6.15. 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.
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.