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
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
See Solid ‣ FDMNES menu.