6.16. Solid Menu

It is a menu related to first principle (band) calculation.

Solid pack is required to use the functions of the solid menu.

6.16.1. Crystal Builder

Create a crystal structure. It is mainly used for the following purposes.

  • Enter the space group, lattice constant, asymmetric element and create crystal structure.
  • Open the CIF file on the crystal builder and replace the axes a, b, c.
  • Open a CIF file containing a noninteger occupancy and allocate atoms.
File menu
New
We will create a new crystal structure.
Open
Open the CIF file.
Save As
Save the crystal structure displayed in the crystal builder in CIF format or XYZ format.
Save As P1 CIF
If checked, save it in P1 when saving in CIF format.
Edit Menu
Exchange Axis
Exchange the coordinates (x, y, z) of the axis (a, b, c) and the asymmetric element. For details, please see International Tables vol.
Discard symmetry
Discard the symmetric operation and let P1 be the space group. At this time, all symmetric elements reproduced by the existing symmetrical operation are recognized as asymmetric elements.
Assign Atoms to Non-Integer Occupancy Sites
Random atoms are generated for each site based on the item (_atom_site_occupancy) defined in the imported CIF file. If you want to create a supercell according to the occupancy rate, use this function after creating a sufficiently large supercell using the repeat function.
View menu
Show Multi-View
We will draw by triple drawing. In the three view, only the upper left window corresponds to free rotation, and the remaining three direction cameras are fixed to the a, b, c axes of the crystal and therefore will not rotate.
Always View Center
When checked, always keep the gaze point on the center of gravity
Orbit/Roll
Specify the rotation method.
Orbit
It performs free rotation.
Roll around a-, b-, c-axis
It rotates around the a, b, c axes.
Show Bond
Displays the join.
Show Element Name
It displays the element symbol.
Show Atoms on Boundary in Duplicate
Display atoms on the boundary.
Show Unit Cell
Display unit lattice.
Make Replicated Atoms Transparent
Transparent display of atoms generated by symmetrical operation.
Crystal System
Select crystal system.
Space Group
Select space group from number or Hermann-Mauguin symbol.
Lattice Constant
Set lattice constants (fields that can be entered depend on the selected space group).
Add
Add an atom that becomes an asymmetric element.
Remove
Delete the atom which becomes the asymmetric element selected on the list.
Atom
Enter/Modify the element symbol.
X, Y, Z
We set the atomic site with the fractional coordinate (fractional coordinate).
OK

Load the created crystal structure into the main window.

If you want to cancel the import, please click Edit ‣ Undo on the main window.

Cancel
Discard the structure entered in the crystal builder and return to the main window.

6.16.2. Build Cluster Model

You can create a slab by calling this function while loading the CIF file of the (bulk) crystal. pymatgen is used internally.

First, click the Generate Slab button, and then click the OK button.

Miller indices
Define the Miller index (hkl) of the surface.
Minimum slab size
Enter the cell size in the face vertical (c-axis) direction.
Supercell
Enter the number of supercells in the surface horizontal direction (a or b-axis).
Force c-axis to be perpendicular to a and b axes
Ensure that the c-axis is perpendicular to the a and b axes.
Convert hexagonal to orthorhombic
Convert Hexagonal to Orthorhombic.
Generate Slab button
This button creates a candidate surface structure based on the items above.
Surface configurations
Select a surface structure from among the candidates.
Slab, Vacuum, Total width
Enter the size of the surface vertical. If you enter ont of Vacuum or Total width, the other will be determined automatically.
Position
Specify the position of the slab perpendicular to the surface.
OK button
Load the created crystal structure into the main window.

Warning

In order to use this feature, you need CygwinWM setup.

6.16.3. Generate Supercell

Duplicate the cell displayed in the main window and create a super cell.

Enter the number of repetitions in a , b , c and click the OK button.

6.16.4. Cleave Plane

Specify the mirror surface and redefine the unit cell.

When creating a slab model, execute Insert Vacuum after executing this function.

View menu
It is the same as Crystal Builder.
Step 1/2 Cutting
Cleave Plane
Define the Miller index (hkl) of the surface.
Offset
Specify the position of the surface by the relative position (percentage) from the upper end to the lower end of the unit cell.
Next >>
Go to Step 2/2 Transform Unit Cell.
Step 2/2 Transform Unit Cell
View Configuration
Set the drawing range.
Lattice Choice

Select the grid definition.

Manual
Specify atom on the origin, a axis, b axis, c axis with Set button.
Filter (Ortho)
Choose from Lattice. Only rectangular candidates will appear in Lattice.
Filter (All)
Choose from Lattice.
Lattice
The grid definition choices are displayed.
Filter
Specify the narrowing condition of Lattice.
OK
Perform the processing.

6.16.5. Insert Vacuum

Insert a vacuum layer above and below the crystal structure and construct a slab model.

When a vacuum layer is inserted using this function, atoms are copied on both sides of the surface touching the layer, but the number of atoms does not change when the layer is inserted using edit ‣ Edit Cell Manually.

View menu
It is the same as Crystal Builder.
Axis
Select the direction in which the vacuum layer is to be inserted from the X, Y, and Z axes.
Bulk
Indicate the thickness of the original cell in Å. (Display only)
Vacuum
Define the vacuum layer thickness in Å.
Total Width
Indicates the sum of Bulk and Vacuum. (Display only)
Automatically shift to center
When this check box is checked, the original crystal structure is fixed at the center of the slab model. When not checked, the Shift function becomes available.
Shift
You can specify the location of the surface structure in the expanded cell. Numeric values in the edit box indicate the position of the reference plane in fractional coordinates.
Reference Plane
Specify the position of the reference plane. For Base, the reference plane is the bottom of the crystal structure. At the center, the reference plane is the center of the crystal structure.
Terminate dangling bonds with hydrogen atoms
The dangling bond is capped with hydrogen on the surface in contact with the vacuum. If you want to modify with a functional group, check this function, return to the main window, and use Replace with Fragment to replace the hydrogen with any functional group.
OK
Perform the processing.

6.16.6. Build Cluster Model

Cut out nanoclusters from the crystal structure.

The atoms of the original unit cell are opaque and atoms outside the unit cell are translucent.

View menu
It is the same as Crystal Builder.
Center
Specify the center point of the cluster in terms of fraction coordinates. With an atom on the graphic window selected, click Set to specify the selected atomic position as the center point. Cluster Radius Specify the radius of the cluster in angstrom units.
Hydrogen
Define the vacuum layer thickness in Å.
OK
Perform the processing.

6.16.7. Convert Lattice

For cells displayed in the main window, perform conversion between primitive cells and conventional cells.

Warning

In order to use this feature, you need CygwinWM setup.

6.16.8. Quantum ESPRESSO

6.16.9. OpenMX

6.16.10. FDMNES