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nanoXplorer IDE User Guides
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1.1. Nanodevice design tutorial

This tutorial takes you step-by-step through creating a nanodevice design, including creating a NanoFile, adding nanoscale components, editing those components and saving the design.

 

Start >> Open the Design Perspective

1.1.1. Open the Design Perspective

The Design Perspective is the home of many of the Views and Editors that you will use during the design process, so start this tutorial by opening it, if it is not already open.

There are two ways to open the Design Perspective. The fastest way is to use the perspective menu located toward the upper right hand corner of the workspace. Alternatively, select Design from the Open Perspective menu item under the application's Window menu.

The Design Perspective is the default perspective of nanoXplorer IDE.

 

     

 

Next >> Open the Workspace View

1.1.2. Open the Workspace View

The Workspace View shows you the resources that you have in your workspace. In particular it is able to look inside NanoFiles (nanodevice design files) and see their contents. It also serves as a sort of control panel for the design process so let's open that, if it is not already visible, by selecting Window > Show View > Workspace.

 


An example Workspace View

 

Next >> Create a new project

1.1.3. Create a new project

Projects are a convenient way to organize nanodevice designs and related files. While the workspace includes a default project, create a new one for this tutorial.

  • Select File > New > Project... from the main application menu.
  • Use the New Project Wizard to name and create the new project.

 

Next >> Create a new folder

1.1.4. Create a new folder

Folders provide a way to further organize files. Create a new folder in our new project and name it "tutorial."

  • Select File > New > Folder... from the main application menu.
  • Use the New Folder Wizard to set its parent project and name and create the folder.

 

Next >> Create a new NanoFile

1.1.5. Create a new NanoFile

A NanoFile is a special file that contains nanodevice designs and related information. Create a new NanoFile so that you can begin creating a new nanodevice design.

There are two ways to create a new NanoFile:

  1. Use the File > New > Other...menu command from nanoXplorer IDE's main menu bar.
  2. Select the NanoFile wizard in the dialog.
  3. Select a name and parent for the new NanoFile and press the Finish button.

or

  1. Open the Design Perspective.
  2. Open the Workspace View, if necessary.
  3. Press the New NanoFile button () on the Workspace View toolbar.
  4. Select a name and parent for the new NanoFile and press the Finish button.

 

Both of these actions will create a new NanoFile and place it in the workspace at the specified location. If the Workspace View is open, the NanoFile will be immediately visible in the project, folder and file hierarchy.

 

Next >> Open the NanoFile

1.1.6. Open the NanoFile

You created a NanoFile in the previous step; now you would like to open it for editing.

Simply locate the Nanofile in the Workspace View and double-click on it. This will open the NanoFile Editor for that NanoFile. Be patient; it may take a few moments for the Editor window to come up as it needs to load the advanced three-dimensional interactive environment.

The NanoFile Editor, once visible, will show empty space because you haven't added anything yet.

 

Next >> Add components to the NanoFile

1.1.7. Add components to the NanoFile

To keep this basic tutorial simple, you will only add one component to the NanoFile. In a real design process, of course, this is where most of the hard work would take place. Selecting, modifying, positioning, orienting, and connecting components with atomistic precision could take days for a complex nanodevice design.

Double-click the Nanotube widget in the Widgets View. This should open the New Nanotube Wizard. If you want to try and set parameters for the nanotube, go ahead and do so, however, for the tutorial all you need to do is press "Finish" to create the default nanotube.

  • For just a taste of the editing capabilites at your disposal, try moving the nanotube (grab the nanotube with left mouse button and drag it somewhere). Or you can change the orientation by dragging with the right mouse button.
  • If you want to change your viewpoint, drag on the scene background.
  • Try to bring up the context menu (right-click on Windows and Linux) for some of the atoms and bonds in the nanotube.

More comprehensive information about the NanoFile Editor is offered outside this tutorial.

 

Next >> Save the NanoFile

1.1.8. Save the NanoFile

Now that you have edited the NanoFile, you may want to save the changes. Make sure the NanoFile Editor has focus (for example, by clicking on its tab) and press the save button on the main application toolbar.

Close the editor window and open the NanoFile a second time. The nanotube should be there just as you left it.

2.1. Nanoscale device design

The promise of nanotechnology is that someday we'll be able to create a myriad of nanoscale devices that can do everything from prevent disease to clean our environment to suffuse our surroundings with massive computing power... and all that would make possible.

Manufacturing technology will have to come a long way before such things are possible. However, designing such nanodevices is possible today, if one does not worry about the hard problems involved in going from blueprint to real world and the mass production that would have to be available for nanoscale devices to make any meaningful impact. Moreover, some simpler real world nanotechnology applications are available today and enhancing actual products, such as nanoparticle coatings, nanofibers in textiles and nanoscale electronic components. Clearly we are at the beginning of a technological revolution that will transform the world, but the scientists and engineers who are trying to turn these possibilities into realities need tools to help them.

The process of nanoscale device design is similar to aircraft design, automobile design and even, in some respects, software design. It requires hierarchical organization, libraries of reusable parts, advanced visualization and interactivity, teams working together, subsystems of varying complexity and the interfaces between them, and a file format for capturing the design, among many other things.

nanoXplorer IDE sits at the cross-section of chemistry and engineering, providing all the tools to do realistic work with nanoscale components while preserving the function of macroscale computer-aided design systems. It enables teams to work with nanoscale device designs efficiently and powerfully, supporting the design process from the very first inkling of an idea all the way to full-fledged complex design that has been simulated in its target environment and is ready for real world prototyping by some yet to be realized desktop nanoscale device factory.

2.2. The Nanodevice Model

A nanodevice may be defined as "molecules with a purpose." It is a device in the sense that it can be used for something (whether simple or complex) and it is "nano" in the sense that it is characterized by parts that are best measured in nanometers (one billionth of a meter, about the size of a small molecule). The term usually implies that human engineering has played some part in its conception, though some interesting nanodevices are also found in nature. This definition encompasses everything from simple nanowires that do nothing but conduct electricity to complex "nanobots" that are perhaps mobile, autonomous and capable of various functions. Thus nanodevices are both routinely available in today's labs and speculative engineering that will unfold over decades to come. nanoXplorer IDE enables design of the full range of nanodevices.

nanoXplorer models nanodevices as a hierarchical collection of nanosystems, connections, molecular devices, interfaces, device components, molecular components and spatial components. Each is described below:

  • Nanosystem - the top-most level of the hierarchy, contains subsystems and subdevices
  • Molecular Device - consists of device components
  • Device Component - consists of molecules and volumes
  • Molecule - small or large
  • Volume - region of space with particular properties and appearance
  • Interface (not shown) - a nanodevice component may include any number of interfaces
  • Connection (not shown) - a connection between two nanodevice component interfaces

 

2.2.1. Nanosystem

A nanosystem is a nanodevice able to perform some number of functions or fulfill some number of purposes and is typically characterized by at least two distinguishable subcomponents, either subsystems or component molecular devices. Nanosystems represent complex nanodevices and because they can recursively contain nanosystems as subcomponents, their potential complexity is unbounded.

An example of a nanosystem would be a nanobot, with subsystems for communication, computation, locomotion and power.

Nanosystems sit atop the nanodevice component hierarchy and can only have other nanosystems or NanoFiles as parents.

 

2.2.2. Molecular device

A molecular device is a nanodevice with a single primary functionality or purpose. It may consist of any number of device components and itself may be part of a larger nanosystem.

An example of a molecular device would be a nanodiode. The nanodiode would perform a single primary function (regulating current flow) but would consist of a number of uniquely identifiable components (such as the anode and cathode). In turn the diode could be part of a larger system, such as a nanotransistor or nanocircuit.

 

2.2.3. Device component

Device components occupy a middle level of the nanodevice hierarchy, bridging the gap between molecules and functional molecular devices. Devices typically consist of a number of identifiable pieces and this is the role of device components, to group related molecules and volumes together as desired for easier manipulation and to facilitate an intuitive conceptual model for design.

Examples of device components would be the anode and cathode of a nanodiode. The nanodiode itself rises to the level of molecular device since it has a specific functionality (regulating current flow), while the anode and cathode are identifiable pieces of that device.

 

2.2.4. Molecular component

Molecules (a.k.a. molecular components) occupy the lowest level of the nanodevice component hierarchy. Any number of molecules (and volumes) may be included in a single device component. For pieces of a nanodevice design that need to be atomically precise, molecular components must be used.

The term "molecule" is a bit misleading as it is not required that all of the constituent atoms be bonded together. The preferred term is "molecular component"; molecular components are understood to contain atomic systems, which in turn could actually contain more than one molecule.

 

2.2.5. Volume

Volumes, like molecular components, occupy the lowest level of the nanodevice component hierarchy. Unlike molecular components however, volumes are used to represent components whose atomistic detail is either unknown or unimportant. This facilitates development of large nanodevice designs and models with atomistic precision only where necessary. A number of primitive volume shapes are available (such as sphere, box, pyramid, etc), which can be combined to make more complex volumes.

 

2.2.6. Interface

Any nanodevice component may contain interfaces. An interface indicates that the component may be connected to other components in some way. Interfaces can only be connected to compatible interfaces.

For example, a chemical interface will identify particular atoms that are available for bonding with outside components. Other types of interfaces are possible, such as electromagnetic. physical and remote.

 

 

2.2.7. Connection

Two nanodevice components may be connected. This connection must occur between two compatible interfaces.

Connections are useful when a close relationship exists between two identifiable components and the components will not be merged into a single component for design or any other reasons. The connection may be chemical in nature and represent bonds between atoms in the two components. The two connected components will remain distinct however, which can aide the design process as each component can still be positioned, oriented and edited individually.

Chemical connections are only one example type of connection. Other connections may be physical, electromagnetic or remote in nature.

 

 

2.3. Workspace

The Workspace View is the main control center in the Design Perspective. The workspace is where you will keep your projects, folders, NanoFiles and other files.

 

Example Workspace View

2.4. Widget

A widget is any component that can be added to a NanoFile. These include the standard components of the nanodevice hierarchy (nanosystem, molecular device, device component, molecular component and volume), but also include specialized components such as nanotubes, DNA, and buckyballs. Available widgets are found in the Widgets View.

 

Typically, a widget will have an associated wizard--launched by double-clicking on the widget in the Widgets View or dragging the Widget icon to the Workspace and dropping it at the desired place in the component hierarchy--that will aid the customization of the component.

Custom widgets can be added to nanoXplorer IDE through the extensibility mechanism.

2.5. NanoFile

The NanoFile is the main working product of the nanodevice design process in nanoXplorer IDE. A NanoFile holds a collection of top-level nanodevices and/or nanodevice components, each of which may have any number of subcomponents.

NanoFiles have the extension ".nano". NanoFiles are actual files that reside on your computer and can be manipulated like any other file. NanoFiles consists of a single nanoML entry that describes the nanodevices and nanodevice components and any number of data files all zipped together into a single file. Due to the compression and the separation of description from data, NanoFiles are an efficent and flexible storage solution for nanodevice designs.

The first step when designing a new nanodevice is to create a new NanoFile, the permanent container for that nanodevice design. Then components can be added to the NanoFile

 

2.6. Shared NanoFile

A shared NanoFile is a NanoFile that has been "published." Multiple networked users can connect to a shared NanoFile, enabling collaborative design and engineering of nanoscale devices.

Any user can publish a NanoFile from his or her workspace.

2.7. nanoML®

nanoML is a markup language--used to represent nanodevice designs and related information--developed by nanoTITAN and placed in the public domain. It has enjoyed widespread application in the nanotechnology community for capturing and communicating information about nanodevices. It is used internally by nanoXplorer IDE as part of the NanoFile specification to store nanodevice information.

2.8. Atomic System

An atomic system is like a molecule, only more generalized. Atomic systems contain nuclei at specific positions and bonds between them. Unlike a molecule, however, not all of the nuclei are necessarily bonded into a single entity.

In nanoXplorer IDE molecular components contain atomic systems rather than molecules to take advantage of this increased flexibility.

The data for atomic systems is kept in an ".ash5" file (a contraction of atomic system and h5, which is the standard extension for Hierarchical Data Format (HDF) files).

 

2.9. Coordinate system

The coordinate system used throughout nanoXplorer IDE is a right-handed orthogonal coordinate system with the x-axis to the right, the y-axis straight up and the z-axis toward the viewer as pictured below. The design universe, the viewer and all nanodevice components have their own associated coordinate systems.

 

3.1. Opening the Design Perspective

The Design Perspective contains a default set of views and editors useful for performing nanoscale device design.

There are two ways to open the Design Perspective. The fastest way is to use the perspective menu located toward the upper right hand corner of the workspace. Alternatively, select Design from the Open Perspective menu item under the application's Window menu.

 

     

3.2. Creating a new NanoFile

There are two ways to create a new NanoFile:

  1. Use the File > New > Other...menu command from nanoXplorer IDE's main menu bar.
  2. Select the NanoFile wizard in the dialog.
  3. Select a name and parent for the new NanoFile and press the Finish button.

or

  1. Open the Design Perspective.
  2. Open the Workspace View, if necessary.
  3. Press the New NanoFile button () on the Workspace View toolbar.
  4. Select a name and parent for the new NanoFile and press the Finish button.

 

Both of these actions will create a new NanoFile and place it in the workspace at the specified location. If the Workspace View is open, the NanoFile will be immediately visible in the project, folder and file hierarchy.

3.3. Editing a NanoFile

To open the NanoFile editor either:

  1. Double-click on the NanoFile (or any of its components) in the Workspace View, or
  2. Select Open from the NanoFile's popup context menu (right mouse click on most operating systems).

 

Using the NanoFile Editor

The NanoFile Editor consists of a number of tabs that enable looking at and editing the NanoFile's contents in various ways. The nVisualizer tab presents the powerful interactive 3D visualization and editing environment where most editing will likely occur.

3.4. Creating a new nanodevice component

To create a new nanodevice component:

  1. Open the Design Perspective, if necessary. (Window > Open Perspective > Design).
  2. Open the Widgets View, if necessary (Window > Show View > Widgets).
  3. Double-click on the desired component widget in the Widgets View or drag the widget to the desired location in Workspace View.
  4. Select a name and parent for the new component.
  5. Set parameters as necessary in the component's creation wizard. Each component's creation wizard will be unique.

 

The newly created nanodevice component will be immediately visible in the Workspace View. If the associated NanoFile editor is open then the newly created component will be selected.

3.5. Editing a nanodevice component

To edit a nanodevice component:

  1. Open the Design Perspective, if necessary. (Window > Open Perspective > Design).
  2. Open the Workspace View, if necessary (Window > Show View > Workspace ).
  3. Double-click on the component in the Workspace View. This will open the editor for the parent NanoFile and select the component.
  4. Edit the component with the nVisualizer editor.

 

Editing nanodevice components with the nVisualizer Editor

The nVisualizer editor (available by selecting the nVisualizer tab of the NanoFile Editor) provides an advanced interactive 3D environment where nanodevice components can be positioned, oriented and modified enabling atomically precise designs.

 

3.6. Editing a molecular component

To edit a molecular component:

  1. Open the Design Perspective, if necessary. (Window > Open Perspective > Design).
  2. Open the Workspace View, if necessary (Window > Show View > Workspace ).
  3. Double-click on the molecular component in the Workspace View. This will open the editor for the parent NanoFile and select the molecular component.
  4. Edit the molecular component with the nVisualizer editor.

 

Editing molecular components with the nVisualizer Editor

The nVisualizer editor (available by selecting the nVisualizer tab of the NanoFile Editor) provides an advanced interactive 3D environment where molecular components can be positioned, oriented and modified, enabling atomically precise designs.

Special editing capabilities for molecular components include:

  • positioning individual atoms
  • editing atom types
  • adding and removing individual atoms; merging atoms
  • adding and removing individual bonds
  • editing bond order, type and length
  • revolving and rotating bonds and branches

Read more about the nVisualizer Editor.

 

 

 

3.7. Sharing a NanoFile

To establish a collaborative session for viewing and editing a NanoFile over a network, follow these steps:

  1. Open the Design Perspective.
  2. Open an existing NanoFile (so that its NanoFile Editor is displayed).
    - double-click on a NanoFile in the Workspace View, or
    - open the context menu for a NanoFile (typically by right-clicking) and select "Open"
  3. Press the Publish NanoFile button () in the application toolbar to open the Share NanoFile Wizard (shown below).



    The Share NanoFile Wizard

  4. Select a name for the shared NanoFile; this is the name that subscribers will see. Also select a port over which the collaborative communication will be established. The network will have to allow traffic between the computers on the specified port; if necessary, contact your network administrator for assistance as some router and/or firewall setting might have to be adjusted.
  5. Make selections for client editing and locking the client view. Enabling client editing means that the NanoFile can be modified by any subscribers, a truly collaborative design environment. Locking the client view means that subscribers are forced to see the same view as the current owner's view; otherwise they are free to navigate on their own.
  6. Press Finish. If the NanoFile is successfully shared, you should see a message like this:


    The NanoFile's icon will change in the Workspace View to indicate that the NanoFile is currently being shared.

 

 

 

3.8. Subscribing to a shared NanoFile

Owners of NanoFiles can publish them so that others can work with them collaboratively over a network. To subscribe to a published NanoFile:

  1. Open the Design Perspective, if necessary.
  2. Open the Workspace View, if necessary.
  3. Press the New NanoFile Button () on the Workspace View. This will open the New NanoFile Wizard.
  4. Enter a name for the new NanoFile.
  5. Press the "Subscribe>>" button near the bottom of the new NanoFile Wizard.



  6. Example New NanoFile Wizard with subscription enabled


  7. Enter the IP address or host name of the computer from which the NanoFile was published. Also enter the port number on which the NanoFile was published. This information will have to be provided by the person who shared the NanoFile.
  8. Press the "Connect" button. After a few seconds the application will indicate either a successful connection or that the published NanoFile was not found.
  9. Once a successful connection has been made, press "Finish." The NanoFile Editor for the shared NanoFile will open and the shared NanoFile will be added to your workspace. Your ability to view and edit the shared NanoFile is controlled by the publisher.

 

3.9. Creating a video

To create a video:

  1. Open the Design Perspective, if necessary.
  2. Open the Workspace View, if necessary.
  3. Open a NanoFile.
  4. In the NanoFile Editor select the nVisualizer tab.
  5. With a 3D scene visible in the nVisualizer Editor, bring up the context menu and select "Create Video..." This will launch the Create Video Wizard.
  6. Create the video uising the Create Video Wizard.

 

 

 

4.1.1.1. NanoFile Editor

The NanoFile Editor is a multi-page editor for manipulating content of NanoFiles, nanodevice design specifications. The main page (nVisualizer Editor) presents an advanced 3D interactive environment in which to design a nanodevice with atomic precision. Additional pages provide supporting information and editing capabilities, such as the nanoML editor that allows direct editing of the internal nanodevice representation.

An asterisk in the tab title indicates that the NanoFile has been edited and should be saved.

The NanoFile multi-page editor includes the following single-page editors:

  • nVisualizer Editor
  • nanoML Editor

 


The NanoFile Editor is a multi-page editor; select a tab on the bottom to go to the desired editor

 

 

4.1.1.1.1. nVisualizer Editor

The nVisualizer Editor, part of the NanoFile multi-page editor, provides an advanced three-dimensional interactive environment for nanodevice design.

  • Toolbar
  • Menus
  • Interactivity
  • Scale
  • Outline View
  • Reference coordinate system

 

The nVisualizer Editor provides an advanced 3D interactive environment for nanodevice design

 

Toolbar

When the nVisualizer Editor is active, the following buttons are available on the application toolbar.

Button
Description
Toggle selection highlights; when pressed the selected components will be fully illuminated in the 3D scene while other components will be more dimly lit.
Return to the "home" view. The home view is, by default, a view of all the components from the front, however the home view can be set by the user (via the scene's pop up menu).
Zoom in on and center the scene's components.
Center the scene's components.
View the scene's components from the front.
View the scene's components from the back.
View the scene's components from the top.
View the scene's components from the bottom.
View the scene's components from the left.
View the scene's components from the right.

 

Menus

Scene Menu

The scene menu can be displayed by right-clicking on scene background (where there are no components).

Atom Menu

The atom menu can be displayed by right-clicking on a nucleus.


Add Atom

Adds a new atom of the same type as the selected atom and bonds it to the selected atom. The new atom's type may be changed via its Property Dialog.

Set Origin Component

Sets the selected atom as the origin of its parent molecular component. Component rotations and translation will thereafter be relative to the selected atom's location.

Delete Atom

Removes the atom from its parent molecular component.

Molecular Component

Displays the molecular component menu.

Properties

Opens the Property Dialog for the atom.

Bond Menu

The bond menu can be displayed by right-clicking on a bond.

Set Bond Length to Default

For a bond with two members, sets the bond's length to the default length of a bond between two atoms of the associated types.

Delete Bond

Removes the bond from the molecular component.

Molecular Component

Displays the molecular component menu.

Properties

Opens the Property Dialog for the bond.

Nanodevice Component Menu

The nanodevice component menu can be displayed by right-clicking on an atom or bond and then selecting the menu item for its parent molecular component (which will contain a menu item for its parent and so on). The options available may vary for different component types, but the following menu is typical:

Delete

Delete the component.

Select/Deselect

Select or deselect the component.

Center

Center the component in the view.

Zoom

Center and zoom in on the component in the view.

Properties

Open the Property Dialog for the component.

Interactivity

The following tables summarize the mouse and keyboard interactivity available through the nVisualizer Editor:

  • Nanodevice component interactivity
  • Molecular component interactivity

Nanodevice component interactivity

Interactivity Mouse/Keyboard Action

Translate a component

  • in the current view's x-direction only
  • in thecurrent view's y-direction only
  • in the current view's z-direction only
  • in the current view's xy-plane
  • in the current view's xz-plane
  • in the current view's yz-plane

<Mouse LEFT DRAG>

  • <Mouse LEFT DRAG> + <Press 'x'>
  • <Mouse LEFT DRAG> + <Press 'y'>
  • <Mouse LEFT DRAG> + <Press 'z'>
  • <Mouse LEFT DRAG> + <Press 'x'> + <Press 'y'>
  • <Mouse LEFT DRAG> + <Press 'x'> + <Press 'z'>
  • <Mouse LEFT DRAG> + <Press 'y'> + <Press 'z'>

Orient a component

  • around the current view's x-axis
  • around the current view's y-axis
  • around the current view's z-axis

<Mouse RIGHT DRAG>

  • <Mouse RIGHT DRAG> + <Press 'x'>
  • <Mouse RIGHT DRAG> + <Press 'y'>
  • <Mouse RIGHT DRAG> + <Press 'z'>
Pop up/context menu <Mouse RIGHT>
Select <Mouse LEFT CLICK>
Extend Select <Mouse LEFT CLICK> + <SHIFT>
Toggle Select <Mouse LEFT CLICK> + <CTRL>

 

Molecular component interactivity

Molecular components include all of the interactivity described above and also all of the following:

Interactivity Mouse/Keyboard Action

Translate an atom

  • in the current view's x-direction only
  • in the current view's y-direction only
  • in the current view's z-direction only
  • in the current view's xy-plane
  • in the current view's xz-plane
  • in the current view's yz-plane

<Mouse LEFT DRAG> + <CTRL>

  • <Mouse LEFT DRAG> + <Press 'x'> + <CTRL>
  • <Mouse LEFT DRAG> + <Press 'y'> + <CTRL>
  • <Mouse LEFT DRAG> + <Press 'z'> + <CTRL>
  • <Mouse LEFT DRAG> + <Press 'x'> + <Press 'y'> + <CTRL>
  • <Mouse LEFT DRAG> + <Press 'x'> + <Press 'z'>+ <CTRL>
  • <Mouse LEFT DRAG> + <Press 'y'> + <Press 'z'> + <CTRL>
Create a new bond <Mouse RIGHT DRAG> + <SHIFT> between two nuclei
Revolve branch <Mouse LEFT DRAG> + <SHIFT> + <CTRL> over a bond
Rotate bond <Mouse LEFT DRAG> + <ALT> + <CTRL> over a bond
Merge atoms <Mouse LEFT DRAG> + <SHIFT> + <CTRL> between two nuclei
Show atom/bond context menu <Mouse RIGHT CLICK> over nucleus/bond
Open atom/bond Property Dialog <Mouse LEFT DOUBLE-CLICK> over nucleus/bond

 

Scale

The scale slider enables quick control over the design length scale, in powers of ten from Ã?ngstroms to meters. The default scale is nanometers. The scale uses the following symbols and icons:

Symbol/Icon
Description
Ã?
Ã?ngstrom; 1x10-10 m or one tenth of a nanometer. Bond lengths between atoms are typically about an Ã?ngstrom in length.
nm
nanometer; 1x10-9 m or one billionth of a meter. The size of small molecules can be conveniently measured in nanometers.
10 nm; 1x10-8 m. About the size of a small DNA molecule.
100 nm; 1x10-7 m. About the size of some viruses.
µm
micrometer; 1x10-6 m or one millionth of a meter. Also called "microns."
10 µm; 1x10-5 m. Approximately the size of a neuron cell.
100 µm; 1x10-4 m. Seeing anything smaller than this typically requires a microscope. Approximately the diameter of a human hair.
mm
millimeter; 1x10-3 m or one thousandth of a meter.
cm
centimeter; 1x10-2 m or one hundredth of a meter.
decimeter; 1x10-1 m or one tenth of a meter. About the size of a human brain.
m
meter; a bit more than three feet.

 

Outline View

The nVisualizer Editor provides an enhanced version of standard Outline View.

 


Enhanced Outline View

 

Toolbar

Hide/Show Component

Toggles the visibility of the selected component in the nVisualizer Editor.

Menu

Refresh

Makes sure the outline is up to date with any outside changes.

Show All

Any hidden components will be shown.

 

 

4.1.1.1.2. nanoML Editor

The nanoML Editor displays the current nanoML description of the components in the associated NanoFile.

In the current version of nanoXplorer IDE, the nanoML text cannot be edited directly and is provided for informational purposes only.

 


An example nanoML description in the nanoML Editor

 

4.1.1.2. Workspace View

The Workspace View displays the projects, folders and files in your current workspace. It shows the components inside of NanoFiles and is designed to facilitate the design process.

  • Icons
  • Toolbar
  • Menus

 


An example Workspace View

 

Icons

The following icons are used to represent content in the Workspace View:

Icon
Description
A project, which can hold any number of files and folders
A folder, which can contain any number of files and subfolders
NanoFile
Nanosystem
Molecular device
Device component
Molecular component or molecule
Volume
Component interface
Component connection
File

Additional icons may be used, such as those added by nanodevice component and widget extensions.

 

Toolbar

Collapse all

Show only the projects in the workspace.

New NanoFile

Opens the New NanoFile Wizard.

 

Menus:

Toolbar Menu

Refresh

Updates the Workspace View contents to match the local filesystem. This can be useful when changes are made outside of nanoXplorer IDE.

Context Menu

The items in the pop up context menu depend upon the type of the content selected in the Workspace View. The following commands may be available:

Open

Launches an editor for the selected content.

Copy

Copies the selected content to the clipboard.

Cut

Removes the selected content from the workspace and places it on the clipboard.

Paste

Adds any content in the clipboard to the selected component (or its first appropriate ancestor).

Rename

Provide a new name for the selected content.

Delete

Remove the selected content (and any children) from the workspace.

Properties

Open the Properties Dialog for the selected content.

 

4.1.1.3. Widgets View

The Widgets View presents all of the components available for creation. Double-click an icon to launch the associated "New Wizard" or drag and drop the icon to the desired place in the content hierarchy in the Workspace View (or directly on to the nVisualizer Editor).

 


An example Widgets View

 

Widget Sets

Widgets are displayed according to the selected widget set. The p[ull down menu enables selction of a particular widget set or managing widget sets with a dialog.

 


The Manage Widget Sets Dialog

 

4.1.2.1. New NanoFile Wizard

The New NanoFile Wizard creates a new NanoFile with a user-specified name and in a user-specified project or folder in the current workspace.

 

Example New NanoFile Wizard

 

It also allows subscribing to a published NanoFile. Join a collaborative session by pressing the "Subscribe >>" button and then specifying the IP address of the host that has published the NanoFile, as well as the port on which the NanoFile was shared. This information will need to be provided by the person who published the NanoFile..

 

Subscribe to a published NanoFile to enter a collaborative session

 

4.1.2.2. Export Scene Wizard

The Export Scene Wizard enables capturing an image of the current scene or saving the current scene graph to a file. A pull down menu presents the supported image formats. Pressing "Finish" will open the standard Save Dialog so that the exported file can be named and located as desired.

 


Export Scene Wizard

 

 

4.1.2.3. Create Video Wizard

The Create Video Wizard presents a two step process for generating a video.

Scripting the Camera

The first step is to define the path and orientation of the camera (or viewpoint) through the scene. This is done by adding nodes along a timeline; each node represents a specific view.

  • Timeline toolbar
  • Timeline
  • Scene

 

Script the camera's movements on the first page of the Create Video Wizard

 

Timeline Toolbar

Duration

Set the duration of the video by choosing from among predefined durations or by adding a custom duration.

Play

Simulates what the video will look like with the current setting by performing a camera "fly-through."

Loop

If selected and the timeline is playing, then the fly-through will repeat once it reaches the end of the timeline.

Add Node

Adds a new node, having the current view (as displayed by the scene preview), at the current time (as set by the slider on the timeline).

Copy Node

Copies a selected node to the clipboard.

Paste Node

Pastes a node from the clipboard on to the timeline at the current time.

Delete Node

Removes the selected node from the timeline.

Timeline

Time Thumb

The current working time is controlled by the thumb slider in the timeline. Drag the time thumb left or right to change the current working time. The scene will render the view at that specific time. The current working time is displayed just above the thumb.

Nodes

Nodes represent specific viewpoints (camera positions and orientations) and are drawn as circles with lines down to the timeline. Their specific place along the timeline indicates that the associated viewpoint used at the specific time.

Add a node at the current time by pressing the Add Node button () on the timeline toolbar.

Nodes can be dragged and dropped to any time along the timeline.

Select a node by clicking on it. Selected nodes can be copied, cut and deleted. Selecting a node causes the current working time to be changed to the node's time.

Scene

The scene reflects the view (camera position and orientation) at the current time selected on the timeline. To enter a new view, navigate in the scene to the desired view and then add a node for that view.

 

Defining the output

The second step to create a video is to define its output parameters, including its name and location, format, dimensions, and frames per second.

 

Set video name and parameters on the Create Video Wizard's creation page

 

File name

Name of the new video file.

Output folder

Location of the new video file.

Format

Format of the new video. QuickTime recommended for best results.

Image quality

Quality of the images used to generate the video. Higher quality will look better but generate a larger vide file.

Video dimensions

The desired size of the new video, which need not be the same as the size of the scene window.

Frames per second

Higher frames per second leads to less flicker and smoother animation, but also longer processing time and a larger video file. For reference, 20-30 frames per second will usually yield acceptable results.

Disable editing during frame capture

If selected, disallows and edits to the scene while images are being captured.

Delete frame files after video creation

If selected, temporary image files are deleted, leaving only the new video file.