6.12. menu
Create an interface model by joining multiple pre-prepared simulation cell files, the structure displayed in the main window, or a vacuum layer. You can switch between the new and legacy versions of this feature in Tools ‣ Preferences menu. The new version provides the following features.
The joined cell is created using the following procedure.
Load the structure specified by Type. If the structure is a primitive cell and Use conventional cell is checked, convert it to a conventional cell.
Wrap the atomic positions using the method specified by Wrapping.
Apply the operations specified in Operations in the following order: Cleave plane, Transform by matrix, and Shift.
If Replicate boundary atoms is checked, atoms located at the cell boundaries are duplicated.
Redefine the cell boundaries using the method specified by Boundary.
Perform all the above operations on every cell.
Join all cells while preserving their fractional coordinates in the original cells, except along the stacking direction. The size of the resulting cell is determined by Interval and In-Plane Axes.
- Interval
Specify the distance between cells (in Å).
- Stacking axis
Specify the stacking direction.
- Order
Specify the stacking order.
- In-Plane Axes
Specify how to adjust the cell dimensions parallel to the interface. If Average in-plane axes is selected, the dimensions are adjusted to the average values of all cells. If Use selected cell axes is selected, the dimensions are adjusted to those of the cell selected from the drop-down menu on the right.
- The +/- buttons for each cell
Increase or decrease the number of cells.
- Type
If Displayed cell is selected, the structure displayed in the main window is loaded into this cell. If File is selected, the structure from the specified file is loaded into this cell. If Vacuum is selected, this cell is set to a vacuum layer with the thickness specified by Height (in Å).
- Operations
Perform the following operations on the loaded cell.
- Reset
Reset the Operations settings.
- Cleave plane
Redefine the cell according to the specified plane orientation. Click Config to configure detailed settings. For specific instructions, see Build Cluster Model.
- Transform by matrix
Redefine the cell using the specified rotation matrix. Click Config to configure detailed settings. For specific instructions, see Transform Unit Cell.
- Shift
Specify the position parallel to the interface. Click Config to configure detailed settings. Clicking Align marked atoms automatically determines the shift required to align the positions of the two selected atoms in the directions parallel to the interface.
- Wrapping
Specify how to handle atoms outside the cell. If Wrap for each molecule is selected, the coordinates are wrapped using periodic boundary conditions so that the center of mass of each molecule is inside the cell. If Wrap for each atom is selected, the coordinates are wrapped using periodic boundary conditions so that all atoms are inside the cell. If Do nothing is selected, no operation is performed.
- Boundary
Specify the boundaries used when joining cells along the stacking direction. The distance between cells is calculated based on the boundaries specified here. If Cell boundary is selected, the boundaries of the loaded cell are used. If Outermost atom is selected, the positions of the atoms with the minimum and maximum coordinates along the stacking direction are used as the boundaries.
- Replicate boundary atoms
If checked, atoms located at the cell boundaries along the stacking direction are duplicated on both sides, taking periodic boundary conditions into account.
- Use conventional cell
If checked and the loaded cell can be converted to a conventional cell, the cell is converted to a conventional cell before further processing.
- Lattice Matching
When there are two cells, automatically calculate rotation matrices that satisfy the specified conditions. After adjusting the parameters, click the Search button. Then, select the desired structure from the list by checking its checkbox and click Apply changes back.
- OK Button
The interface model is created based on the settings.
The legacy version provides the following features. Create an interface model by joining two pre-prepared simulation cell files or structures displayed in the main window.
- 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
Loads models from structural files in various formats and specifies them as phases.
- 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.