Fitting pd-neut-tof Si-SEPD¶

This example shows how to refine the crystal structure parameters of Si from neutron diffraction data in a time-of-flight experiment performed on SEPD diffractometer at Argonne.

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(type='tof')
print(job.type)

job = ed.Job(type='tof') print(job.type)

Job type: pd-tof-unp-1d-neut

Define a model¶

Create a phase object

In [4]:

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

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

Set space group

In [5]:

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

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

Set cell parameters

In [6]:

phase.cell.length_a = 5.43146

phase.cell.length_a = 5.43146

Add atoms

In [7]:

phase.atom_sites.append(label='Si',
                        type_symbol='Si',
                        fract_x=0,
                        fract_y=0,
                        fract_z=0,
                        occupancy=1,
                        b_iso_or_equiv=0.529)

phase.atom_sites.append(label='Si', type_symbol='Si', fract_x=0, fract_y=0, fract_z=0, occupancy=1, b_iso_or_equiv=0.529)

Add phase to the job object

In [8]:

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

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

Several values of it_coordinate_system_code have been defined:
2, 1
The default value has been choosen:'2'.

Several values of it_coordinate_system_code have been defined:
2, 1
The default value has been choosen:'2'.
Collection of 1 phases: ['si']

Show phase info in CIF format

In [9]:

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

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

data_si
_cell_length_a 5.43146
_cell_length_b 5.43146
_cell_length_c 5.43146
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_space_group_name_H-M_ref 'F d -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
Si Si 0.00000000 0.00000000 0.00000000 1.00000000 Biso 0.529

Display the crystal structure of a given model

In [10]:

job.show_crystal_structure(id='si')

job.show_crystal_structure(id='si')

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Define an experiment¶

Download the data file from the EasyDiffraction repository on GitHub

In [11]:

ed.download_from_repository('sepd.xye', destination='data')

ed.download_from_repository('sepd.xye', destination='data')

Show content of the downloaded file (first 5 lines)

In [12]:

with open('data/sepd.xye') as f:
    print(''.join(f.readlines()[:5]))

with open('data/sepd.xye') as f: print(''.join(f.readlines()[:5]))

2000.0 213.8 3.3
2005.0 213.8 3.3
2010.0 210.1 3.3
2015.0 213.3 3.3
2020.0 211.9 3.3

Load experimentally measured data from a file in XYE format

In [13]:

job.add_experiment_from_file('data/sepd.xye')

job.add_experiment_from_file('data/sepd.xye')

Display the experimentally measured data

In [14]:

job.show_experiment_chart(show_legend=False)

job.show_experiment_chart(show_legend=False)