Structure Refinement: Taurine, SENJU¶

Crystal structure refinement of Taurine using time-of-flight single crystal neutron diffraction data from SENJU at J-PARC.

Import Library¶

In [2]:

import easydiffraction as ed

import easydiffraction as ed

Step 1: Define Project¶

In [3]:

# Create minimal project without name and description
project = ed.Project()

# Create minimal project without name and description project = ed.Project()

Step 2: Define Structure¶

In [4]:

# Download CIF file from repository
structure_path = ed.download_data(id=21, destination='data')

# Download CIF file from repository structure_path = ed.download_data(id=21, destination='data')

Getting data...

Data #21: Taurine (crystal structure)

✅ Data #21 downloaded to 'data/ed-21.cif'

In [5]:

project.structures.add_from_cif_path(structure_path)

project.structures.add_from_cif_path(structure_path)

In [6]:

project.structures.show_names()

project.structures.show_names()

Defined structures 🧩

['taurine']

In [7]:

structure = project.structures['taurine']

structure = project.structures['taurine']

In [8]:

# structure.show_as_cif()

# structure.show_as_cif()

Step 3: Define Experiment¶

In [9]:

data_path = ed.download_data(id=22, destination='data')

data_path = ed.download_data(id=22, destination='data')

Getting data...

Data #22: Taurine, SENJU (J-PARC)

✅ Data #22 downloaded to 'data/ed-22.xye'

In [10]:

project.experiments.add_from_data_path(
    name='senju',
    data_path=data_path,
    sample_form='single crystal',
    beam_mode='time-of-flight',
    radiation_probe='neutron',
)

project.experiments.add_from_data_path( name='senju', data_path=data_path, sample_form='single crystal', beam_mode='time-of-flight', radiation_probe='neutron', )

Data loaded successfully

Experiment 🔬 'senju'. Number of data points: 286.

In [11]:

experiment = project.experiments['senju']

experiment = project.experiments['senju']

In [12]:

experiment.linked_crystal.id = 'taurine'
experiment.linked_crystal.scale = 1.0

experiment.linked_crystal.id = 'taurine' experiment.linked_crystal.scale = 1.0

In [13]:

experiment.extinction.mosaicity = 1000.0
experiment.extinction.radius = 100.0

experiment.extinction.mosaicity = 1000.0 experiment.extinction.radius = 100.0

Step 4: Perform Analysis¶

In [14]:

project.plot_meas_vs_calc(expt_name='senju')

project.plot_meas_vs_calc(expt_name='senju')

In [15]:

experiment.linked_crystal.scale.free = True
experiment.extinction.radius.free = True

experiment.linked_crystal.scale.free = True experiment.extinction.radius.free = True

In [16]:

# experiment.show_as_cif()

# experiment.show_as_cif()

In [17]:

# Start refinement. All parameters, which have standard uncertainties
# in the input CIF files, are refined by default.
project.analysis.fit()

# Start refinement. All parameters, which have standard uncertainties # in the input CIF files, are refined by default. project.analysis.fit()

Using experiment 🔬 'senju' for 'single' fitting

🚀 Starting fit process with 'lmfit (leastsq)'...

📈 Goodness-of-fit (reduced χ²) change:

	iteration	χ²	improvement [%]
1	1	748.12
2	64	465.20	37.8% ↓
3	123	93.07	80.0% ↓
4	182	34.96	62.4% ↓
5	241	24.65	29.5% ↓
6	300	24.21	1.8% ↓
7	359	23.78	1.8% ↓
8	1003	23.56

🏆 Best goodness-of-fit (reduced χ²) is 23.56 at iteration 958

✅ Fitting complete.

In [18]:

# Show fit results summary
project.analysis.show_fit_results()

# Show fit results summary project.analysis.show_fit_results()

Fit results

❌ Success: False

⏱️ Fitting time: 20.90 seconds

📏 Goodness-of-fit (reduced χ²): 23.56

📏 R-factor (Rf): 21.59%

📏 R-factor squared (Rf²): 16.98%

📏 Weighted R-factor (wR): 17.74%

📈 Fitted parameters:

	datablock	category	entry	parameter	start	fitted	uncertainty	units	change
1	taurine	atom_site	S1	fract_x	0.2000	0.2044	N/A		2.18 % ↑
2	taurine	atom_site	S1	fract_y	0.3500	0.3469	N/A		0.90 % ↓
3	taurine	atom_site	S1	fract_z	0.3500	0.3482	N/A		0.52 % ↓
4	taurine	atom_site	S1	b_iso	1.5791	1.1417	N/A	Ų	27.70 % ↓
5	taurine	atom_site	O1	fract_x	0.3130	0.3181	N/A		1.62 % ↑
6	taurine	atom_site	O1	fract_y	0.2400	0.2414	N/A		0.57 % ↑
7	taurine	atom_site	O1	fract_z	0.3510	0.3521	N/A		0.31 % ↑
8	taurine	atom_site	O1	b_iso	2.7635	2.7912	N/A	Ų	1.00 % ↑
9	taurine	atom_site	O2	fract_x	0.9380	0.9396	N/A		0.17 % ↑
10	taurine	atom_site	O2	fract_y	0.3370	0.3381	N/A		0.32 % ↑
11	taurine	atom_site	O2	fract_z	0.2940	0.2928	N/A		0.41 % ↓
12	taurine	atom_site	O2	b_iso	3.6320	3.7348	N/A	Ų	2.83 % ↑
13	taurine	atom_site	O3	fract_x	0.2220	0.2248	N/A		1.25 % ↑
14	taurine	atom_site	O3	fract_y	0.4120	0.4093	N/A		0.66 % ↓
15	taurine	atom_site	O3	fract_z	0.5070	0.5071	N/A		0.02 % ↑
16	taurine	atom_site	O3	b_iso	1.8950	2.1451	N/A	Ų	13.20 % ↑
17	taurine	atom_site	N1	fract_x	0.2640	0.2637	N/A		0.10 % ↓
18	taurine	atom_site	N1	fract_y	0.6280	0.6273	N/A		0.12 % ↓
19	taurine	atom_site	N1	fract_z	0.3310	0.3326	N/A		0.48 % ↑
20	taurine	atom_site	N1	b_iso	2.1318	2.1431	N/A	Ų	0.53 % ↑
21	taurine	atom_site	H1	fract_x	0.1330	0.1364	N/A		2.53 % ↑
22	taurine	atom_site	H1	fract_y	0.5880	0.5844	N/A		0.61 % ↓
23	taurine	atom_site	H1	fract_z	0.4210	0.4159	N/A		1.20 % ↓
24	taurine	atom_site	H1	b_iso	3.3951	2.4978	N/A	Ų	26.43 % ↓
25	taurine	atom_site	H2	fract_x	0.1910	0.1874	N/A		1.89 % ↓
26	taurine	atom_site	H2	fract_y	0.7150	0.7140	N/A		0.14 % ↓
27	taurine	atom_site	H2	fract_z	0.3120	0.3078	N/A		1.33 % ↓
28	taurine	atom_site	H2	b_iso	4.5795	4.2614	N/A	Ų	6.95 % ↓
29	taurine	atom_site	H3	fract_x	0.4400	0.4321	N/A		1.80 % ↓
30	taurine	atom_site	H3	fract_y	0.6240	0.6255	N/A		0.24 % ↑
31	taurine	atom_site	H3	fract_z	0.3490	0.3482	N/A		0.22 % ↓
32	taurine	atom_site	H3	b_iso	4.6585	4.9394	N/A	Ų	6.03 % ↑
33	taurine	atom_site	C1	fract_x	0.3440	0.3479	N/A		1.12 % ↑
34	taurine	atom_site	C1	fract_y	0.4400	0.4402	N/A		0.04 % ↑
35	taurine	atom_site	C1	fract_z	0.2020	0.2025	N/A		0.22 % ↑
36	taurine	atom_site	C1	b_iso	1.7371	1.6820	N/A	Ų	3.17 % ↓
37	taurine	atom_site	H11	fract_x	0.5520	0.5466	N/A		0.98 % ↓
38	taurine	atom_site	H11	fract_y	0.4330	0.4341	N/A		0.26 % ↑
39	taurine	atom_site	H11	fract_z	0.2430	0.2403	N/A		1.09 % ↓
40	taurine	atom_site	H11	b_iso	3.3951	3.4650	N/A	Ų	2.06 % ↑
41	taurine	atom_site	H12	fract_x	0.3200	0.3264	N/A		2.00 % ↑
42	taurine	atom_site	H12	fract_y	0.3880	0.3774	N/A		2.74 % ↓
43	taurine	atom_site	H12	fract_z	0.0810	0.0851	N/A		5.02 % ↑
44	taurine	atom_site	H12	b_iso	3.3162	3.2415	N/A	Ų	2.25 % ↓
45	taurine	atom_site	C2	fract_x	0.2000	0.1949	N/A		2.56 % ↓
46	taurine	atom_site	C2	fract_y	0.5570	0.5548	N/A		0.40 % ↓
47	taurine	atom_site	C2	fract_z	0.1820	0.1786	N/A		1.88 % ↓
48	taurine	atom_site	C2	b_iso	1.7371	1.8770	N/A	Ų	8.06 % ↑
49	taurine	atom_site	H21	fract_x	0.2760	0.2722	N/A		1.39 % ↓
50	taurine	atom_site	H21	fract_y	0.6000	0.5975	N/A		0.42 % ↓
51	taurine	atom_site	H21	fract_z	0.0770	0.0737	N/A		4.27 % ↓
52	taurine	atom_site	H21	b_iso	2.1318	2.3711	N/A	Ų	11.23 % ↑
53	taurine	atom_site	H22	fract_x	0.9990	0.9998	N/A		0.08 % ↑
54	taurine	atom_site	H22	fract_y	0.5490	0.5544	N/A		0.99 % ↑
55	taurine	atom_site	H22	fract_z	0.1610	0.1667	N/A		3.57 % ↑
56	taurine	atom_site	H22	b_iso	4.9743	4.4547	N/A	Ų	10.45 % ↓
57	senju	extinction		radius	100.0000	2.0159	N/A	µm	97.98 % ↓
58	senju	linked_crystal		scale	1.0000	1.3517	N/A		35.17 % ↑

In [19]:

# experiment.show_as_cif()

# experiment.show_as_cif()

In [20]:

project.experiments.show_names()

project.experiments.show_names()

Defined experiments 🔬

['senju']

In [21]:

project.plot_meas_vs_calc(expt_name='senju')

project.plot_meas_vs_calc(expt_name='senju')

Step 5: Show Project Summary¶

In [22]:

project.summary.show_report()

project.summary.show_report()

————————————
PROJECT INFO
————————————

Title

Untitled Project

—————————————————————
CRYSTALLOGRAPHIC DATA
—————————————————————

Phase datablock

🧩 taurine

Space group

P 21/c

Cell parameters

	Parameter	Value
1	a	5.27290
2	b	11.65650
3	c	7.83830
4	alpha	90.00000
5	beta	94.01100
6	gamma	90.00000

Atom sites

	label	type	x	y	z	occ	Biso
1	S1	S	0.20436	0.34685	0.34817	1.00000	1.14166
2	O1	O	0.31806	0.24136	0.35209	1.00000	2.79115
3	O2	O	0.93958	0.33809	0.29279	1.00000	3.73482
4	O3	O	0.22478	0.40927	0.50709	1.00000	2.14513
5	N1	N	0.26375	0.62726	0.33259	1.00000	2.14310
6	H1	H	0.13636	0.58442	0.41594	1.00000	2.49781
7	H2	H	0.18740	0.71402	0.30784	1.00000	4.26140
8	H3	H	0.43207	0.62553	0.34824	1.00000	4.93944
9	C1	C	0.34787	0.44016	0.20245	1.00000	1.68200
10	H11	H	0.54661	0.43411	0.24035	1.00000	3.46501
11	H12	H	0.32640	0.37737	0.08507	1.00000	3.24146
12	C2	C	0.19488	0.55477	0.17858	1.00000	1.87705
13	H21	H	0.27217	0.59751	0.07371	1.00000	2.37111
14	H22	H	0.99978	0.55443	0.16674	1.00000	4.45472

———————————
EXPERIMENTS
———————————

Experiment datablock

🔬 senju

Experiment type

single crystal, neutron, time-of-flight

———————
FITTING
———————

Calculation engine

  senju: CalculatorEnum.CRYSPY

Minimization engine

lmfit

Fit quality

	metric	value
1	Goodness-of-fit (reduced χ²)	23.56