Getting started

Int3D has three basic objects that are present in almost all of the tasks it can perform: the instrument, the crystal and the scans. This section contains, among other things, a description of how to set and work with these three objects.

User interface

The user interface of Int3D is shown in Fig. 1. Its main components are: the menu bar, the scan loader, the file explorer, the scan viewer and the terminal.

The menu bar has six menus: File, Edit, Single Crystal, Powder, Calibration and Utilities. The File menu is used to create, open and close projects. The Edit menu allows to edit the project information, the instrument parameters, the crystal data and the general settings. The Single Crystal and Powder menus contain the programs needed to perform the data reduction of single crystal and powder data respectively. The Calibration menu is used to calibrate the detector efficiency of XtremeD. Finally, the Utilities menu contains the utility Rspace, a graphical tool to work in the reciprocal space. If the FullProf Suite is already installed, it can be run from this menu.

The scan loader is used to load or remove scans. It also displays the main information contained in the scan files. The different programs used in the data reduction take the scans to be processed from the scan loader. In other words, if you want to process a particular scan, it must first be loaded with the scan loader.

The file explorer is useful for viewing the output files produced by the Fortran programs. If a text editor has been configured in Settings, then double clicking a text file on the file explorer will open it in the text editor.

The scan viewer displays the detector counts in 2D (frame by frame) or in 3D (the whole scan at once). The 2D viewer is the main viewer used during the data reduction. It allows you to visualize the detected peaks as well as the integration results, i.e., predicted peak positions, integration boxes, masks and ellipsoids.

The terminal displays the standard output of the Fortran programs, and it is very useful for detecting possible errors.

The scan loader, the scan viewer and the terminal can be resized by placing the mouse between two of these elements and holding down the left mouse button. The elements can be expanded horizontally or vertically.

Fig. 1 Main window of Int3D.

Creating a project

The data reduction can be carried out with or without defining a project. However, a project helps to organize the information and allows you to retrieve the scans, instrument and crystal data when starting a new session.

A project is created by clicking New Project in the File menu. Int3D then displays the project window (Fig. 2), in which the user must enter the project name, the project directory, the scans directory, the instrument and the experiment. It is always good practice to work with directories and names without white spaces and non ASCII-characters.

All the scans located in the scans directory are automatically loaded in the scan loader when the project is created or opened.

Every project has three files with fixed names, located in the project directory:

• project_name.pro: the project settings (Fig. 2). This is the file that has to be selected to reopen the project.

• instrument_name.geom: the instrument definition.

• project_name.cry: the crystal parameters.

Every project folder has several sub-folders. For a single crystal project the sub-folders are Peaks/, UB/ and Integration/. For a powder project, the sub-folders are Process/ and Integration/. The content of these sub-folders is explained in Single crystal data reduction and Powder data reduction sections respectively.

Fig. 2 Project window.

Instrument

The instrument window, shown in Fig. 3, is opened by clicking Instrument in the Edit menu. The instrument definition follows the Busing-Levy convention (Acta Cryst. (1967). 22, 457-464). The instrument parameters are described in the panel below.

Name

Type: string

The available instruments are D9, D10, D16, D19, XtremeD from ILL, DMC and Zebra from PSI and Wombat from ANSTO.

Busing-Levy frame

Type: string

Busing-Levy axes convention. The reference system is right-handed, with the y axis along the beam direction. If we look from the sample toward the detector, and the positive θ direction is to our right, then the Busing-Levy convention sets the z-axis upward (z-up). Otherwise, the z-axis is directed downward (z-down).

Wavelength

Type: float

If not specified, Int3D takes the wavelength from the scan file.

Type

Type: string

The detector type. Two types are available: Flat and H-Banana (horizontally curved). The type determines the equations for moving from real to reciprocal space. If the user is interested in how the conversion is done, details can be found in the routine psd_convert of CrysFML08 library.

Sample-detector distance

Type: float

Distance between the sample and the detector in mm.

Pixel origin

Type: string

Origin for pixel numbering, assuming the detector is viewed from the sample position. Four possible values: BottomLeft, BottomRight, TopLeft, and TopRight.

Gamma detector,Nu detector

Type: float

Gamma and Nu values specifying the position of the center of the detector with respect to the incident beam. These fields are usually left empty and the values are read from the scan file.

Number of pixels

Type: int

Number of detector pixels along x (horizontal) and z (vertical) dimension.

Pixel size

Type: int

Pixel size in mm along x (horizontal) and z (vertical) dimension.

Offsets

Type: float

Detector offsets in mm along detector coordinates (x, z) and beam direction (y).

Angles

Type: float

Lower limit, upper limit and offset of the different angles involved in the experiment. These angles are used for computing the accesible reflections. They can be disabled by checking the small boxes on the right if they are not needed.

Instrument path

Type: string

Folder where the instrument file is located. Inside a project, it is fixed and takes the value /path/to/the/project. Outside a project, the path must be set by the user.

Instrument file

Type: string

Name of the instrument file. It is fixed, equal to the name of the instrument followed by the extension .geom. The instrument parameters are saved on this file, used by the different Fortran programs run by Int3D.

Most of the parameters, with the exception of the wavelength and offsets, are fixed and do not have to be changed by the user. Default values for a given instrument can be set by clicking on the Default Values button.

An instrument file can be loaded by clicking on the Import button.

Fig. 3 Instrument window.

Crystal

The crystal window, shown in Fig. 4, is opened by clicking Crystal in the Edit menu. The crystal parameters are described in the panel below.

Phase

Type: int

Phase index. In principle more than one phase can be added, but in practice only one phase is used.

Cell Parameters

Type: float

a, b and c lattice parameters in Å and α, β and γ lattice angles in degrees.

Generators

Type: string

Generator of the space group. The generator can be for instance the standard symbol of the space group, a series of symmetry operators or the Hall symbol. It also admits the specification of a particular setting. The space group can be a crystallographic space group, a Shubnikov group or a superspace group. The different ways to provide the generator can be displayed by clicking on the Help button. If no generator is given, Int3D assumes space group P1.

Domain

Type: int

A crystal domain. Each crystal domain is described by a UB matrix. Every phase must have at least one crystal domain. There are two ways to provide the UB matrix:

• Typing it into the text editor. It must be written as a 3x3 matrix, i.e. on three separate lines. Copy and paste from an editor or from the scan loader works.
• Using the Import UB. This button opens a file browser. After selecting a file, Int3D will search a line starting with UBMAT. When such a line is found, Int3D expects the UB matrix given in the three next lines.

Color Main

Type: string

Color used for representing the main reflections predicted by the UB matrix.

Color Satellites

Type: string

Color used for representing the satellite reflections predicted by the UB matrix and the k-vectors.

Indexing UB

Type: bool

If True (box checked), that UB matrix is the one used for indexing pixels in the 2D viewer.

Basis vectors

Type: float

Basis vectors used to build the propagation vectors.

q-coefficients

Type: int

Coefficients of the linear coombinations of basis vectors that describe the propagation vectors. The example shown in Fig. 4 defines four propagation vectors from two basis vectors:

• k1=(0.25,0.00,0.00)
• k2=(0.50,0.00,0.00)
• k3=(0.00,0.25,0.00)
• k3=(0.25,0.25,0.00)

Crystal path

Type: string

Folder where the crystal file is located. Inside a project, it is fixed and takes the value /path/to/the/project. Outside a project, the path must be set by the user.

Crystal file

Type: string

Name of the instrument file. It is fixed, equal to the name of the project folder followed by the extension .cry. The crystal parameters are saved on this file, used by the different Fortran programs run by Int3D.

Fig. 4 Crystal window.

Scans

Scans are loaded into and removed from the application with the scan loader, shown in Fig. 1 and Fig. 5.

Scans can be loaded / removed manually with the buttons Load and Removerespectively. Scans are loaded / removed automatically when opening / closing a project.

The scan loader assigns an item text to every loaded scan. This item contains at least the name of the scan file, the scan type and the number of steps. For D9 and D10 the Miller indexes of the measured reflection are added. If the temperature, pressure or magnetic field are specified in the scan file, they are also included in the item text.

A single click on an item fills the fields below the scan list with the scan data. The button Explore HDF allows to explore the content of the scan file to look for some data not shown in these fields.

A double click on an item displays the scan on the 2D Viewer.

Several items can be selected simultaneously. As usual, ctrl key is used to select items alternately, and shift key allows to select items in a continuous range. After selection, the Remove button can be used to remove these items from the list.

The filter

It is used to filter out some of the loaded scans. This makes it much easier to deal with scans when the scan list is very long, which is often the case for instruments with small detectors. The filtering is done by pattern matching between the text introduced by the user and the items. Let’s see at some examples:

0222       # List scans starting by 0222
T=15       # List scans collected at 15 K. White-spaces around the equal sign are not significant. T = 15 or T =15 will work as well
T=15 + H=1 # List scans collected at T = 15 and H = 1
ome        # List omega scans
ome + T=15 # List omega scans collected at T=15

Fig. 5 Scan loader window.

Settings

Settings can be edited by clicking on Settings action in Edit menu (Fig. 6). The settings window contains some user preferences read by int3d when it is launched. The settings are organized in three groups:

Instrument

Busing-Levy frame, Detector origin

Type: string

Default values for each instrument. These values are only used when the instrument has not been configured.

External programs

FullProf Suite

Type: path to a folder

Folder where the FullProf suite is installed. This folder is automatically found by Int3D if the environment variable FULLPROF is set.

Text Editor

Type: path to an executable

Text editor for opening text files from the file explorer of Int3D.

Web browser

Type: path to an executable

Web browser for opening the online manual of Int3D from the menu Help.

Calibration files

XtremeD

Type: path to a file

Calibration file for XtremeD. It should be supplied by the instrument scientist.

Settings are saved written in the file to the file int3d.ini (see below).

Fig. 6 Settings window.

Initialization Files

Each time int3d initialises, it looks for two files called int3d.ini and settings.txt located in the user home directory.

int3d.ini

It contains the last ten projects opened by the user and the last working directory. After initialization, the working directory is taking from this file if it exists, and the list of recent projects are added to the menu Open Recent in the File menu.