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

If Tools ‣ Preferences menu has Use New Slab Builder checked, it works as follows.

Miller indices

Define the Miller index (hkl) of the surface.

Force orthorhombic cell

If unchecked, the first basic lattice found by the internal process that satisfies the specified Miller index will appear. If checked, the internal process is executed until a basic lattice of rectangles satisfying the specified Miller index is found, at which point the structure appears.

Supercell

Enter the number of supercells in the surface horizontal direction (a or b-axis).

Set slab width by length

Specify the thickness of the slab in angstroms, and enter the location of the lower and upper bound of the slab in the Lower bound and Upper bound.

Set slab width by repeat units

Specify the thickness of the slab in basic cell units, and enter the location of the lower and upper bound of the slab in the Lower bound and Upper bound.

Vacuum

Enter the thickness of the vacuum layer; if Vacuum is entered, the Total width is automatically changed.

Total width

Enter the length of the cell in the c-axis direction; if Total width is entered, Vacuum is automatically changed.

Position

Specify the position of the slab perpendicular to the surface.

Terminate dangling bonds width hydrogen

If checked, hydrogen atoms are added to the bonds that are broken on the slab surface. If more hydrogen is added than expected, use Delete or Delete atom after using this function to delete excess hydrogen atoms.

Do not insert vacuum

If checked, no vacuum layer is inserted. This is used when you do not want to create a slab and just want to re-create the basic lattice with a mirror index.

Maximum slab width internally generated

Specifies the maximum thickness of the slab to be generated by the internal process if the basic grid is not found at the specified Miller index, such as in the case of a high-index surface. The value (absolute value) set in Lower bound or Upper bound must be less than half of this value.

OK button

Creates a slab model and displays it in the main window.

If Tools ‣ Preferences menu does not check Use New Slab Builder, it works as follows.

Calling this function with a (bulk) crystal CIF file loaded will create a slab. Internally, it uses pymatgen or an in-house routine that simulates pymatgen.

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

Creates a slab model and displays it in 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

Modifies hydrogen on cluster surface.

OK

Perform the processing.

6.15.5. Convert Lattice (Primitive-Conventional)

Converts between primitive cells-conventional cells for cells displayed in the main window. Uses spglib in the background.

6.15.6. Convert lattice to equivalent rectangular cells

Convert to equivalent rectangular cells for cells displayed in the main window. Useful for converting hexagons to rectangular cells. Uses atomsk in the background.

Warning

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

6.15.7. Transform Unit Cell

The rotation matrix is used to deform the unit grid vectors in each of the a, b, and c axes. Since each element of the rotation matrix is an integer, the transformed cell is also a unit cell. This is useful when you want to re-transform the unit cell lattice vectors.

6.15.8. Refine Lattice

This function detects the symmetry of a cell displayed in the main window with a set tolerance, and then slightly adjusts the coordinates to conform to that symmetry, which may help avoid symmetry-related problems in Quantum ESPRESSO and other applications. It uses spglib in the background.

6.15.9. Quantum ESPRESSO

6.15.10. OpenMX

6.15.11. FDMNES