3. How to Use

In this chapter we'll look at how to work with easyDiffraction.

3.1. easyDiffraction user interface

Here you can see what the program looks like. The application window is divided into parts that provide you with quick and easy access to everything you'll need. The parts are Toolbar, Main Window and Sidebar described in the following sections.

3.1.1. Toolbar

The toolbar at the top of the application window contains the buttons which represent the data analysis workflow. When you create a new project, all toolbar buttons but Home are disabled. When each step in the workflow is completed, the toolbar button which corresponds to the next step becomes enabled.

The following buttons (workflow steps) are present in the easyDiffraction toolbar:

  1. Home to manage your project (create new, open existing, etc.)
  2. Experimental Data to load experimentally measured data files.
  3. Sample Model to describe sample phases.
  4. Analysis to perform refinement of structural parameters.
  5. Summary to view and export summary report.

3.1.2. Main window

The Main Window of the program is located below the Toolbar and it can contain several tabs depending on the current step in the data analysis workflow. An example of the Main Window for the analysis step is shown in the figure below. You can switch between the Fitting and Text View at any time clicking on the required tab.

3.1.3. Sidebar

The Sidebar is located at the right side of the application window, below the Toolbar. It has 2 tabs: Basic controls and Advanced controls. Their contents depend on the selected tab in the Toolbar and the respective tab in the Main Window. You can switch between them at any time clicking on the required tab.

  1. Basic controls tab provides an access to essential actions and information fields.
  2. Advanced controls tab describes additional actions recommended for advanced users.

The content of the Basic controls and Advanced controls tabs for every workflow step are described in the sections below.

3.2. Data processing workflow

This section describes all the steps in the data processing with easyDiffraction, starting from the loading of input data files and ending with saving the calculated parameters.

3.2.1. Select between modeling and analysis

The selection can be performed just after the start of easyDiffraction, see the screenshot below:

3.2.2. Create/Open project

All manipulations with project can be performed on the Home tab.

To start with easyDiffraction, please click Open another project button in sidebar and select main.rcif file from one of the provided examples.

Supported file formats

Currently, easyDiffraction allows to work with the STAR/CIF data format. Click here to learn more about that.

Application main window

The application's main window shows:

  • Project name.
  • Project related information (Keywords, Phases labels, etc.).
  • Figures of the crystal structure and refinement curves.

Application sidebar

The application's sidebar contains the following groups:

  • Get Started group contains buttons to create, open, clone or save the project. Currently, the only enabled button is Open another project.
  • Recent Projects group is currently disabled.
  • Examples group is currently disabled.
  • Program Preferences are available here.

The very bottom of the sidebar contains the following buttons:

  • Experimental Data to go to the next step in the data processing.
  • Save Current State of the project (currently disabled).
  • Get Online Help for the current tab.
  • Report a bug or issue online.

3.2.3. Load experimental data

All manipulations with experimentally measured data can be performed on the Experimental Data tab.

Supported file formats

The instrument description is taken from the experiments.cif file. An example is given below: data_pnd

_diffrn_radiation_wavelength 0.84
_diffrn_radiation_polarization 0.0
_diffrn_radiation_efficiency 1.0
_diffrn_ambient_field 1.0

_pd_2theta_range_min 4.000
_pd_2theta_range_max 80.000
_pd_calib_2theta_offset -0.1()

_pd_instr_resolution_u 16.9776
_pd_instr_resolution_v -2.8357
_pd_instr_resolution_w 0.5763
_pd_instr_resolution_x 0.0
_pd_instr_resolution_y 0.0

_pd_chi2_sum True
_pd_chi2_diff False
_pd_chi2_up False
_pd_chi2_down False

loop_
_pd_phase_label
_pd_phase_scale
_pd_phase_igsize
Fe3O4 0.0238 0.0

loop_
_pd_background_2theta
_pd_background_intensity
4.5 255.95
40.0 157.96
80.0 64.78

Currently, easyDiffraction only supports the polarized powder diffraction data. An example of the data section of the experiments.cif file is shown below: loop_
_pd_meas_angle_2theta
_pd_meas_intensity_up
_pd_meas_intensity_up_sigma
_pd_meas_intensity_down
_pd_meas_intensity_down_sigma
4.0 465.8 128.97 301.88 129.3
4.2 323.78 118.22 206.06 120.0
4.4 307.14 115.9 230.47 116.53
4.6 172.13 115.84 236.52 113.74
4.8 164.31 110.75 291.6 110.73
5.0 166.47 106.51 426.73 109.08
5.2 217.67 104.66 183.24 107.79
5.4 84.01 99.91 179.87 99.98
5.6 220.87 98.72 297.76 99.83
5.8 223.46 98.77 149.78 98.18
6.0 408.25 96.89 356.86 96.41
6.2 381.21 94.03 287.26 96.94
...

  • _pd_meas_angle_2theta: Angular position of the Bragg peak.
  • _pd_meas_intensity_up: Intensity of scattered beam of neutrons polarized with spin "UP".
  • _pd_meas_intensity_up_sigma: Standard deviation of intensity "UP".
  • _pd_meas_intensity_down: Intensity of scattered beam of neutrons polarized with spin "DOWN".
  • _pd_meas_intensity_down_sigma: Standard deviation of intensity "DOWN".

Application main window

The application's main window contains the following tabs:

  1. Plot View shows the experimental data plots.
  2. Table View contains a table with the extracted data.
  3. Text View displays the content of the data file.

An interaction with the plot is performed as follows:

  • Show coordinates: Hover mouse pointer over the data point.
  • Zoom in: Drag with left mouse button pressed.
  • Reset zoom: Click right mouse button.

Application sidebar

The application's sidebar contains the following groups:

  • Data explorer shows experimental data file name and directory.
  • Instrument contains information about the neutron scattering instrument.
  • Peak profile contains information about the peak profile.
  • Misc contains miscellaneous information.

The very bottom of the sidebar contains the following buttons:

  • Home to go to the previous step in the data processing.
  • Sample Model to go to the next step in the data processing.
  • Save Current State of the project (currently disabled).
  • Get Online Help for the current tab.
  • Report a bug or issue online.

3.2.4. Define sample model

All manipulations with sample phases can be performed on the Sample Model tab.

Supported file formats

Currently, the structural model is taken from the phases.cif file, where it is described in the same way as in pure CIF. An example is shown below. Explanations about the full syntax can be found elsewhere. data_phase_1

_chemical_name_common 'Fe3O4'
_cell_length_a 8.56210
_cell_length_b 8.56210
_cell_length_c 8.56210
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_space_group_name_H-M_alt 'F d -3 m'
_space_group_IT_number 227

loop_
 _atom_site_label
 _atom_site_type_symbol
 _atom_site_fract_x
 _atom_site_fract_y
 _atom_site_fract_z
 _atom_site_occupancy
 _atom_site_adp_type
 _atom_site_B_iso_or_equiv
 Fe3A Fe 0.125000 0.125000 0.125000 1.0 Uiso 0.00000
 Fe3B Fe 0.500000 0.500000 0.500000 1.0 Uiso 0.00000
 O1   O  0.255210 0.255210 0.255210 1.0 Uiso 0.00000

Application main window

The application's main window contains the following tabs:

  1. Structure View shows a 3D crystal structure model.
  2. Text View displays the structure model in the CIF format.

An interaction with the plot is performed as follows:

  • Rotate structure: Drag with right mouse button pressed.
  • Zoom in/out: Scroll using mouse wheel.
  • Reset zoom and rotation: Click left mouse button.

Application sidebar

The application's sidebar contains the following groups:

  • Structural phases group shows the table of crystalline phases present in the sample. The parameters of the selected phase are given in the groups below.
  • Symmetry and cell parameters group contains information about space group crystal system, number, name and setting, as well as unit cell lengths and angles.
  • Atoms, atomic coordinates and occupations group contains details about the atom sites, such as label, color in the structure plot, coordinates and occupancy.
  • Atomic displacement parameters, also known as atomic vibration parameters or thermal parameters, are presented here.
  • Magnetic susceptibility parameters, or atomic site susceptibility tensor within local susceptibility approach, are given here.

The very bottom of the sidebar contains the following buttons:

  • Experimental Data to go to the previous step in the data processing.
  • Analysis to go to the next step in the data processing.
  • Save Current State of the project (currently disabled).
  • Get Online Help for the current tab.
  • Report a bug or issue online.

3.2.5. Perform data analysis

Data analysis (structure refinement) is performed in the Analysis tab.

Application main window

The application's main window contains the following tabs:

  1. Fitting shows plot of the data and model using current parameters.
  2. Text View displays the results of structure refinement in the START/CIF format.

An interaction with the plot shown in the Fitting tab is performed as follows:

  • View data point: Hover mouse over data point.
  • Zoom in: Hold left click and drag a box over desired area.
  • Reset view: Right mouse button.

Application sidebar

Each of the tabs of the main window have independent sidebar options.

The Fitting sidebar contains the following elements:

  • Parameters group shows the table of parameters. Starting values are shown, along with a checkbox for selecting the variable for fitting.
  • Start/Stop fitting button that initiates and stops fitting.
  • Accept refined parameters button (not implemented yet).

The Text View sidebar contans the following elements:

  • Find Search in the RCIF file (currently disabled).

The very bottom of the sidebar contains the following buttons of each tab:

  • Sample Model to go to the previous step in the data processing.
  • Summary to go to the next step in the data processing.
  • Save Current State of the project (currently disabled).
  • Get Online Help for the current tab.
  • Report a bug or issue online.

3.2.6. Generate summary report

Here you can view and export the summary report.

Application main window

The application's main window contains the following tabs:

  1. Report shows the report for the performed data analysis.

The report contains the following:

  • Project related information.
  • Parameters displays table with all parameters.
  • Fitting shows plot of data and model with current parameters.
  • Structure contains 3D view of structure.

Application sidebar

The application's sidebar contains the following elements:

  • Export as... contains export button, field for custom report name and drop down menu for file format.
  • Export elements has checkboxes for each element in the report to select those that should be exported (currently disabled).

The very bottom of the sidebar contains the following buttons of each tab:

  • Analysis to go to the previous step in the data processing.
  • Save Current State of the project (currently disabled).
  • Get Online Help for the current tab.
  • Report a bug or issue online.