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Structure

The Structure in EasyDiffraction represents the crystallographic structure used to calculate the diffraction pattern, which is then fitted to the experimentally measured data to refine the structural parameters.

EasyDiffraction allows you to:

  • Load an existing model from a file (CIF format).
  • Manually define a new structure by specifying crystallographic parameters.

Below, you will find instructions on how to define and manage crystallographic models in EasyDiffraction. It is assumed that you have already created a project object, as described in the Project section.

Adding a Model from CIF

This is the most straightforward way to define a structure in EasyDiffraction. If you have a crystallographic information file (CIF) for your structure, you can add it to your project using the add_from_cif_path method of the project.structures collection. In this case, the name of the model will be taken from CIF.

# Load a phase from a CIF file
project.structures.add_from_cif_path('data/lbco.cif')

Accessing the model after loading it will be done through the structures collection of the project instance. The name of the model will be the same as the data block id in the CIF file. For example, if the CIF file contains a data block with the id lbco,

data_lbco

_space_group.name_H-M_alt  "P m -3 m"
...

you can access it in the code as follows:

# Access the structure by its name
project.structures['lbco']

Defining a Model Manually

If you do not have a CIF file or prefer to define the model manually, you can use the create method of the structures object of the project instance. In this case, you will need to specify the name of the model, which will be used to reference it later.

# Add a structure with default parameters
# The structure name is used to reference it later.
project.structures.create(name='nacl')

The add method creates a new structure with default parameters. You can then modify its parameters to match your specific crystallographic structure. All parameters are grouped into the following categories, which makes it easier to manage the model:

  1. Space Group Category: Defines the symmetry of the crystal structure.
  2. Cell Category: Specifies the dimensions and angles of the unit cell.
  3. Atom Sites Category: Describes the positions and properties of atoms within the unit cell.

1. Space Group Category

# Set space group
project.structures['nacl'].space_group.name_h_m = 'F m -3 m'

2. Cell Category

# Define unit cell parameters
project.structures['nacl'].cell.length_a = 5.691694

3. Atom Sites Category

# Add atomic sites
project.structures['nacl'].atom_sites.create(
    label='Na',
    type_symbol='Na',
    fract_x=0,
    fract_y=0,
    fract_z=0,
    occupancy=1,
    b_iso_or_equiv=0.5,
)
project.structures['nacl'].atom_sites.create(
    label='Cl',
    type_symbol='Cl',
    fract_x=0,
    fract_y=0,
    fract_z=0.5,
    occupancy=1,
    b_iso_or_equiv=0.5,
)

Listing Defined Models

To check which structures have been added to the project, use:

# Show defined structures
project.structures.show_names()

Expected output:

Defined structures 🧩
['lbco', 'nacl']

Viewing a Model as CIF

To inspect a structure in CIF format, use:

# Show structure as CIF
project.structures['lbco'].show_as_cif()

Example output:

Structure 🧩 'lbco' as cif
╒═══════════════════════════════════════════╕
│ data_lbco                                 │
│                                           │
│ _space_group.IT_coordinate_system_code  1 │
│ _space_group.name_H-M_alt  "P m -3 m"     │
│                                           │
│ _cell.angle_alpha  90                     │
│ _cell.angle_beta  90                      │
│ _cell.angle_gamma  90                     │
│ _cell.length_a  3.88                      │
│ _cell.length_b  3.88                      │
│ _cell.length_c  3.88                      │
│                                           │
│ loop_                                     │
│ _atom_site.ADP_type                       │
│ _atom_site.B_iso_or_equiv                 │
│ _atom_site.fract_x                        │
│ _atom_site.fract_y                        │
│ _atom_site.fract_z                        │
│ _atom_site.label                          │
│ _atom_site.occupancy                      │
│ _atom_site.type_symbol                    │
│ _atom_site.Wyckoff_letter                 │
│ Biso 0.5 0.0 0.0 0.0 La 0.5 La a          │
│ Biso 0.5 0.0 0.0 0.0 Ba 0.5 Ba a          │
│ Biso 0.5 0.5 0.5 0.5 Co 1.0 Co b          │
│ Biso 0.5 0.0 0.5 0.5 O 1.0 O c            │
╘═══════════════════════════════════════════╛

Saving a Model

Saving the project, as described in the Project section, will also save the model. Each model is saved as a separate CIF file in the structures subdirectory of the project directory. The project file contains references to these files.

Below is an example of the saved CIF file for the lbco model:

data_lbco

_space_group.name_H-M_alt              "P m -3 m"
_space_group.IT_coordinate_system_code 1

_cell.length_a      3.8909
_cell.length_b      3.8909
_cell.length_c      3.8909
_cell.angle_alpha  90
_cell.angle_beta   90
_cell.angle_gamma  90

loop_
_atom_site.label
_atom_site.type_symbol
_atom_site.fract_x
_atom_site.fract_y
_atom_site.fract_z
_atom_site.Wyckoff_letter
_atom_site.occupancy
_atom_site.adp_type
_atom_site.B_iso_or_equiv
La La   0   0   0     a   0.5  Biso 0.4958
Ba Ba   0   0   0     a   0.5  Biso 0.4943
Co Co   0.5 0.5 0.5   b   1    Biso 0.2567
O  O    0   0.5 0.5   c   1    Biso 1.4041


Now that the crystallographic model has been defined and added to the project, you can proceed to the next step: Experiment.