6.15. Solid Menu

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

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

6.15.1. 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.

Lattice
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).

Asymmetric unit
Add atom

Add an atom that becomes an asymmetric element.

Delete atom

Delete the atom which becomes the asymmetric element selected on the list.

Element

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.

6.15.2. 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.

6.15.3. 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.

6.15.4. 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 cluster center point in fractional coordinates. With an atom selected on the graphic screen, click Set to specify the selected atom position as the center point.

Cluster Radius

Specifies the radius of the cluster in angstroms.

Hydrogen

Define the vacuum layer thickness in Å.

OK

Perform the processing.

6.15.5. 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.

6.15.6. Quantum ESPRESSO

6.15.7. OpenMX

6.15.8. FDMNES