3. Graphical Interface Introduction

The Device Studio graphical interface is shown in fig. 3.1.

fig. 3.1 Device Studio Graphical Interface

3.1. Menu Bar

The Device Studio menu bar graphical interface is shown in fig. 3.2.

fig. 3.2 Menu Bar

3.1.1. File

Click on File, and the interface is shown in fig. 3.3.

fig. 3.3 File

• New Project: Opens the new project interface where users can create a new project with the file extension .hpf. Users can name the project as needed, such as DeviceStudio.hpf, or use the default name, such as Untitled.hpf. After naming, click the “Save” button to create the project; otherwise, if you don’t want to create a new project, click the “Cancel” button.

• Open Project: Opens the project interface where users can open an existing project, such as the DeviceStudio.hpf project. Find and select the project file, then click the “Open” button to open it; otherwise, if you don’t want to open the project, click the “Cancel” button.

• Save Project: Saves the current project.

• New: Users can choose to build device, crystal, or molecular structures as needed.

• Import: Opens the structure file import interface where users can choose to import device, crystal, or molecular structures from local or online databases.

• Export: Opens the structure file export interface where users can name the structure file as needed or use the default name and choose the storage location.

• Options: Opens the options interface where users can choose the pseudopotential basis set file, set the background color of Device Studio, and refresh time.

• Exit: Closes the Device Studio software.

3.1.2. Edit

Click on Edit, and the interface is shown in fig. 3.4.

fig. 3.4 Edit

• Undo: Undoes.

• Redo: Redoes.

• Copy: Copies.

• Paste: Pastes.

• Delete Atom: Deletes the selected atom.

• Atom Selection: Selects specific atoms of a specific element in the selected atoms. Users can select specific atoms as needed. For example: First, select a part of the atoms, then select all C atoms in the selected part of the atoms.

3.1.3. View

Click on View, and the interface is shown in fig. 3.5.

fig. 3.5 View

• Toolbars: Users can choose whether to display the Project, Standard, 3D View modules in the toolbar. If displayed, select the corresponding modules; otherwise, do not select.

• Explorers: Users can choose whether to display the Project Explorer, Properties Explorer, and Job Manager modules on the software. If displayed, select the corresponding modules; otherwise, do not select.

• Status Bars: Select to display the module on the software; otherwise, do not display.

• Display Style: Opens the DisplayStyle setting interface. For atoms, users can choose not to display, display in line form, or display in ball stick form. For lattice basis vectors, users can choose not to display, display in solid line, or display in dashed line. If displayed in solid line, users can set the line thickness as needed.

• generate GIF: Opens the generategif interface where users can import a series of existing pictures and generate a dynamic graph with the file extension .gif, then export the dynamic graph.

3.1.4. Build

Click on Build, and the interface is shown in fig. 3.6.

fig. 3.6 Build

• Molecule: Builds a 3D molecular structure.

• Molecule2D: Builds a 2D molecular structure.

• Decomposition: Decomposes a molecular structure.

• Device: Builds a device structure. Device types include L-R structure, L-C-R structure, B-T structure, etc. Users can choose to build according to their needs.

• Convert to Device: Builds a device structure on the basis of molecular or crystal structure.

• Bending of Device: Performs bending operation on two-port device structure.

• Interface Builder: Builds heterojunction structure.

• Fill Junction With Atoms: Builds multilayer membrane structure.

• CAD to Atomic: Builds multilayer membrane structure through 2D CAD.

• Crystal: Builds a crystal structure.

• Redefine Crystal: Crystal cell redefinition and expansion.

• Surface/Slab: Crystal structure cut surface/slice.

• Symmetry: Performs space group recognition on crystal structure.

• StandardizeCell: Super cell recognition primitive cell.

• Gr_Nanoribbon: Builds nanoribbon structure.

• Gr_Nanotube: Builds nanotube structure.

• Grain Boundary: Builds crystal boundary structure on basis of unit cell.

• Nanotube: Builds nanotube on basis of crystal structure.

• Nanowire: Builds nanowire on basis of crystal structure.

• Disordered Graphene-like: Builds disordered graphene-like structure.

• Disordered Zinc-blende-like: Builds disordered zinc-blende-like structure.

• Icosahedron: Builds regular icosahedron structure.

• Cubooctahedron: Builds regular cubooctahedron structure.

• WulffCluster: Builds WulffCluster structure on basis of unit cell.

• Bond Options: Bond setting.

• Convert Files: Structure file conversion.

3.1.5. Simulator

Click on Simulator, and the interface is shown in fig. 3.7. Users can choose the corresponding module according to their needs to generate input files for corresponding software, calculate, and visualize data.

fig. 3.7 Simulator

• BDF: Quantum chemistry calculation software BDF.

• DS-PAW: First-principles plane wave calculation software DS-PAW.

3.1.6. Window

Click on Window, and the interface is shown in fig. 3.8.

fig. 3.8 Window

• Title Horizontally: Horizontally arranges 3D Viewer windows of structure files.

• Title Vertically: Vertically arranges 3D Viewer windows of structure files.

• Cascade: Stacks 3D Viewer windows of structure files.

• Arrange Icons: Minimizes 3D Viewer windows of structure files.

• Close All: Closes 3D Viewer windows of structure files.

• Next: Selects the next 3D Viewer window of structure file.

• Previous: Selects the previous 3D Viewer window of structure file.

3.1.7. Help

Click on Help, and the interface is shown in fig. 3.9.

fig. 3.9 Help

• Getting Started With Device Studio: Connects Device Studio Quick Start Guide.

• Device Studio Tutorials: Connects Device Studio Usage Tutorial.

• Feed Back Report: Opens the Hongzhiwei Customer Information Feedback Collection Interface where users can provide product suggestions to Hongzhiwei.

• Hzwtech Homepage: Connects Hongzhiwei Technology (Shanghai) Co., Ltd. Homepage.

• About Device Studio: Opens the About Device Studio window to understand the Device Studio version number, issuing company, License usage period, etc.

• Article Reference Template: Opens the Device Studio Article Reference Template to facilitate correct citation of Device Studio in articles.

3.2. Toolbars

The Device Studio toolbars are shown in fig. 3.10. The numbers from left to right are numbered from 1 to 38. The English name of the icon can be viewed by placing the mouse arrow on the icon.

fig. 3.10 Toolbars

Number	Icon	Icon English Name	Function Description
1		Open Project	Opens Device Studio project file
2		Save Project	Saves current project and structure
3		New	Builds new structure, through which you can select to build device, crystal | or molecular structure
4		Import Local	Imports structure file from local
5		Undo	Undoes
6		Redo	Redoes
7		3D Viewer Selection Mode	Selects, clicks to enter selection mode, can select atoms by mouse click or drag to select
8		3D Viewer Rotation Mode	Rotates, clicks to enter rotation mode, can rotate 3D view of atom structure by dragging mouse
9		3D Viewer Zoom Mode	Zooms in or out, clicks to enter zoom mode, can zoom 3D view of atom structure by scrolling mouse middle key
10		3D Viewer Translation Mode	Translates, clicks to enter translation mode, can translate 3D view of atom structure by dragging mouse
11		3D Viewer zy View	Clicks to reset 3D view of structure (z-y plane), clicks down to select from different perspectives to view 3D view of structure
12		3D Viewer Fit to View	Clicks to move 3D view of structure to appropriate position according to screen
13		Display Style	Clicks to set display mode of atom structure
14		Structure Refinement Module	Clicks to enter atom structure refinement module, this module has fully upgraded 3D display effect of atom structure, displays atom structure in the form of equivalent atoms, and supports ball stick/polyhedron display mode, users can customize color, radius, and lighting parameters, create exclusive personal template
15		Add Atom	Adds atom, clicks to enter Device Studio periodic table, selects element, clicks in 3D view of structure to add atom
16		Add New Atom	Adds atom in the middle of selected multiple atoms. This icon needs to select multiple atoms to activate
17		Hydrogen passivation	Uses hydrogen atom to passivate crystal structure. Currently, only effective for Si and C elements
18		Delete Atom	Deletes selected atom
19		Replace Atom	Replaces selected atom
20		Edit Atom With Selected	Sets distance between 2 atoms or angle between 3 atoms. This icon needs to select 2 or more atoms to activate
21		Move Atom	Moves selected atom. This icon needs to select atom to activate
22		Rotate Atom	Rotates selected atom. This icon needs to select 2 or more atoms to activate
23		Mirror Atom	Mirrors selected atom. This icon needs to select atom to activate
24		Stretch Cell	Stretches or compresses primitive cell while keeping fractional coordinates unchanged
25		alternate axes	Rotates lattice basis vectors A, B, C of structure
26		alternate coordinate	Rotates X, Y, Z of structure
27		Wrap	Wraps atoms outside lattice along unit axis to lattice, clicks down to select Wrap Along a/b/c
28		Center	Centers all atoms or selected atoms as a whole in lattice cell, clicks down to select Center Along a/b/c
29		Fit Cell	Automatically matches minimum unit lattice basis vector, clicks down to select Fit Cell Along a/b/c
30		Minimize Structure	Performs structure optimization on molecular structure through molecular force field calculation, clicks down to select suitable force field. This icon can only activate when structure to be displayed is molecular structure
31		Convert to Molecule	Converts current structure to molecular
32		Convert to Crystal	Converts current structure to crystal
33		Convert to Device	Converts current structure to device
34		Distance	Measures distance between 2 atoms
35		Angle	Measures angle between 3 atoms
36		Dihedral angle	Measures dihedral angle between 4 atoms
37		Vector between two atoms	Measures vector between 2 atoms
38		Recalculate LinkerBond	Recalculates bond

Note

The Device Studio toolbars are important, so it is recommended that users read the function of each icon in Toolbars before using Device Studio. Also, for convenience of users’ use, Device Studio has categorized the icons in the toolbars, and when the icon is gray, it cannot be activated unless the condition is met. If help is needed, consult the Hongzhiwei professional solution center team.

Project Management Area is shown in fig. 3.11. If the project name is DeviceStudio, there are 3 structure files under this project, namely Au-Alkanethiol-Au.hzw, NaCl.hzw, and azulene.hzw. For structure files, such as Au-Alkanethiol-Au.hzw, as shown in the red frame of Figure 3.3-1, this area can manage input files for corresponding structure calculation, such as self-consistent calculation input file scf.input. Users can open and view the input file by right-clicking on the input file and selecting Open with, or find the file storage location in the computer by right-clicking on the input file and selecting Open Containing Folder. For structure files, if related calculation input files have been generated, they cannot be renamed; otherwise, if no related calculation input files have been generated, users can rename them by right-clicking on the structure file and selecting Rename, then renaming them.

fig. 3.11 Project Management Area

To create or open an existing project, import or export structure files in the Project Management Area, please refer to the detailed description of File.

Note

Device Studio has optimized Project, so it is recommended that users name project files, structure files, etc. in English without spaces, Chinese characters, asterisks, etc. when submitting homework for calculation. After submitting homework, including after submitting homework, do not change file names. If you want to change them, it is recommended to change them before submitting homework for calculation.

Structure 3D Display Area is shown in fig. 3.12. If the structure Au-Alkanethiol-Au.hzw is displayed in this area, users can open the structure file in the project management area by double-clicking on the structure file. In this area, users can zoom the 3D view of the structure by scrolling the mouse middle key; they can first select the 3D Viewer Translation Mode shortcut icon in the toolbar or press the middle mouse button, and then drag the mouse to translate the 3D view of the structure in this area; they can first select the 3D Viewer Rotation Mode shortcut icon or press the right mouse button, and then drag the mouse to rotate the 3D view of the structure in this area.

Users can perform various operations such as adding, deleting, modifying, etc. on the structure in this area, and the 3D view of the structure can be displayed in real time in this area. Users can perform structure operations according to the function description of each shortcut icon in Toolbars.

fig. 3.12 Au-Alkanethiol-Au’s 3D Display

If structure Au-Alkanethiol-Au.hzw is displayed in the 3D display area, Structure Attribute Area shows the system information of the structure as shown in GraphicalInterface_13; if a specific atom of Au-Alkanethiol-Au.hzw structure is selected, Structure Attribute Area shows the atom information of the structure as shown in GraphicalInterface_14, users can modify the coordinate position or replace the atom of the selected atom by double-clicking on the mouse.

As shown in fig. 3.13, Calculation Task Monitoring Management Area contains 5 modules, with the function descriptions as follows. When the task is in queue, calculating, or completed, Status is Queued, Running, Completed respectively. After calculation is completed, part of calculation results will be automatically pulled back to local. If more calculation results are needed, click the download button to download and return.

fig. 3.13 Calculation Task Monitoring Management Area

• Description: Structure name.

• Script: Location of task input file.

• Commit Status: Task file transmission progress.

• Status: Task calculation status.

• Actions: Task calculation operation.

• Process: Views task calculation log file to determine whether task calculation is completed through log file.

JobManager icon function is as follows table:

Number	Icon	Icon English Name	Function Description
1		/	Clicks to enter Xshell exe file directory setting
2		Open WinSCP	Clicks to connect current supercomputing server through WinSCP, as shown in fig. 7.19
3		Open PuTTY	Clicks to connect current supercomputing server through PuTTY, as shown in fig. 7.18
4		Reset IP	Clicks to enter MachineOptions interface, in which users can choose local or supercomputing server, or customize connection server. Connection server operation can refer to Nanodcal Connection Server section content
5		Reload to server	Reconnects server
6		refresh	Refreshes, clicks to refresh Calculation Task Monitoring Management Area status
7		Download	Downloads, clicks to enter Calculation Result Download Interface as shown in fig. 7.17
8		Cancel	Cancels, clicks to cancel calculation task
9		Inspect simulation data in real time	Clicks to view calculation result log file in real time