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Model

The Model in EasyDiffraction represents the crystallographic structure used to calculate the diffraction pattern. This pattern is then compared to the experimental data to analyze and refine the structural parameters.

EasyDiffraction allows you to:

  • Load an existing model from a CIF file.
  • Manually define a new model 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 imported the easydiffraction package and created a Job object, as described in the Getting started section.

Defining a Model Manually

You can manually define a model by specifying the space group, unit cell parameters, and atomic positions.

Example: Creating a NaCl Model

# Create a phase object
phase = ed.Phase(name='nacl')

# Set space group
phase.space_group.name_hm_alt = 'F m -3 m'

# Define unit cell parameters
phase.cell.length_a = 5.691694

# Add atomic sites
phase.atom_sites.append(label='Na',
                        type_symbol='Na',
                        fract_x=0,
                        fract_y=0,
                        fract_z=0,
                        occupancy=1,
                        b_iso_or_equiv=0.5)
phase.atom_sites.append(label='Cl',
                        type_symbol='Cl',
                        fract_x=0,
                        fract_y=0,
                        fract_z=0.5,
                        occupancy=1,
                        b_iso_or_equiv=0.5)

Loading a Model from a CIF File

Instead of defining the model manually, you can load a crystallographic information file (CIF) directly:

# Load a phase from a CIF file
job.add_phase_from_file('data/lbco.cif')

Listing Defined Phases

To check which phases have been added to the Job, use:

print(job.phases)

Expected output:

Collection of 2 phases: ['nacl', 'lbco']

Viewing a Phase as a CIF File

To inspect a phase in CIF format, use:

print(job.phases['lbco'].cif)

Example output:

data_lbco
_cell_length_a 3.88
_cell_length_b 3.88
_cell_length_c 3.88
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_space_group_name_H-M_ref 'P m -3 m'
_space_group_IT_coordinate_system_code 1

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
La La 0.00000000 0.00000000 0.00000000 0.5 Biso 0.1
Ba Ba 0.00000000 0.00000000 0.00000000 0.5 Biso 0.1
Co Co 0.5 0.5 0.5 1.00000000 Biso 0.1
O O 0.00000000 0.5 0.5 1.00000000 Biso 0.1

Now that the Model has been defined, you can proceed to the next step: Experiment.