Simulation pd-xray NaCl¶

This example demonstrates how to simulate a powder diffraction pattern of NaCl for the X-ray case.

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='pd-xray')
print(job.type)

job = ed.Job(type='pd-xray') print(job.type)

Job type: pd-cwl-unp-1d-xray

Define a model¶

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,
                        u_iso_or_equiv=0.01)
phase.atom_sites.append(label='Cl',
                        type_symbol='Cl',
                        fract_x=0,
                        fract_y=0,
                        fract_z=0.5,
                        occupancy=1,
                        u_iso_or_equiv=0.01)

phase.atom_sites.append(label='Na', type_symbol='Na', fract_x=0, fract_y=0, fract_z=0, occupancy=1, u_iso_or_equiv=0.01) phase.atom_sites.append(label='Cl', type_symbol='Cl', fract_x=0, fract_y=0, fract_z=0.5, occupancy=1, u_iso_or_equiv=0.01)

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_U_iso_or_equiv
Na Na 0.00000000 0.00000000 0.00000000 1.00000000 Uiso 0.01
Cl Cl 0.00000000 0.00000000 0.5 1.00000000 Uiso 0.01

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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Define an experiment¶

Although in this example we only simulate the diffraction pattern, some parameters for the ‘virtual experiment’ still need to be set. For example, the wavelength of the X-ray beam, the range of 2-theta angles, etc.

Let's start by setting the range and step of the 2-theta angles. The other parameters will be set later.

In [11]:

job.instrument.twotheta_range_min = 20
job.instrument.twotheta_range_max = 160
job.instrument.twotheta_range_inc = 0.05

job.instrument.twotheta_range_min = 20 job.instrument.twotheta_range_max = 160 job.instrument.twotheta_range_inc = 0.05

Perform an analysis¶

Display the analysis chart before changing the values of other parameters from their default values.

In [12]:

job.show_simulation_chart()

job.show_simulation_chart()

Show the names of all parameters, their values, etc. Parameter names can be used to access the parameter and change its value.

In [13]:

job.show_parameters()

job.show_parameters()

	name	value		error	min	max	vary
1	.phases['nacl'].cell.length_a	5.691694	Å		0.0	inf
2	.phases['nacl'].atom_sites['Na'].occupancy	1.000000			-inf	inf
3	.phases['nacl'].atom_sites['Na'].fract_x	0.000000			-inf	inf
4	.phases['nacl'].atom_sites['Na'].fract_y	0.000000			-inf	inf
5	.phases['nacl'].atom_sites['Na'].fract_z	0.000000			-inf	inf
6	.phases['nacl'].atom_sites['Na'].u_iso_or_equiv	0.010000	Ų		0.0	inf
7	.phases['nacl'].atom_sites['Cl'].occupancy	1.000000			-inf	inf
8	.phases['nacl'].atom_sites['Cl'].fract_x	0.000000			-inf	inf
9	.phases['nacl'].atom_sites['Cl'].fract_y	0.000000			-inf	inf
10	.phases['nacl'].atom_sites['Cl'].fract_z	0.500000			-inf	inf
11	.phases['nacl'].atom_sites['Cl'].u_iso_or_equiv	0.010000	Ų		0.0	inf
12	.phases['nacl'].scale	1.000000			0.0	inf	True
13	.instrument.wavelength	1.540560	Å		-inf	inf
14	.instrument.resolution_u	0.000200			-inf	inf
15	.instrument.resolution_v	-0.000200			-inf	inf
16	.instrument.resolution_w	0.012000			-inf	inf
17	.instrument.resolution_x	0.000000			-inf	inf
18	.instrument.resolution_y	0.000000			-inf	inf
19	.instrument.reflex_asymmetry_p1	0.000000			-inf	inf
20	.instrument.reflex_asymmetry_p2	0.000000			-inf	inf
21	.instrument.reflex_asymmetry_p3	0.000000			-inf	inf
22	.instrument.reflex_asymmetry_p4	0.000000			-inf	inf
23	.pattern.zero_shift	0.000000	deg		-inf	inf

Change the default value of the wavelength used in the experiment and display the analysis chart again

In [14]:

job.instrument.wavelength = 1.5
job.show_simulation_chart()

job.instrument.wavelength = 1.5 job.show_simulation_chart()

Change the default values of the peak profile related parameters and display the analysis chart again

In [15]:

job.instrument.resolution_u = 0.1
job.instrument.resolution_v = -0.1
job.instrument.resolution_w = 0.2
job.show_simulation_chart()

job.instrument.resolution_u = 0.1 job.instrument.resolution_v = -0.1 job.instrument.resolution_w = 0.2 job.show_simulation_chart()

Change the value of the unit cell parameter and display the analysis chart again

In [16]:

job.phases['nacl'].cell.length_a = 5.0
job.show_simulation_chart()

job.phases['nacl'].cell.length_a = 5.0 job.show_simulation_chart()