Define a model¶

This example shows how to define a model of a crystal structure in EasyDiffraction.

Import EasyDiffraction¶

In [2]:

import easydiffraction as ed

import easydiffraction as ed

Create a job¶

Create a job — the main object to store all the information

In [3]:

job = ed.Job()

job = ed.Job()

Define a model¶

Set manually¶

Create a phase object

In [4]:

phase = ed.Phase(name='nacl')

phase = ed.Phase(name='nacl')

Set space group

In [5]:

phase.space_group.name_hm_alt = 'F m -3 m'

phase.space_group.name_hm_alt = 'F m -3 m'

Set cell parameters

In [6]:

phase.cell.length_a = 5.691694

phase.cell.length_a = 5.691694

Add atoms

In [7]:

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)

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)

Add phase to the job object

In [8]:

job.add_phase(phase=phase)
print(job.phases)

job.add_phase(phase=phase) print(job.phases)

Collection of 1 phases: ['nacl']

Show phase info in CIF format

In [9]:

phase = job.phases['nacl']
print(phase.cif)

phase = job.phases['nacl'] print(phase.cif)

data_nacl
_cell_length_a 5.691694
_cell_length_b 5.691694
_cell_length_c 5.691694
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_space_group_name_H-M_ref 'F m -3 m'

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
Na Na 0.00000000 0.00000000 0.00000000 1.00000000 Biso 0.5
Cl Cl 0.00000000 0.00000000 0.5 1.00000000 Biso 0.5

Display the crystal structure of a given model

In [10]:

job.show_crystal_structure(id='nacl')

job.show_crystal_structure(id='nacl')

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Load from CIF¶

Download the CIF file from the EasyDiffraction repository on GitHub

In [11]:

ed.download_from_repository('lbco.cif', destination='data')

ed.download_from_repository('lbco.cif', destination='data')

Load a phase from the downloaded CIF file

In [12]:

job.add_phase_from_file('data/lbco.cif')
print(job.phases)

job.add_phase_from_file('data/lbco.cif') print(job.phases)

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

Show phase info in CIF format

In [13]:

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

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

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'

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

Display the crystal structure of a given model

In [14]:

job.show_crystal_structure(id='lbco')

job.show_crystal_structure(id='lbco')

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