算双电极体系的透射谱、本征通道、态密度、分子投影自洽哈密顿(MPSH)轨道和 态密度实空间分布 11、 能计算体系的电荷密度和有效势 12、 能计算双电极体系的电流-电压(I-V)曲线 13、 对周期性结构和双电极体系实现了 Monkhorst-Pack k 点取样方法 14、 对透射谱和电流进行了 k 点取样的处理 15、 通过在中心区施加外势场来近似处理门电压并模拟三端器件的电学性质 16、 提供了元素周期表中从 H(1)-Lr(103)各种元素的从头模守恒赝势 17、 在电子结构自洽计算过程中，采用了 Broyden 或 Pulay 混合算法 18、 基于密度泛函理论计算原子所受的力， 并采用共轭梯度(CG)方法优化和驰豫原子位置，
以及采用类似的方法来处理双电极体系在外置偏压情况下的几何结构优化问题 19、 通过 Fermi 分布来指定电子气的温度 20、 可处理双电极体系中的两端电极由不同材料组成时的情况 21、 Mulliken 布居分析 22、 输入文件采用了自由、弹性和简单的文本格式 23、 对计算结果按 NetCDF 格式输出 ATK(包括了 TranSIESTA-C)的成功应用案例： 1、分子接触器件和隧道器件的 I-V 特征曲线 2、分子电子器件的功放和转换性质。 3、分子线、半导体纳米线和碳纳米管的电子输运性质 4、金属-纳米管接触结和纳米管-纳米管接触结的电阻和电容性质 5、原子线中的电子迁移性质 6、碳纳米管的场致发散性质 7、MOS 器件中漏电流问题 8、界面处的自旋输运问题和磁阻效应的计算 9、生物体系中电荷转移问题
Virtual NanoLab Virtual NanoLab (VNL)是 Atomistix ToolKit (ATK)对应的图形界面软件，它具有友好的 图形界面操作环境， 以轻松进行纳米器件在原子尺度模拟的建模、 计算和数据分析等可视化 操作。 其中 VNL 的计算 引擎是内嵌的 ATK。 VNL 中的操作流程与真实实验中的情况类似， 它为用户提供了多种工具并通过原子尺度模拟来轻松建立“虚拟的实验平台”： 构造纳米器件 的原子几何结构、模拟器件的电子结构和电学性质。目前发行的稳定版本是 VNL1.2，它包 括了原子操作模块 (Atomic Manipulator) 、纳米结构透视模块 (Nanoscope) 、晶体构造模块 (Crystal Grower)、纳米管构造模块(Nanotube Grower)和能谱计算模块(Energy Spectrometer)。 即将 2006 年 12 月正式发布的 VNL1.3 版本中晶体构造模块(Crystal Grower)替换为晶体结构 库模块(Crystal Cupboard)，在 1.2 版本的基础上提供了更多的晶体结构。 功能： 1. 可视化 ATK 输入文件中所定义的体系的几何结构。 2. 可视化 ATK 计算输出的 netCDF 格式文件。 3. 能导入按 xyz 格式描述的原子坐标文件，并显示相应体系的几何结构。 4. 提供了 500 多种晶体的结构图，可以直接在 VNL 中进行显示和表面结构的建模。 5. 直接构造和显示碳纳米管的结构并可以导出它的原子坐标，采用紧束缚近似快速计算并 显示它的能带结构。 6. 通过对电极材料进行表面结构建模，对中心区（或导体区）采用鼠标操作来调整中心区 吸附分子或导体的位置和取向，可简单、轻松构造所要模拟的双电极体系。 7. 能快速建立所要模拟的分子、体材料和双电极体系的 ATK 输入文件，并通过鼠标操作来 引导内嵌的 ATK 的运行并进行所模拟体系的几何结构优化、电子结构计算或电子输运性质 计算。
8. 可视化电荷密度和有效势在实空间分布的等高线图、等值面图和体积图。 9. 可视化分子轨道的 3D 图和显示周期性体系的布络赫(Bloch)波函数。 10.支持大多数运行于 32 和 64 位的 Intel 和 AMD 处理器上的 Linux 和 Windows 操作系统
Semiconductor Nanowires Case Study 15.Feb.2007 00:22 Category: VNL & ATK Case Studies
The electronic properties of semiconductors are strongly modified when their dimensions approach the nanoscale. Because of the weak screening in semiconductors, a large portion of the nanowire is influenced by the constriction size and shape. Surface effects are in general much more important in nanocomponents, since the surface-to-volume ratio is much larger than in macroscopic systems.
Figure 6b Materials such as ZnO also have other characteristics which make them promising candidates for various nanoelectronics. For instance, they could be used to measure the flow in small blood veins in the human body, without inhibiting the flow itself. Moreover, it is expected that ZnO nanowires will be less effected by degradation due to the influence of oxygen in the atmospheric air (a process which is a real concern for many nanodevices), as they are already oxidized.
Semiconductor nanowires are typically quite rigid at these length scales, as opposed to nanotubes and metallic contacts, and they are therefore often referred to as nanorods. There are also good possibilities to take advantage of the carrier confinement, which can be relative strong in these wires, which results in an increase in the band gap. Furthermore, ZnO in general is a large band gap semiconductor and has high excitonic binding energies. All together this makes ZnO nanowires a candidate for the first UV light emitting nanodevice.
The transport in nanowires is dominated by states on the surface of the wire. It is therefore expected that the conductance is highly sensitive to surface functionalization, making these systems strong candidates for various nanosensor applications.
Figure 6: a) VNL visualization of the density of states of semiconducting ZnO nanowire. This calculation, which took about 12 hours on a 16-node PC cluster, involved more than 500 atoms and roughly 5000 electrons.
Figure 6b) The effective potential of a cross section of the wire.
Metallic Contacts Case Study 15.Feb.2007 00:22 Category: VNL & ATK Case Studies
Microelectronic components are becoming smaller and smaller every year, and the electronic industry is soon reaching the point where quantum effects will begin to play a fundamental role.
Figure 5 Studying atomically narrow metal wires provides an opportunity to investigate what happens to conventional wiring as the dimensions shrink. Techniques for fabrication and characterization of atomically thin metallic wires are among the most established methods for detailed studies of electronics at the nanoscale, and coupled with modeling, this has allowed researchers to understand many basic properties of electronics at the atomic scale.
The current flowing through an atomic wire creates a force
on the constituent atoms. This process, known as electromigration, has been studied by researchers at the Technical University of Denmark.  They studied the detailed energetics of a gold nanowire under the effect of an applied bias voltage. Importantly, a novel mechanism for the breaking of atomic wires under current flow was proposed: an applied bias voltage favors the population of anti-bonding orbitals in the wire, thus repelling atoms form one another and leading to breakage.
Metallic contacts can both realign and broaden the energy levels of adsorbate molecules. Prof. Ruitenbeek and colleagues at the Kamerlingh Ohnes Laboratories have for a long time specialized in fabrication and characterization of atomically thin metal wires. With their mechanical break-junction technique, they were able to detect the presence of a single hydrogen molecule and analyze its electronic properties.  The hydrogen molecule has a large HOMO-LUMO gap, and it was not expected to be a good conductor, while the experiment instead found a large conductance probability. Thygesen and co-workers used atomistic modeling to show that this large conductance is
due to transmission through the anti-bonding state of the hydrogen molecule. 
Metallic gold nanotubes of gold have been discovered in detailed SEM studies of atomic scale wires.  Researchers at placename Bilkent University have used atomistic modeling to study the stability of different Au nanotubes of different chirality to determine which nanotube is most likely to form in nature.  The electronic properties of the most stable structures were then studied to understand the role that chirality plays in electron transport.
 M. Brandbyge et al., Physics Review B 67, 193104 (2003).
 R. H. M. Smit et. al., Nature 419, 906 (2002).
 Thygesen et al., Physics Review Letters 94, 036807 (2005).
 Y. Oshima et al., Physics Review Letters 91, 205503 (2003).
 R. T. Senger et al., Physics Review Letters 93, 196807 (2005).
 S. K. Nielsen et al., Physics Review Letters 89, 66804 (2002).
Figure 3a Calculated (circles) and measured (solid line) I–V characteristics of Au and Pt atomic wires.  The theoretical results are in excellent agreement with the experimental results.
Figure 3b Visualization of a molecular projected self-consistent Hamiltonian (MPSH) orbital of a thin Au wire grown from an Au (100) surface. These orbitals give a description of the delocalized electron channels used for transport. Using ATK, one can study the changes in the orbitals as a finite bias is
applied. As the bias is increased, the forces between the atoms in the wire increases, a phenomenon related to electromigration.
Figure 4 An MPSH orbital of an H2 molecule between two Pt (111) surfaces. Studies show that the large conductance observed in this system experimentally is due to transport through the anti-bonding orbital that is shown here.
Figure 5 Visualization of a Bloch state of a (4,4) Au nanotube. While the structure of Au nanotubes are related to that of carbon nanotubes, the electronic properties are different -orbitals.?since transport in the Au nanotubes is not dominated by the Back to: Virtual NanoLab
Complex Switching Mechanisms Case Study 15.Feb.2007 00:22 Category: VNL & ATK Case Studies
Researchers at Yale University have discovered giant negative differential resistance (NDR) in a class of organic molecules [1,2], raising great interest in the possibility of using molecular NDR to build logic components.
Figure 7b The mechanism was only seen when the molecule in question had been functionalized with an electron acceptor side group. Researchers at the Technical University of Denmark performed detailed comparative analyses of the molecule functionalized with different side groups.  By calculating the transmission spectrum of the molecules between metal contacts, two characteristic peaks were
identified in all molecules, independent of the side groups. Detailed inspection of the peaks showed that they correspond to the intrinsic delocalized orbitals of the molecule, and that functionalization does not significantly change the conductance mechanism. Calculations of the interaction energies of the molecules revealed that monolayers of molecules with the acceptor side group have a metastable low-conductance state where the molecule is twisted, which is stabilized with respect to the high conductance state when a bias is applied.
This work highlights the importance of having reliable information about the electron transport properties and the total energy of the system.
 J. Chen et al., Science, 286, 1550 (1999).
 Z. L. Donhauser et al., Science 292, 2303 (2001).
 J. Taylor et al., Physics Review B 68, 121101 (2003).
Figure 7a Visualization of a monolayer of oligo-ethynylene-phenylene molecules between Au (111) surfaces.
Figure 7b Total energies of the system as a function the rotational angle of the middle ring. For molecules functionalized with NO sidegroups a rotation of the middle ring is stabilized by interactions with neighboring molecules. Such rotations strongly increase the electrical resistance of the molecule.
Molecular Diodes Case Study 15.Feb.2007 00:22 Category: VNL & ATK Case Studies
The birth of molecular electronics, some say, was a proposal as early as 1974 by Aviram and Ratner , to construct a molecular diode by locally changing its electronic properties with donor and acceptor groups. This would, the idea was, create the molecular equivalent of a p-n junction, i.e. a moletronic device. Only recently, however, has it been possible with the use of modern nanotechnology to perform controlled moletronic experiments where the results can be directly compared to calculated quantities, and a series of experiments has demonstrated that molecules can indeed be used to rectify current.  The mechanism is, however, slightly different than what originally was imagined, and the answer was provided by the modeling.
Figure 8b At the Technical University of Denmark, researchers looked at two different mechanisms for current rectification. In both cases, using
numerical simulations of the same kind that are available in ATK to look at a concrete example of a molecular rectifier, made it possible to extract the general behavior of the system and make simplified models that would govern the device behavior.
The key to understanding these systems was to have a control parameter that one can vary to gauge the effect of perturbing the system using an external probe. In one case, it was the molecule-metal interaction and in another, it was the applied bias.
A simplified model of asymmetric molecule-electrode coupling strength derived from atomistic modeling results made it possible to understand a wide range of molecular rectification experiments.  The construction of a moletronic device is at least a two-step process. Molecules are adsorbed onto a substrate and then another electrode is attached in some way. This asymmetry in molecular absorption leads to molecular rectification. By tuning the strength of the asymmetry, either by modifying the substrate adsorption or how the second electrode is attached, one can tune the performance of the rectifier.
The operation of a molecular p-n junction, or donor-sigma-acceptor bridge, was studied using atomistic modeling.  The mechanism relies
on two levels in the molecule, a donor and acceptor level. As the applied bias is increased in one direction, the energies of the two levels align and a resonant tunneling occurs. In the other bias polarity, the levels are repelled and current decreases. This was indeed observed in the simulation. From this study, it emerged that two key parameters govern the behavior of the device: the difference in donor and acceptor level energies, and the dielectric constant and width of the sigma bridge. Adjusting these parameters will play a role in optimizing the rectification properties of these devices.
 A. Aviram and M.A. Ratner, Chemical Physics Letters 29, 277 (1974).
 A. Dhirani et al., Journal of Chemical Physics 106, 5249 (1997).
 J. Taylor et al., Physics Review Letters 89, 138301 (2002)
 K. Stokbro et al., Journal of the American Chemical Society 125, 3674 (2003).
Calculated current-voltage characteristics of a p-n molecular junction. The rectification in the system is very low.
Figure 8b Visualization of a current carrying orbital, i.e. a scattering state. Due to the sigma bridge between the two conjugated parts of the molecule, only a small fraction of the orbital is transmitted through the system.
Absorption Geometry and Fluctuations Case Study 15.Feb.2007 00:22 Category: VNL & ATK Case Studies
The interface between organic molecules and metallic surfaces in moletronic devices is complex and the detailed structure of the
metal-molecule-metal system is often unknown. Organic molecules are typically not rigid at room temperature and it is expected that fluctuations may play a role in such devices. While it is impossible to measure or manipulate the detailed structure experimentally, it is natural to use modeling software to create a number of target structures and study in detail how the energetics and electronic properties are correlated with the structure. Prof. Marc Ratner and colleagues have performed studies of the effect of fluctuations on current in different absorption geometries, concluding that the local symmetry of the molecule/metal contact can have great influence on the current changes under fluctuations. 
Researchers at the Chinese Academy of Sciences compared current conduction in two different molecules: an insulating alkane chain and a bi-pyridine molecule with a delocalized molecular p state.  Transport in the alkane occurs through non-resonant tunneling and its electronic properties are much more robust to changes in adsorbtion geometry. The transport in the pi-system occurs by
resonant tunneling through the delocalized pi-states, a mechanism which is much more sensitive to the local geometry.
 H. Basch et al., NanoLetters 5, 1668 (2005).
 Y. Hu et al., Physics Review Letters 95, 156803 (2005).