Materials

Materials can be used in HEXRDGUI for a variety of purposes, including calibration and drawing overlays.

Loading and Saving

Materials may be loaded from an HDF5 file via File->Open->Materials. This will replace all current materials with the ones from the file. An example materials file may be found here.

Similarly, materials may be written to an HDF5 file via File->Save->Materials.

Individual materials may be created and imported through the Material List Editor.

Materials Panel

The materials panel provides many editable settings for materials.

The material name displayed in the combo box at the top (in this case, CeO2) is the material that is currently being edited and used for any material-specific options, such as the Reflections Table, General settings, etc. If you are editing material settings, be sure you have the correct material selected!

The tool button to the far right on the same row opens up the Material List Editor, which can be used to add/delete materials.

The Overlay Manager button opens up the global Overlay Manager settings. See overlays for more details about overlays.

Show Overlays is a global option to turn on/off overlays in the canvas. It applies to all materials, including the currently selected one.

The Min d-spacing (computed) is the minimum d-spacing that is actually computed in HEXRD for the selected material. Reflections with a lower d-spacing will not be computed. In addition, this number is used when computing Laue overlays.

The Min d-spacing (displayed) will limit the selectable rows in the Reflections Table. The Max 2θ below it is just the 2θ value corresponding to the Min d-spacing (displayed) (each option edits the other). If Limit Active is unchecked, these two options will be disabled.

Material List Editor

The material list editor is accessible via the tool button in the top-right corner of the materials panel (next to the current material name). This editor allows reordering, deleting, copying, and adding new materials.

If a row is selected, the up or down buttons may be used for reordering, delete deletes the material, and copy makes a deep copy of the material. add creates a new default material. The materials may also be renamed in this list.

Materials may be imported from CIF files as well by using the Import from CIF button. HEXRDGUI also ships with a set of default materials which may be imported via the Import from Defaults button at the bottom.

Reflections Table

The reflections table may be used for a few reasons:

1. To view information about each available reflection
2. To show/hide the reflection for powder overlays
3. To select reflections to use in calibration methods
4. To select reflections to use in various steps in the HEDM workflow

Shift-click can be used to select multiple rows simultaneously, and ctrl-click may be used to add/remove individual rows. The rows may also be sorted by clicking on the various columns at the top.

If a powder overlay is visible for the selected material, then only the reflections corresponding to the selected rows will be drawn. These HKL selections also determine which HKLs are used for the various calibration methods.

In the columns of the table, |F|² is the structure factor, and Iₚ is the powder intensity. They are both normalized so that the maximum is 100.

Setting the min d-spacing in the materials panel will affect the number of rows in the reflections table. If an HKL falls below the Min d-spacing (computed), it will not be displayed in the table at all. If an HKL falls below the Min d-spacing (displayed), it will appear in the table, but it will be grayed out and not selectable.

Copy to Clipboard

After selecting rows, if a row in the table is right-clicked, a context menu will appear that provides an option to copy the selected rows to the clipboard:

If "Copy to Clipboard" is clicked, the clipboard will contain the selected rows in CSV format. The above selection produces the following text in the clipboard:

ID,{hkl},d-spacing (Å),2θ (°),|F|²,Iₚ,Multiplicity
0,1 1 1,3.12,3.17,100.00,100.00,8
3,3 1 1,1.63,6.08,19.52,15.93,24
5,4 0 0,1.35,7.33,10.77,1.51,6

This can be pasted into spreadsheet software, such as Microsoft Excel.

General Settings

The general settings of the material include everything within the General tab.

The Space Group Info section is used to select the space group. The Lattice Type must first be used to select the correct lattice type, and then either the Space Group number, Hall Symbol, or Hermann-Mauguin may be used to select the space group within that lattice type.

The Lattice Parameters are automatically enabled/disabled depending on the selected lattice type. For instance, for a cubic lattice type, only a will be enabled, since all sides are the same and all angles are 90.

For tetragonal, trigonal, and hexagonal space groups, the c/a ratio may be fixed in order to simplify exploration of values. If the c/a ratio is fixed, modifying a or c will cause the other to update so to keep the ratio fixed, and modifying the ratio value will cause a to change to reflect the new ratio value.

Material Structure

The space group and lattice parameters of a material are sufficient to determine the list of allowed reflections and the $2\theta$ values for these reflections. However, in order to compute the correct structure factors, additional information is required about the positions of atoms in the unit cell. The structure tab lets the user input this information.

The following information is needed to fully define the atomic structure of a material:

1. fractional coordinates of the site
2. site occupancy
3. Debye-waller factor for the atoms

The user can select or remove a site. However, at least one site is required. The default name of the site is Site1, Site2 etc. These are editable fields and double-clicking on the site will let the user edit its name as shown below

Each site has a unique position in the unit cell given by the fractional coordinates. The user can specify this location in the Fractional Coords parameters. Remember that the space group symmetry introduces degeneracy in the different positions. For e.g. for an FCC crystal the coordinates [0, 0, 0] is equivalent to [1/2, 1/2, 0], [1, 0, 0], [1/2, 1, 0], $\cdots$ etc.

Within each site, the user can select the atom that sits on that site. The selection can be made using the Select Atom Types button. The button opens a periodic table that lets the user select the atom type at the site location as shown below:

Typically, one atom sits at each site. However, It is possible for multiple atoms to occupy the same atomic site with fractional occupancy (summing up to 1). A relevant material system where this is the case are disordered alloys. In this case the user needs to select multiple atoms for the same site position and set the occupancies correctly.

Finally, the thermal factor can either be specified as the U which represents the mean-squared displacement or B which is referred to as the B-factor in literature. The two numbers are related to each other via the relationship

$$B = 8\pi^{2}U$$

It is assumed that the temperature factors are isotropic by default. however, anisotropic thermal parameters can also be specified as a full tensor.

The structure tab also provides some helper functions to ensure accuracy of the material. The remove duplicate atoms is one such function. This button will check the equivalence of different sites and remove the ones which are too close to each other by crystal symmetry. Finally, if the user are happy with the changes made in the structure tab and want to apply those changes to the material, they need to press the Apply button. If the user is unhappy about the changes made, they can always go back to the starting structure using the Reset button.

Material Properties

The properties tab has two primary functions:

1. Summarize the property of the material based on the space group, lattice parameters and atomic coordinates.
2. Let the user input other material properties such as the Elastic Tensor.

An example properties tab for ambient condition Nickel is shown below

The top panel can be used to specify the elastic constants of the material using either the stiffness or compliance tensor. The units for the entries are in GPa or GPa$^{-1}$ respectively. Due to cubic crystal symmetry of Nickel, the Elastic Constant has only three independent variables, namely the $C_{11}$, $C_{12}$ and $C_{44}$. Depending on the crystal structure, the number of independent component of stiffness or compliance matrix will automatically be adjusted.

The space group, lattice parameters and atomic coordinates are used to compute the theoretical density (g/cm$^{3}$), the volume of the unit cell ($\mathring{\text{A}}^{3}$) and the volume of unit cell per atom ($\mathring{\text{A}}^{3}$). These quantities are displayed in the material properties tab as well.

The properties tab also implements a third order Birch-Murnaghan (BM) equation of state to compute the change in volume of the unit cell based on an input pressure-temperature condition. The Show PT Slider button opens up the window. A JCPDS (Joint Committee on Powder Diffraction Standards) file or manual input of BM EOS parameters is required. An example for Ni at 38 GPa is shown in the image below. The lattice parameters, density and volume of the unit cell are automatically updated depending on the pressure-temperature values.