5. Structure Editing and Information Measurement

For structure manipulation, users should first carefully read the descriptions of each shortcut icon in Toolbars, then perform the corresponding operations as needed. The structure view after the operation can be viewed in the 3D display area.

Device Studio supports viewing the 3D structure from ZY, XY, XZ, YZ, YX, and ZX planes, as shown in the NaCl (111) crystal structure in the 3D display area (NaCl(111).hzw). Users can reset the structure to the ZY plane by clicking the 3D Viewer zy View shortcut icon in the toolbar. Clicking the dropdown button of this shortcut icon allows selection of XY, XZ, YZ, YX, or ZX planes to view the 3D structure of the NaCl (111) crystal. The 3D views of the NaCl (111) crystal structure from the ZY, XY, XZ, YZ, YX, and ZX planes in the 3D display area are shown in fig. 5.1, fig. 5.2, fig. 5.3, fig. 5.4, fig. 5.5, and fig. 5.6, respectively.

fig. 5.1 3D View of NaCl (1 1 1) ZY Plane	fig. 5.2 3D View of NaCl (1 1 1) XY Plane
fig. 5.3 3D view of NaCl (1 1 1) XZ plane	fig. 5.4 3D view of NaCl (111) YZ plane
fig. 5.5 3D view of NaCl (1 1 1) YX plane	fig. 5.6 3D view of NaCl (1 1 1) ZX plane

In the 3D structure display area, users can zoom in or out of the 3D view of the structure by scrolling the middle mouse button; they can pan the 3D view of the structure in this area by first selecting the 3D Viewer Translation Mode shortcut icon in the toolbar or holding down the middle mouse button and dragging the mouse; they can rotate the 3D view of the structure in this area by first selecting the 3D Viewer Rotation Mode shortcut icon in the toolbar or holding down the right mouse button and dragging the mouse.

Taking crystalline MoS₂ as an example to illustrate a series of structural modification operations, prepare the structure file (MoS2.hzw). Drag and drop this file into the Project Explorer area of the software to import the structure. The 3D view of the structure in the zy plane is shown in StructureOperation_7 (a).

5.1. Adding Atoms

To add a Cr atom to crystalline MoS₂, as shown in red in fig. 5.7, click the Add Atom shortcut icon in the Toolbars. The periodic table will pop up. Select Cr in the periodic table and click OK. Click the left mouse button at position (4) in the interface shown in fig. 5.7. Then click the Recalculate LinkerBond shortcut icon to recalculate bond lengths. This completes the operation of adding a Cr atom to MoS₂. The completed 3D view is shown in StructureOperation_8 (b).

fig. 5.7 Add atomic operation interface

5.2. Delete Atom

To delete an S atom, as shown in the structure in StructureOperation_8 (b), follow the steps illustrated in the red portion of fig. 5.8. Select the S atom to be deleted, click the Delete Atom shortcut icon on the toolbar, or press the Delete key. Then, click the Recalculate LinkerBond shortcut icon to recalculate bond lengths. The 3D view after deleting the S atom is shown in StructureOperation_9 (c).

fig. 5.8 Remove Atom Operation Interface

5.3. Replacement Atom

To replace a Cr atom with a W atom in the structure shown in StructureOperation_9 (c), follow the steps shown in red in fig. 5.9. Select the Cr atom to be replaced, click the Replace Atom shortcut icon in the Toolbars, select W from the periodic table that appears, click OK, and then click the Recalculate LinkerBond shortcut icon to complete the replacement. The 3D view of the resulting structure is shown in StructureOperation_10 (d).

fig. 5.9 Replace Atomic Operation Interface

5.4. Modifying Atomic Coordinates

To modify the coordinates of the W atom from (0.79757905, 1.84840857, 7.24943971) in StructureOperation_10 (d) to (1.0, 1.5, 12.0), follow the steps shown in red in fig. 5.10. First, select the W atom with the mouse. The coordinates of the selected W atom, (0.5951619, 1.47565329, 7.18570423), will be displayed in the Properties Explorer. Then, double-click the appropriate fields and enter 1.0, 1.5, and 12.0 respectively to modify the W atom’s coordinates. Finally, click the Recalculate LinkerBond shortcut icon to recalculate bond lengths. The 3D view of the structure after modifying the atomic coordinates is shown in StructureOperation_11 (e).

fig. 5.10 Modify Atomic Coordinates Operation Interface

5.5. Move the selected atom

For the structure shown in StructureOperation_11 (e), move the two leftmost atoms as shown in the red portion of fig. 5.11. First, select the two leftmost atoms with the mouse. Click the Move Atom shortcut icon to open the Move Atom dialog. Enter the distance to move in the dialog and click to move along the positive Z direction (+z). After moving, click the Recalculate LinkerBond shortcut icon to recalculate the bond lengths. The 3D view of the structure after moving is shown in StructureOperation_12 (f).

fig. 5.11 Move the selected atomic operation interface

note

This only describes a portion of the structural modification operations. Users can refer to the descriptions of each shortcut icon in Toolbars for details and perform corresponding structural operations as needed.

A series of operations for measuring structural information is described using the Si8 crystal structure as an example. Prepare the structure file (Si8.hzw), and drag and drop it into the Project Explorer of the software to import the structure. The 3D view of the structure’s zy plane is shown in fig. 5.12.

fig. 5.12 Si8 Crystal Structure

Note

To measure structural information, multiple atoms often need to be selected. It is recommended that users first select the corresponding shortcut icon on the Toolbars and then hold down the Ctrl key while individually selecting atoms in the structure. Without holding down the Ctrl key, multiple atom selection via mouse clicks is not possible, and therefore structural information measurement cannot be performed.

5.6. Measuring the distance between two atoms

For the crystal structure shown in fig. 5.12, click the Distance shortcut icon on the Toolbars, hold down the Ctrl key on the keyboard, and then select two atoms in the structure with the mouse to measure the distance between the selected two atoms, as shown in StructureOperation_15 (a). If you do not want to keep the measurement numbers, right-click and select “Clear Annotation”.

5.7. Measuring the vector between two atoms

For a crystal structure as shown in fig. 5.12, click the Vector between two atoms shortcut icon on the Toolbars, hold down the Ctrl key on the keyboard, and then select two atoms in the structure with the mouse to measure the vector between the selected two atoms, as shown in StructureOperation_16 (b).

5.8. Measuring the Angle Between Three Atoms

For a crystal structure as shown in fig. 5.12, click the Angle shortcut icon on the Toolbars, hold down the Ctrl key on the keyboard, and then select three atoms in the structure with the mouse to measure the angle between the selected three atoms, as shown in StructureOperation_17 (c).

5.9. Measuring the dihedral angle between four atoms

For a crystal structure as shown in fig. 5.12, click the Dihedral angle shortcut icon on the Toolbars, hold down the Ctrl key on the keyboard, and then select four atoms in the structure with the mouse to measure the dihedral angle between the selected four atoms, as shown in StructureOperation_18 (d).