6.12. menu
Join the two simulation cell files (mol2 or cif format) prepared in advance to create an interface model. Tools ‣ Preferences menu allows you to switch between the new and old features. The features of the new spec are as follows
- Cell Tab
Specify the two phases (Cell1 and Cell2) across the interface.
- Use displayed cell
Specify the model displayed in the main window as a phase.
- Load from file
Specify the phase as a model saved in CIF or mol2 format.
- Direction Tab
- Axis perpendicular to interface
Specifies the axis in the vertical direction of the interface.
- Order
Specify the order of Cell1 and Cell2 joined.
- Interval
Specify the interval between Cell1 and Cell2.
- Specify interval between cell boundaries
The entered value is the distance between cell boundaries.
- Place atoms on cell boundaries on both sides
If checked, the atoms placed just above the cell boundary are copied and placed on both sides of the interface vertical. If Axis perpendicular to interface is c-axis, atoms with a fractional coordinate of 0 or 1 on the c-axis (or z-axis in the case of a rectangular cell) are copied to position 1 or 0 respectively.
- Specify interval on selected axis between outermost atoms
The specified value is the Axis perpendicular to interface is the distance between the outermost atoms on the selected axis.
- Adjusting cell size parallel to interface
Specifying how to adjust the horizontal cell size of the interface
- Scaling cells to average size
Doing Affine deformation so that the horizontal cell size of the created interface model is the average of the cell sizes of Cell 1 and Cell 2.
- Scale to size of…
Doing Affine deformation of the atomic positions to match the selected cell size to the other cell size.
- Extend size of smaller cell while keeping atomic positions
The atomic positions are not changed, but the smaller cell size is changed to the larger cell size.
- Repeat Tab
- Number of cells
Specify the number of supercells in Cell 1 and Cell 2 when creating the interface model. Clicking the Suggest button and the ratio of the cell size is shown for the numbers of Cell1 and Cell2. It is recommended to choose a combination for which Ratio close to 1.
- Operation for atoms outside each cell
Specify how to handle atoms that are located outside the cell.
- Wrap for each molecule
Molecules are moved inside the cell taking into account the periodic boundary.
- Wrap for each atom
Atoms are moved inside the cell taking into account the periodic boundary.
- Do nothing
Do nothing
- Build button
The interface model is created based on the settings.
The features of the previous version are as follows
- Cell Files
Specify the information of the two cells (Cell 1 and 2) to be joined. After setting each item, click the [Next] button.
- Cell 1 and Cell 2
- [Browse]
Specify the file (mol 2 or cif format) to be joined. It is also possible to specify files by dragging and dropping them.
- [Lattice Constants]
- [a],[b],[c],[Alpha],[Beta],[Gamma]
The cell constant is displayed.
- Direction
Specify the direction to join the cells and the spacing between the cells. After setting each item, click the [Next] button.
- Direction
- [a-axis]
Combine two cells along the a-axis direction.
- [b-axis]
Combine two cells along the b-axis direction.
- [C-axis]
Combine two cells along the c-axis direction.
- Order
- [Normal]
Place Cell 2 on Cell 1.
- [Reverse]
Overlay Cell 1 on Cell 2.
- [Interval]
Specify the interval between cells. It is not the distance between the two sides but the length along the axis.
- [Scaling cells to average size]
If there is a difference in cell size, it stretches to the average size.
- [Padding small cell to the size of large cell]
If there is a difference in the size of the cell, put a vacuum in the smaller cell and align it with the larger cell.
- Repeat
Specify the number of repeats for each cell. Finally click the [Build] button.
- Number of Cell 1 and Cell 2
- [a-axis]
Specify the number of reports in cell 1 or cell 2 in the a-axis direction.
- [b-axis]
Specify the number of repeats in cell 1 or cell 2 in the b axis direction.
- [C-axis]
Specify the number of repeats in cell 1 or cell 2 in the c-axis direction.
- [Suggest]
We will present a combination of repeat numbers so that Cell 1 and Cell 2 are closer in size. The combination with Ratio close to 1 reduces the distortion of both cells. Click on the column and press the Set button, or double-click it to take effect.
- Lattice Constrants
- [a],[b],[c],[Alpha],[Beta],[Gamma]
The lattice constant of the cell after bonding is displayed.
- [Build]
Save the joined cells. Processing time may be prolonged if the size of the system is large.