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 edi

import easydiffraction as edi

📦 Define Project¶

In [3]:

# Create a minimal project with a short name
project = edi.Project(name='taurine_senju')

# Create a minimal project with a short name project = edi.Project(name='taurine_senju')

🧩 Define Structure¶

In [4]:

# Download CIF file from repository
structure_path = edi.download_data('struct-taurine', destination='data')

# Download CIF file from repository structure_path = edi.download_data('struct-taurine', destination='data')

Getting data...

Data 'struct-taurine': Taurine (crystal structure)

✅ Data 'struct-taurine' downloaded to '../../../data/struct-taurine.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_text()

structure.show_as_text()

Structure 🧩 'taurine' as text

	Edi
1	data_taurine
2
3	_cell.length_a 5.2729
4	_cell.length_b 11.6565
5	_cell.length_c 7.8383
6	_cell.angle_alpha 90.
7	_cell.angle_beta 94.011
8	_cell.angle_gamma 90.
9
10	_space_group.name_h_m "P 21/c"
11	_space_group.coord_system_code b1
12
13	_geom.min_bond_distance_cutoff 0.
14	_geom.bond_distance_inc 0.25
15
16	loop_
17	_atom_site.id
18	_atom_site.type_symbol
19	_atom_site.fract_x
20	_atom_site.fract_y
21	_atom_site.fract_z
22	_atom_site.wyckoff_letter
23	_atom_site.multiplicity
24	_atom_site.occupancy
25	_atom_site.adp_iso
26	_atom_site.adp_type
27	S1 S 0.2000(10) 0.3500(10) 0.3500(10) e 4 1. 1.57910(10) Biso
28	O1 O 0.3130(10) 0.2400(10) 0.3510(10) e 4 1. 2.76350(10) Biso
29	O2 O 0.9380(10) 0.3370(10) 0.2940(10) e 4 1. 3.63200(10) Biso
30	O3 O 0.2220(10) 0.4120(10) 0.5070(10) e 4 1. 1.89500(10) Biso
31	N1 N 0.2640(10) 0.6280(10) 0.3310(10) e 4 1. 2.13180(10) Biso
32	H1 H 0.1330(10) 0.5880(10) 0.4210(10) e 4 1. 3.39510(10) Biso
33	H2 H 0.1910(10) 0.7150(10) 0.3120(10) e 4 1. 4.57950(10) Biso
34	H3 H 0.4400(10) 0.6240(10) 0.3490(10) e 4 1. 4.65850(10) Biso
35	C1 C 0.3440(10) 0.4400(10) 0.2020(10) e 4 1. 1.73710(10) Biso
36	H11 H 0.5520(10) 0.4330(10) 0.2430(10) e 4 1. 3.39510(10) Biso
37	H12 H 0.3200(10) 0.3880(10) 0.0810(10) e 4 1. 3.31620(10) Biso
38	C2 C 0.2000(10) 0.5570(10) 0.1820(10) e 4 1. 1.73710(10) Biso
39	H21 H 0.2760(10) 0.6000(10) 0.0770(10) e 4 1. 2.13180(10) Biso
40	H22 H 0.9990(10) 0.5490(10) 0.1610(10) e 4 1. 4.97430(10) Biso

In [9]:

project.display.structure(struct_name='taurine')

project.display.structure(struct_name='taurine')

Structure 🧩 'taurine' (Atom view type: 'covalent')

Loading plot…

drag = rotate
wheel = zoom
right-drag = pan

🔬 Define Experiment¶

In [10]:

# Download data file from repository
data_path = edi.download_data('meas-taurine-senju', destination='data')

# Download data file from repository data_path = edi.download_data('meas-taurine-senju', destination='data')

Getting data...

Data 'meas-taurine-senju': Taurine, SENJU (J-PARC)

✅ Data 'meas-taurine-senju' downloaded to '../../../data/meas-taurine-senju.xye'

In [11]:

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 [12]:

experiment = project.experiments['senju']

experiment = project.experiments['senju']

In [13]:

experiment.linked_structure.structure_id = 'taurine'
experiment.linked_structure.scale = 1.0

experiment.linked_structure.structure_id = 'taurine' experiment.linked_structure.scale = 1.0

In [14]:

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

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

🚀 Perform Analysis¶

ADP iso¶

In [15]:

project.display.pattern(expt_name='senju')

project.display.pattern(expt_name='senju')

Loading plot…

In [16]:

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

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

In [17]:

project.analysis.minimizer.show_supported()

project.analysis.minimizer.show_supported()

Minimizer types

		Type	Description
1		bumps	BUMPS library using the default Levenberg-Marquardt method
2		bumps (amoeba)	BUMPS library with Nelder-Mead simplex method
3		bumps (de)	BUMPS library with differential evolution method
4		bumps (dream)	BUMPS library with DREAM Bayesian sampling
5		bumps (lm)	BUMPS library with Levenberg-Marquardt method
6		dfols	DFO-LS library for derivative-free least-squares optimization
7		emcee	emcee affine-invariant ensemble Bayesian sampling
8		lmfit	LMFIT library using the default Levenberg-Marquardt method
9		lmfit (least_squares)	LMFIT library with SciPy's trust region reflective algorithm
10	*	lmfit (leastsq)	LMFIT library with Levenberg-Marquardt least squares method

In [18]:

project.analysis.minimizer.type = 'bumps'

project.analysis.minimizer.type = 'bumps'

⚠️ Switching minimizer type removes these settings:
• gradient_tolerance

Current minimizer changed to

bumps

In [19]:

# Limit number of iterations to prevent long calculation time in this tutorial.
project.analysis.minimizer.max_iterations = 500

# Limit number of iterations to prevent long calculation time in this tutorial. project.analysis.minimizer.max_iterations = 500

In [20]:

project.analysis.minimizer.chi_square_change_tolerance = 1e-2

project.analysis.minimizer.chi_square_change_tolerance = 1e-2

In [21]:

# 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()

Standard fitting

📋 Using experiment 🔬 'senju' for 'single' fitting

🚀 Starting fit process with 'bumps (lm)'...

📈 Goodness-of-fit progress:

	iteration	time (s)	χ²	change / status
1	1	0.01	748.12
2	62	0.62	465.67	37.8% ↓
3	121	1.19	93.43	79.9% ↓
4	180	1.77	34.99	62.5% ↓
5	239	2.33	24.65	29.6% ↓
6	298	2.88	24.22	1.8% ↓
7	357	3.43	23.78	1.8% ↓
8	419	8.97	23.71

🏆 Best goodness-of-fit (reduced χ²) is 23.71 at iteration 419

✅ Fitting complete.

In [22]:

# Show fit results summary
project.display.fit.results()

# Show fit results summary project.display.fit.results()

⚙️ Settings used:

	Name	Value	Description
1	max_iterations	500	Maximum solver iterations.
2	chi_square_change_tolerance	0.01	Relative change in the objective (chi-square) used to stop fitting.
3	parameter_change_tolerance	1e-08	Relative change in fitted parameters used to stop fitting.

📋 Least-squares fit results:

	Metric	Value
1	🧪 Minimizer	bumps
2	✅ Overall status	success
3	⏱️ Fitting time (seconds)	8.97
4	📏 Goodness-of-fit (reduced χ²)	23.71
5	📏 R-factor (Rf, %)	21.33
6	📏 R-factor squared (Rf², %)	16.83
7	📏 Weighted R-factor (wR, %)	14.22

📈 Refined parameters:

	datablock	category	entry	parameter	units	start	value	s.u.	change
1	taurine	atom_site	S1	fract_x		0.2000	0.2013	0.0044	0.66 % ↑
2	taurine	atom_site	S1	fract_y		0.3500	0.3483	0.0022	0.48 % ↓
3	taurine	atom_site	S1	fract_z		0.3500	0.3484	0.0019	0.44 % ↓
4	taurine	atom_site	S1	adp_iso	Ų	1.5791	1.2727	0.2785	19.40 % ↓
5	taurine	atom_site	O1	fract_x		0.3130	0.3178	0.0032	1.54 % ↑
6	taurine	atom_site	O1	fract_y		0.2400	0.2406	0.0012	0.27 % ↑
7	taurine	atom_site	O1	fract_z		0.3510	0.3516	0.0013	0.17 % ↑
8	taurine	atom_site	O1	adp_iso	Ų	2.7635	2.7794	0.2019	0.58 % ↑
9	taurine	atom_site	O2	fract_x		0.9380	0.9392	0.0027	0.13 % ↑
10	taurine	atom_site	O2	fract_y		0.3370	0.3372	0.0021	0.06 % ↑
11	taurine	atom_site	O2	fract_z		0.2940	0.2939	0.0014	0.03 % ↓
12	taurine	atom_site	O2	adp_iso	Ų	3.6320	3.5463	0.2769	2.36 % ↓
13	taurine	atom_site	O3	fract_x		0.2220	0.2249	0.0024	1.31 % ↑
14	taurine	atom_site	O3	fract_y		0.4120	0.4099	0.0015	0.52 % ↓
15	taurine	atom_site	O3	fract_z		0.5070	0.5076	0.0011	0.11 % ↑
16	taurine	atom_site	O3	adp_iso	Ų	1.8950	2.0671	0.1976	9.08 % ↑
17	taurine	atom_site	N1	fract_x		0.2640	0.2634	0.0019	0.22 % ↓
18	taurine	atom_site	N1	fract_y		0.6280	0.6280	0.0008	0.01 % ↑
19	taurine	atom_site	N1	fract_z		0.3310	0.3321	0.0007	0.33 % ↑
20	taurine	atom_site	N1	adp_iso	Ų	2.1318	2.1030	0.1448	1.35 % ↓
21	taurine	atom_site	H1	fract_x		0.1330	0.1365	0.0046	2.60 % ↑
22	taurine	atom_site	H1	fract_y		0.5880	0.5858	0.0020	0.37 % ↓
23	taurine	atom_site	H1	fract_z		0.4210	0.4170	0.0021	0.95 % ↓
24	taurine	atom_site	H1	adp_iso	Ų	3.3951	2.8313	0.3425	16.61 % ↓
25	taurine	atom_site	H2	fract_x		0.1910	0.1886	0.0048	1.28 % ↓
26	taurine	atom_site	H2	fract_y		0.7150	0.7132	0.0026	0.25 % ↓
27	taurine	atom_site	H2	fract_z		0.3120	0.3077	0.0024	1.37 % ↓
28	taurine	atom_site	H2	adp_iso	Ų	4.5795	4.1615	0.4489	9.13 % ↓
29	taurine	atom_site	H3	fract_x		0.4400	0.4338	0.0082	1.40 % ↓
30	taurine	atom_site	H3	fract_y		0.6240	0.6261	0.0031	0.33 % ↑
31	taurine	atom_site	H3	fract_z		0.3490	0.3485	0.0033	0.14 % ↓
32	taurine	atom_site	H3	adp_iso	Ų	4.6585	4.9040	0.5305	5.27 % ↑
33	taurine	atom_site	C1	fract_x		0.3440	0.3470	0.0020	0.88 % ↑
34	taurine	atom_site	C1	fract_y		0.4400	0.4398	0.0010	0.05 % ↓
35	taurine	atom_site	C1	fract_z		0.2020	0.2021	0.0009	0.06 % ↑
36	taurine	atom_site	C1	adp_iso	Ų	1.7371	1.6823	0.1586	3.15 % ↓
37	taurine	atom_site	H11	fract_x		0.5520	0.5478	0.0053	0.76 % ↓
38	taurine	atom_site	H11	fract_y		0.4330	0.4337	0.0028	0.17 % ↑
39	taurine	atom_site	H11	fract_z		0.2430	0.2404	0.0024	1.05 % ↓
40	taurine	atom_site	H11	adp_iso	Ų	3.3951	3.5150	0.3890	3.53 % ↑
41	taurine	atom_site	H12	fract_x		0.3200	0.3271	0.0050	2.23 % ↑
42	taurine	atom_site	H12	fract_y		0.3880	0.3809	0.0027	1.83 % ↓
43	taurine	atom_site	H12	fract_z		0.0810	0.0852	0.0025	5.24 % ↑
44	taurine	atom_site	H12	adp_iso	Ų	3.3162	3.3508	0.3764	1.04 % ↑
45	taurine	atom_site	C2	fract_x		0.2000	0.1966	0.0025	1.72 % ↓
46	taurine	atom_site	C2	fract_y		0.5570	0.5556	0.0011	0.25 % ↓
47	taurine	atom_site	C2	fract_z		0.1820	0.1797	0.0011	1.24 % ↓
48	taurine	atom_site	C2	adp_iso	Ų	1.7371	1.8327	0.1622	5.51 % ↑
49	taurine	atom_site	H21	fract_x		0.2760	0.2735	0.0048	0.91 % ↓
50	taurine	atom_site	H21	fract_y		0.6000	0.5982	0.0020	0.30 % ↓
51	taurine	atom_site	H21	fract_z		0.0770	0.0737	0.0021	4.24 % ↓
52	taurine	atom_site	H21	adp_iso	Ų	2.1318	2.3761	0.2807	11.46 % ↑
53	taurine	atom_site	H22	fract_x		0.9990	0.9968	0.0058	0.22 % ↓
54	taurine	atom_site	H22	fract_y		0.5490	0.5509	0.0029	0.35 % ↑
55	taurine	atom_site	H22	fract_z		0.1610	0.1644	0.0032	2.10 % ↑
56	taurine	atom_site	H22	adp_iso	Ų	4.9743	4.6849	0.5078	5.82 % ↓
57	senju	extinction		radius	μm	100.0000	0.2304	56.7093	99.77 % ↓
58	senju	linked_structure		scale		1.0000	1.3466	0.0780	34.66 % ↑

• start = parameter value before refinement
• value = refined value from least-squares minimization
• s.u. = standard uncertainty (one sigma), from the covariance matrix
• change = relative change from start, in %; ↑ = increase, ↓ = decrease

⚠️ Red s.u.: exceeds the refined value (consider adding constraints)

In [23]:

structure.show_as_text()

structure.show_as_text()

Structure 🧩 'taurine' as text

	Edi
1	data_taurine
2
3	_cell.length_a 5.2729
4	_cell.length_b 11.6565
5	_cell.length_c 7.8383
6	_cell.angle_alpha 90.
7	_cell.angle_beta 94.011
8	_cell.angle_gamma 90.
9
10	_space_group.name_h_m "P 21/c"
11	_space_group.coord_system_code b1
12
13	_geom.min_bond_distance_cutoff 0.
14	_geom.bond_distance_inc 0.25
15
16	loop_
17	_atom_site.id
18	_atom_site.type_symbol
19	_atom_site.fract_x
20	_atom_site.fract_y
21	_atom_site.fract_z
22	_atom_site.wyckoff_letter
23	_atom_site.multiplicity
24	_atom_site.occupancy
25	_atom_site.adp_iso
26	_atom_site.adp_type
27	S1 S 0.2013(44) 0.3483(22) 0.3484(19) e 4 1. 1.27(28) Biso
28	O1 O 0.3178(32) 0.2406(12) 0.3516(13) e 4 1. 2.78(20) Biso
29	O2 O 0.9392(27) 0.3372(21) 0.2939(14) e 4 1. 3.55(28) Biso
30	O3 O 0.2249(24) 0.4099(15) 0.5076(11) e 4 1. 2.07(20) Biso
31	N1 N 0.2634(19) 0.62805(78) 0.33211(73) e 4 1. 2.10(14) Biso
32	H1 H 0.1365(46) 0.5858(20) 0.4170(21) e 4 1. 2.83(34) Biso
33	H2 H 0.1886(48) 0.7132(26) 0.3077(24) e 4 1. 4.16(45) Biso
34	H3 H 0.4338(82) 0.6261(31) 0.3485(33) e 4 1. 4.90(53) Biso
35	C1 C 0.3470(20) 0.43980(96) 0.20212(86) e 4 1. 1.68(16) Biso
36	H11 H 0.5478(53) 0.4337(28) 0.2404(24) e 4 1. 3.52(39) Biso
37	H12 H 0.3271(50) 0.3809(27) 0.0852(25) e 4 1. 3.35(38) Biso
38	C2 C 0.1966(25) 0.5556(11) 0.1797(11) e 4 1. 1.83(16) Biso
39	H21 H 0.2735(48) 0.5982(20) 0.0737(21) e 4 1. 2.38(28) Biso
40	H22 H 0.9968(58) 0.5509(29) 0.1644(32) e 4 1. 4.68(51) Biso

In [24]:

project.experiments.show_names()

project.experiments.show_names()

Defined experiments 🔬

['senju']

In [25]:

project.display.pattern(expt_name='senju')

project.display.pattern(expt_name='senju')

Loading plot…

ADP aniso¶

In [26]:

for atom_site in structure.atom_sites:
    atom_site.adp_type = 'Uani'

for atom_site in structure.atom_sites: atom_site.adp_type = 'Uani'

In [27]:

adp_components = ('adp_11', 'adp_22', 'adp_33', 'adp_12', 'adp_13', 'adp_23')
for atom_site in structure.atom_site_aniso:
    for component in adp_components:
        getattr(atom_site, component).free = True

adp_components = ('adp_11', 'adp_22', 'adp_33', 'adp_12', 'adp_13', 'adp_23') for atom_site in structure.atom_site_aniso: for component in adp_components: getattr(atom_site, component).free = True

In [28]:

structure.show_as_text()

structure.show_as_text()

Structure 🧩 'taurine' as text

	Edi
1	data_taurine
2
3	_cell.length_a 5.2729
4	_cell.length_b 11.6565
5	_cell.length_c 7.8383
6	_cell.angle_alpha 90.
7	_cell.angle_beta 94.011
8	_cell.angle_gamma 90.
9
10	_space_group.name_h_m "P 21/c"
11	_space_group.coord_system_code b1
12
13	_geom.min_bond_distance_cutoff 0.
14	_geom.bond_distance_inc 0.25
15
16	loop_
17	_atom_site.id
18	_atom_site.type_symbol
19	_atom_site.fract_x
20	_atom_site.fract_y
21	_atom_site.fract_z
22	_atom_site.wyckoff_letter
23	_atom_site.multiplicity
24	_atom_site.occupancy
25	_atom_site.adp_iso
26	_atom_site.adp_type
27	S1 S 0.2013(44) 0.3483(22) 0.3484(19) e 4 1. 0.01611943 Uani
28	O1 O 0.3178(32) 0.2406(12) 0.3516(13) e 4 1. 0.03520173 Uani
29	O2 O 0.9392(27) 0.3372(21) 0.2939(14) e 4 1. 0.04491399 Uani
30	O3 O 0.2249(24) 0.4099(15) 0.5076(11) e 4 1. 0.02618024 Uani
31	N1 N 0.2634(19) 0.62805(78) 0.33211(73) e 4 1. 0.02663485 Uani
32	H1 H 0.1365(46) 0.5858(20) 0.4170(21) e 4 1. 0.0358593 Uani
33	H2 H 0.1886(48) 0.7132(26) 0.3077(24) e 4 1. 0.05270599 Uani
34	H3 H 0.4338(82) 0.6261(31) 0.3485(33) e 4 1. 0.06210953 Uani
35	C1 C 0.3470(20) 0.43980(96) 0.20212(86) e 4 1. 0.02130661 Uani
36	H11 H 0.5478(53) 0.4337(28) 0.2404(24) e 4 1. 0.0445182 Uani
37	H12 H 0.3271(50) 0.3809(27) 0.0852(25) e 4 1. 0.04243794 Uani
38	C2 C 0.1966(25) 0.5556(11) 0.1797(11) e 4 1. 0.02321194 Uani
39	H21 H 0.2735(48) 0.5982(20) 0.0737(21) e 4 1. 0.03009422 Uani
40	H22 H 0.9968(58) 0.5509(29) 0.1644(32) e 4 1. 0.05933481 Uani
41
42	loop_
43	_atom_site_aniso.id
44	_atom_site_aniso.adp_11
45	_atom_site_aniso.adp_22
46	_atom_site_aniso.adp_33
47	_atom_site_aniso.adp_12
48	_atom_site_aniso.adp_13
49	_atom_site_aniso.adp_23
50	S1 0.01611943() 0.01611943() 0.01611943() 0.() 0.() 0.()
51	O1 0.03520173() 0.03520173() 0.03520173() 0.() 0.() 0.()
52	O2 0.04491399() 0.04491399() 0.04491399() 0.() 0.() 0.()
53	O3 0.02618024() 0.02618024() 0.02618024() 0.() 0.() 0.()
54	N1 0.02663485() 0.02663485() 0.02663485() 0.() 0.() 0.()
55	H1 0.0358593() 0.0358593() 0.0358593() 0.() 0.() 0.()
56	H2 0.05270599() 0.05270599() 0.05270599() 0.() 0.() 0.()
57	H3 0.06210953() 0.06210953() 0.06210953() 0.() 0.() 0.()
58	C1 0.02130661() 0.02130661() 0.02130661() 0.() 0.() 0.()
59	H11 0.0445182() 0.0445182() 0.0445182() 0.() 0.() 0.()
60	H12 0.04243794() 0.04243794() 0.04243794() 0.() 0.() 0.()
61	C2 0.02321194() 0.02321194() 0.02321194() 0.() 0.() 0.()
62	H21 0.03009422() 0.03009422() 0.03009422() 0.() 0.() 0.()
63	H22 0.05933481() 0.05933481() 0.05933481() 0.() 0.() 0.()

In [29]:

project.display.parameters.free()

project.display.parameters.free()

Free parameters for both structures (🧩 data blocks) and experiments (🔬 data blocks)

	datablock	category	entry	parameter	value	uncertainty	min	max	units
1	taurine	atom_site	S1	fract_x	0.20131	0.00437	-inf	inf
2	taurine	atom_site	S1	fract_y	0.34831	0.00216	-inf	inf
3	taurine	atom_site	S1	fract_z	0.34845	0.00188	-inf	inf
4	taurine	atom_site	O1	fract_x	0.31782	0.00320	-inf	inf
5	taurine	atom_site	O1	fract_y	0.24064	0.00118	-inf	inf
6	taurine	atom_site	O1	fract_z	0.35161	0.00132	-inf	inf
7	taurine	atom_site	O2	fract_x	0.93922	0.00274	-inf	inf
8	taurine	atom_site	O2	fract_y	0.33720	0.00208	-inf	inf
9	taurine	atom_site	O2	fract_z	0.29393	0.00140	-inf	inf
10	taurine	atom_site	O3	fract_x	0.22490	0.00241	-inf	inf
11	taurine	atom_site	O3	fract_y	0.40986	0.00153	-inf	inf
12	taurine	atom_site	O3	fract_z	0.50756	0.00106	-inf	inf
13	taurine	atom_site	N1	fract_x	0.26341	0.00193	-inf	inf
14	taurine	atom_site	N1	fract_y	0.62805	0.00078	-inf	inf
15	taurine	atom_site	N1	fract_z	0.33211	0.00073	-inf	inf
16	taurine	atom_site	H1	fract_x	0.13646	0.00462	-inf	inf
17	taurine	atom_site	H1	fract_y	0.58580	0.00200	-inf	inf
18	taurine	atom_site	H1	fract_z	0.41701	0.00211	-inf	inf
19	taurine	atom_site	H2	fract_x	0.18855	0.00476	-inf	inf
20	taurine	atom_site	H2	fract_y	0.71324	0.00265	-inf	inf
21	taurine	atom_site	H2	fract_z	0.30773	0.00245	-inf	inf
22	taurine	atom_site	H3	fract_x	0.43384	0.00819	-inf	inf
23	taurine	atom_site	H3	fract_y	0.62608	0.00315	-inf	inf
24	taurine	atom_site	H3	fract_z	0.34853	0.00334	-inf	inf
25	taurine	atom_site	C1	fract_x	0.34703	0.00205	-inf	inf
26	taurine	atom_site	C1	fract_y	0.43980	0.00096	-inf	inf
27	taurine	atom_site	C1	fract_z	0.20212	0.00086	-inf	inf
28	taurine	atom_site	H11	fract_x	0.54783	0.00527	-inf	inf
29	taurine	atom_site	H11	fract_y	0.43372	0.00278	-inf	inf
30	taurine	atom_site	H11	fract_z	0.24044	0.00244	-inf	inf
31	taurine	atom_site	H12	fract_x	0.32715	0.00500	-inf	inf
32	taurine	atom_site	H12	fract_y	0.38089	0.00269	-inf	inf
33	taurine	atom_site	H12	fract_z	0.08525	0.00247	-inf	inf
34	taurine	atom_site	C2	fract_x	0.19657	0.00246	-inf	inf
35	taurine	atom_site	C2	fract_y	0.55559	0.00108	-inf	inf
36	taurine	atom_site	C2	fract_z	0.17975	0.00112	-inf	inf
37	taurine	atom_site	H21	fract_x	0.27350	0.00477	-inf	inf
38	taurine	atom_site	H21	fract_y	0.59817	0.00201	-inf	inf
39	taurine	atom_site	H21	fract_z	0.07373	0.00206	-inf	inf
40	taurine	atom_site	H22	fract_x	0.99678	0.00575	-inf	inf
41	taurine	atom_site	H22	fract_y	0.55090	0.00288	-inf	inf
42	taurine	atom_site	H22	fract_z	0.16438	0.00317	-inf	inf
43	taurine	atom_site_aniso	S1	adp_11	0.01612		-inf	inf	Ų
44	taurine	atom_site_aniso	S1	adp_22	0.01612		-inf	inf	Ų
45	taurine	atom_site_aniso	S1	adp_33	0.01612		-inf	inf	Ų
46	taurine	atom_site_aniso	S1	adp_12	0.00000		-inf	inf	Ų
47	taurine	atom_site_aniso	S1	adp_13	0.00000		-inf	inf	Ų
48	taurine	atom_site_aniso	S1	adp_23	0.00000		-inf	inf	Ų
49	taurine	atom_site_aniso	O1	adp_11	0.03520		-inf	inf	Ų
50	taurine	atom_site_aniso	O1	adp_22	0.03520		-inf	inf	Ų
51	taurine	atom_site_aniso	O1	adp_33	0.03520		-inf	inf	Ų
52	taurine	atom_site_aniso	O1	adp_12	0.00000		-inf	inf	Ų
53	taurine	atom_site_aniso	O1	adp_13	0.00000		-inf	inf	Ų
54	taurine	atom_site_aniso	O1	adp_23	0.00000		-inf	inf	Ų
55	taurine	atom_site_aniso	O2	adp_11	0.04491		-inf	inf	Ų
56	taurine	atom_site_aniso	O2	adp_22	0.04491		-inf	inf	Ų
57	taurine	atom_site_aniso	O2	adp_33	0.04491		-inf	inf	Ų
58	taurine	atom_site_aniso	O2	adp_12	0.00000		-inf	inf	Ų
59	taurine	atom_site_aniso	O2	adp_13	0.00000		-inf	inf	Ų
60	taurine	atom_site_aniso	O2	adp_23	0.00000		-inf	inf	Ų
61	taurine	atom_site_aniso	O3	adp_11	0.02618		-inf	inf	Ų
62	taurine	atom_site_aniso	O3	adp_22	0.02618		-inf	inf	Ų
63	taurine	atom_site_aniso	O3	adp_33	0.02618		-inf	inf	Ų
64	taurine	atom_site_aniso	O3	adp_12	0.00000		-inf	inf	Ų
65	taurine	atom_site_aniso	O3	adp_13	0.00000		-inf	inf	Ų
66	taurine	atom_site_aniso	O3	adp_23	0.00000		-inf	inf	Ų
67	taurine	atom_site_aniso	N1	adp_11	0.02663		-inf	inf	Ų
68	taurine	atom_site_aniso	N1	adp_22	0.02663		-inf	inf	Ų
69	taurine	atom_site_aniso	N1	adp_33	0.02663		-inf	inf	Ų
70	taurine	atom_site_aniso	N1	adp_12	0.00000		-inf	inf	Ų
71	taurine	atom_site_aniso	N1	adp_13	0.00000		-inf	inf	Ų
72	taurine	atom_site_aniso	N1	adp_23	0.00000		-inf	inf	Ų
73	taurine	atom_site_aniso	H1	adp_11	0.03586		-inf	inf	Ų
74	taurine	atom_site_aniso	H1	adp_22	0.03586		-inf	inf	Ų
75	taurine	atom_site_aniso	H1	adp_33	0.03586		-inf	inf	Ų
76	taurine	atom_site_aniso	H1	adp_12	0.00000		-inf	inf	Ų
77	taurine	atom_site_aniso	H1	adp_13	0.00000		-inf	inf	Ų
78	taurine	atom_site_aniso	H1	adp_23	0.00000		-inf	inf	Ų
79	taurine	atom_site_aniso	H2	adp_11	0.05271		-inf	inf	Ų
80	taurine	atom_site_aniso	H2	adp_22	0.05271		-inf	inf	Ų
81	taurine	atom_site_aniso	H2	adp_33	0.05271		-inf	inf	Ų
82	taurine	atom_site_aniso	H2	adp_12	0.00000		-inf	inf	Ų
83	taurine	atom_site_aniso	H2	adp_13	0.00000		-inf	inf	Ų
84	taurine	atom_site_aniso	H2	adp_23	0.00000		-inf	inf	Ų
85	taurine	atom_site_aniso	H3	adp_11	0.06211		-inf	inf	Ų
86	taurine	atom_site_aniso	H3	adp_22	0.06211		-inf	inf	Ų
87	taurine	atom_site_aniso	H3	adp_33	0.06211		-inf	inf	Ų
88	taurine	atom_site_aniso	H3	adp_12	0.00000		-inf	inf	Ų
89	taurine	atom_site_aniso	H3	adp_13	0.00000		-inf	inf	Ų
90	taurine	atom_site_aniso	H3	adp_23	0.00000		-inf	inf	Ų
91	taurine	atom_site_aniso	C1	adp_11	0.02131		-inf	inf	Ų
92	taurine	atom_site_aniso	C1	adp_22	0.02131		-inf	inf	Ų
93	taurine	atom_site_aniso	C1	adp_33	0.02131		-inf	inf	Ų
94	taurine	atom_site_aniso	C1	adp_12	0.00000		-inf	inf	Ų
95	taurine	atom_site_aniso	C1	adp_13	0.00000		-inf	inf	Ų
96	taurine	atom_site_aniso	C1	adp_23	0.00000		-inf	inf	Ų
97	taurine	atom_site_aniso	H11	adp_11	0.04452		-inf	inf	Ų
98	taurine	atom_site_aniso	H11	adp_22	0.04452		-inf	inf	Ų
99	taurine	atom_site_aniso	H11	adp_33	0.04452		-inf	inf	Ų
100	taurine	atom_site_aniso	H11	adp_12	0.00000		-inf	inf	Ų
101	taurine	atom_site_aniso	H11	adp_13	0.00000		-inf	inf	Ų
102	taurine	atom_site_aniso	H11	adp_23	0.00000		-inf	inf	Ų
103	taurine	atom_site_aniso	H12	adp_11	0.04244		-inf	inf	Ų
104	taurine	atom_site_aniso	H12	adp_22	0.04244		-inf	inf	Ų
105	taurine	atom_site_aniso	H12	adp_33	0.04244		-inf	inf	Ų
106	taurine	atom_site_aniso	H12	adp_12	0.00000		-inf	inf	Ų
107	taurine	atom_site_aniso	H12	adp_13	0.00000		-inf	inf	Ų
108	taurine	atom_site_aniso	H12	adp_23	0.00000		-inf	inf	Ų
109	taurine	atom_site_aniso	C2	adp_11	0.02321		-inf	inf	Ų
110	taurine	atom_site_aniso	C2	adp_22	0.02321		-inf	inf	Ų
111	taurine	atom_site_aniso	C2	adp_33	0.02321		-inf	inf	Ų
112	taurine	atom_site_aniso	C2	adp_12	0.00000		-inf	inf	Ų
113	taurine	atom_site_aniso	C2	adp_13	0.00000		-inf	inf	Ų
114	taurine	atom_site_aniso	C2	adp_23	0.00000		-inf	inf	Ų
115	taurine	atom_site_aniso	H21	adp_11	0.03009		-inf	inf	Ų
116	taurine	atom_site_aniso	H21	adp_22	0.03009		-inf	inf	Ų
117	taurine	atom_site_aniso	H21	adp_33	0.03009		-inf	inf	Ų
118	taurine	atom_site_aniso	H21	adp_12	0.00000		-inf	inf	Ų
119	taurine	atom_site_aniso	H21	adp_13	0.00000		-inf	inf	Ų
120	taurine	atom_site_aniso	H21	adp_23	0.00000		-inf	inf	Ų
121	taurine	atom_site_aniso	H22	adp_11	0.05933		-inf	inf	Ų
122	taurine	atom_site_aniso	H22	adp_22	0.05933		-inf	inf	Ų
123	taurine	atom_site_aniso	H22	adp_33	0.05933		-inf	inf	Ų
124	taurine	atom_site_aniso	H22	adp_12	0.00000		-inf	inf	Ų
125	taurine	atom_site_aniso	H22	adp_13	0.00000		-inf	inf	Ų
126	taurine	atom_site_aniso	H22	adp_23	0.00000		-inf	inf	Ų
127	senju	extinction		radius	0.23044	56.70926	-inf	inf	μm
128	senju	linked_structure		scale	1.34662	0.07803	-inf	inf

In [30]:

project.analysis.fit()

project.analysis.fit()

Standard fitting

📋 Using experiment 🔬 'senju' for 'single' fitting

🚀 Starting fit process with 'bumps (lm)'...

📈 Goodness-of-fit progress:

	iteration	time (s)	χ²	change / status
1	1	0.02	38.65
2	131	2.38	27.51	28.8% ↓
3	260	4.71	17.73	35.5% ↓
4	389	7.06	11.89	33.0% ↓
5	500	9.12	11.89

⚠️ Parameter 'taurine.atom_site_aniso.S1.adp_11' (-0.02049645) is below its physical lower limit (0.0).

⚠️ Parameter 'taurine.atom_site_aniso.C2.adp_11' (-0.00438188) is below its physical lower limit (0.0).

🏆 Best goodness-of-fit (reduced χ²) is 11.89 at iteration 500

✅ Fitting complete.

In [31]:

project.display.fit.results()

project.display.fit.results()

⚙️ Settings used:

	Name	Value	Description
1	max_iterations	500	Maximum solver iterations.
2	chi_square_change_tolerance	0.01	Relative change in the objective (chi-square) used to stop fitting.
3	parameter_change_tolerance	1e-08	Relative change in fitted parameters used to stop fitting.

📋 Least-squares fit results:

	Metric	Value
1	🧪 Minimizer	bumps
2	❌ Overall status	failed
3	⏱️ Fitting time (seconds)	9.12
4	📏 Goodness-of-fit (reduced χ²)	11.89
5	📏 R-factor (Rf, %)	13.26
6	📏 R-factor squared (Rf², %)	9.10
7	📏 Weighted R-factor (wR, %)	8.38

📈 Refined parameters:

	datablock	category	entry	parameter	units	start	value	s.u.	change
1	taurine	atom_site	S1	fract_x		0.2013	0.2032	N/A	0.93 % ↑
2	taurine	atom_site	S1	fract_y		0.3483	0.3506	N/A	0.65 % ↑
3	taurine	atom_site	S1	fract_z		0.3484	0.3491	N/A	0.18 % ↑
4	taurine	atom_site	O1	fract_x		0.3178	0.3209	N/A	0.96 % ↑
5	taurine	atom_site	O1	fract_y		0.2406	0.2407	N/A	0.01 % ↑
6	taurine	atom_site	O1	fract_z		0.3516	0.3503	N/A	0.37 % ↓
7	taurine	atom_site	O2	fract_x		0.9392	0.9422	N/A	0.32 % ↑
8	taurine	atom_site	O2	fract_y		0.3372	0.3355	N/A	0.49 % ↓
9	taurine	atom_site	O2	fract_z		0.2939	0.2943	N/A	0.14 % ↑
10	taurine	atom_site	O3	fract_x		0.2249	0.2260	N/A	0.51 % ↑
11	taurine	atom_site	O3	fract_y		0.4099	0.4125	N/A	0.64 % ↑
12	taurine	atom_site	O3	fract_z		0.5076	0.5089	N/A	0.26 % ↑
13	taurine	atom_site	N1	fract_x		0.2634	0.2610	N/A	0.91 % ↓
14	taurine	atom_site	N1	fract_y		0.6280	0.6276	N/A	0.07 % ↓
15	taurine	atom_site	N1	fract_z		0.3321	0.3325	N/A	0.10 % ↑
16	taurine	atom_site	H1	fract_x		0.1365	0.1356	N/A	0.66 % ↓
17	taurine	atom_site	H1	fract_y		0.5858	0.5940	N/A	1.39 % ↑
18	taurine	atom_site	H1	fract_z		0.4170	0.4213	N/A	1.03 % ↑
19	taurine	atom_site	H2	fract_x		0.1886	0.1843	N/A	2.24 % ↓
20	taurine	atom_site	H2	fract_y		0.7132	0.7053	N/A	1.12 % ↓
21	taurine	atom_site	H2	fract_z		0.3077	0.3042	N/A	1.16 % ↓
22	taurine	atom_site	H3	fract_x		0.4338	0.4418	N/A	1.83 % ↑
23	taurine	atom_site	H3	fract_y		0.6261	0.6340	N/A	1.27 % ↑
24	taurine	atom_site	H3	fract_z		0.3485	0.3555	N/A	2.01 % ↑
25	taurine	atom_site	C1	fract_x		0.3470	0.3505	N/A	0.99 % ↑
26	taurine	atom_site	C1	fract_y		0.4398	0.4393	N/A	0.11 % ↓
27	taurine	atom_site	C1	fract_z		0.2021	0.2037	N/A	0.79 % ↑
28	taurine	atom_site	H11	fract_x		0.5478	0.5403	N/A	1.37 % ↓
29	taurine	atom_site	H11	fract_y		0.4337	0.4416	N/A	1.82 % ↑
30	taurine	atom_site	H11	fract_z		0.2404	0.2405	N/A	0.04 % ↑
31	taurine	atom_site	H12	fract_x		0.3271	0.3314	N/A	1.30 % ↑
32	taurine	atom_site	H12	fract_y		0.3809	0.3861	N/A	1.37 % ↑
33	taurine	atom_site	H12	fract_z		0.0852	0.0861	N/A	0.95 % ↑
34	taurine	atom_site	C2	fract_x		0.1966	0.2063	N/A	4.93 % ↑
35	taurine	atom_site	C2	fract_y		0.5556	0.5556	N/A	0.01 % ↑
36	taurine	atom_site	C2	fract_z		0.1797	0.1806	N/A	0.49 % ↑
37	taurine	atom_site	H21	fract_x		0.2735	0.2738	N/A	0.11 % ↑
38	taurine	atom_site	H21	fract_y		0.5982	0.6016	N/A	0.57 % ↑
39	taurine	atom_site	H21	fract_z		0.0737	0.0772	N/A	4.65 % ↑
40	taurine	atom_site	H22	fract_x		0.9968	0.9948	N/A	0.20 % ↓
41	taurine	atom_site	H22	fract_y		0.5509	0.5558	N/A	0.89 % ↑
42	taurine	atom_site	H22	fract_z		0.1644	0.1643	N/A	0.04 % ↓
43	taurine	atom_site_aniso	S1	adp_11	Ų	0.0161	-0.0205	N/A	227.15 % ↓
44	taurine	atom_site_aniso	S1	adp_22	Ų	0.0161	0.0028	N/A	82.62 % ↓
45	taurine	atom_site_aniso	S1	adp_33	Ų	0.0161	0.0297	N/A	84.50 % ↑
46	taurine	atom_site_aniso	S1	adp_12	Ų	0.0000	-0.0193	N/A	N/A
47	taurine	atom_site_aniso	S1	adp_13	Ų	0.0000	0.0016	N/A	N/A
48	taurine	atom_site_aniso	S1	adp_23	Ų	0.0000	-0.0000	N/A	N/A
49	taurine	atom_site_aniso	O1	adp_11	Ų	0.0352	0.0375	N/A	6.62 % ↑
50	taurine	atom_site_aniso	O1	adp_22	Ų	0.0352	0.0263	N/A	25.37 % ↓
51	taurine	atom_site_aniso	O1	adp_33	Ų	0.0352	0.0430	N/A	22.02 % ↑
52	taurine	atom_site_aniso	O1	adp_12	Ų	0.0000	-0.0027	N/A	N/A
53	taurine	atom_site_aniso	O1	adp_13	Ų	0.0000	0.0120	N/A	N/A
54	taurine	atom_site_aniso	O1	adp_23	Ų	0.0000	-0.0117	N/A	N/A
55	taurine	atom_site_aniso	O2	adp_11	Ų	0.0449	0.0317	N/A	29.50 % ↓
56	taurine	atom_site_aniso	O2	adp_22	Ų	0.0449	0.0022	N/A	95.11 % ↓
57	taurine	atom_site_aniso	O2	adp_33	Ų	0.0449	0.0544	N/A	21.09 % ↑
58	taurine	atom_site_aniso	O2	adp_12	Ų	0.0000	-0.0019	N/A	N/A
59	taurine	atom_site_aniso	O2	adp_13	Ų	0.0000	0.0187	N/A	N/A
60	taurine	atom_site_aniso	O2	adp_23	Ų	0.0000	-0.0079	N/A	N/A
61	taurine	atom_site_aniso	O3	adp_11	Ų	0.0262	0.0409	N/A	56.07 % ↑
62	taurine	atom_site_aniso	O3	adp_22	Ų	0.0262	0.0305	N/A	16.63 % ↑
63	taurine	atom_site_aniso	O3	adp_33	Ų	0.0262	0.0172	N/A	34.42 % ↓
64	taurine	atom_site_aniso	O3	adp_12	Ų	0.0000	0.0104	N/A	N/A
65	taurine	atom_site_aniso	O3	adp_13	Ų	0.0000	0.0002	N/A	N/A
66	taurine	atom_site_aniso	O3	adp_23	Ų	0.0000	0.0009	N/A	N/A
67	taurine	atom_site_aniso	N1	adp_11	Ų	0.0266	0.0144	N/A	45.98 % ↓
68	taurine	atom_site_aniso	N1	adp_22	Ų	0.0266	0.0348	N/A	30.78 % ↑
69	taurine	atom_site_aniso	N1	adp_33	Ų	0.0266	0.0263	N/A	1.15 % ↓
70	taurine	atom_site_aniso	N1	adp_12	Ų	0.0000	-0.0052	N/A	N/A
71	taurine	atom_site_aniso	N1	adp_13	Ų	0.0000	0.0032	N/A	N/A
72	taurine	atom_site_aniso	N1	adp_23	Ų	0.0000	-0.0018	N/A	N/A
73	taurine	atom_site_aniso	H1	adp_11	Ų	0.0359	0.0450	N/A	25.44 % ↑
74	taurine	atom_site_aniso	H1	adp_22	Ų	0.0359	0.0275	N/A	23.22 % ↓
75	taurine	atom_site_aniso	H1	adp_33	Ų	0.0359	0.0389	N/A	8.62 % ↑
76	taurine	atom_site_aniso	H1	adp_12	Ų	0.0000	-0.0047	N/A	N/A
77	taurine	atom_site_aniso	H1	adp_13	Ų	0.0000	0.0128	N/A	N/A
78	taurine	atom_site_aniso	H1	adp_23	Ų	0.0000	-0.0110	N/A	N/A
79	taurine	atom_site_aniso	H2	adp_11	Ų	0.0527	0.0645	N/A	22.38 % ↑
80	taurine	atom_site_aniso	H2	adp_22	Ų	0.0527	0.0959	N/A	81.87 % ↑
81	taurine	atom_site_aniso	H2	adp_33	Ų	0.0527	0.0293	N/A	44.44 % ↓
82	taurine	atom_site_aniso	H2	adp_12	Ų	0.0000	0.0441	N/A	N/A
83	taurine	atom_site_aniso	H2	adp_13	Ų	0.0000	-0.0087	N/A	N/A
84	taurine	atom_site_aniso	H2	adp_23	Ų	0.0000	0.0103	N/A	N/A
85	taurine	atom_site_aniso	H3	adp_11	Ų	0.0621	0.0191	N/A	69.27 % ↓
86	taurine	atom_site_aniso	H3	adp_22	Ų	0.0621	0.0773	N/A	24.39 % ↑
87	taurine	atom_site_aniso	H3	adp_33	Ų	0.0621	0.0764	N/A	22.94 % ↑
88	taurine	atom_site_aniso	H3	adp_12	Ų	0.0000	0.0055	N/A	N/A
89	taurine	atom_site_aniso	H3	adp_13	Ų	0.0000	-0.0066	N/A	N/A
90	taurine	atom_site_aniso	H3	adp_23	Ų	0.0000	-0.0177	N/A	N/A
91	taurine	atom_site_aniso	C1	adp_11	Ų	0.0213	0.0352	N/A	65.30 % ↑
92	taurine	atom_site_aniso	C1	adp_22	Ų	0.0213	0.0093	N/A	56.26 % ↓
93	taurine	atom_site_aniso	C1	adp_33	Ų	0.0213	0.0187	N/A	12.26 % ↓
94	taurine	atom_site_aniso	C1	adp_12	Ų	0.0000	0.0147	N/A	N/A
95	taurine	atom_site_aniso	C1	adp_13	Ų	0.0000	0.0056	N/A	N/A
96	taurine	atom_site_aniso	C1	adp_23	Ų	0.0000	-0.0053	N/A	N/A
97	taurine	atom_site_aniso	H11	adp_11	Ų	0.0445	0.0662	N/A	48.72 % ↑
98	taurine	atom_site_aniso	H11	adp_22	Ų	0.0445	0.0056	N/A	87.50 % ↓
99	taurine	atom_site_aniso	H11	adp_33	Ų	0.0445	0.0543	N/A	21.87 % ↑
100	taurine	atom_site_aniso	H11	adp_12	Ų	0.0000	0.0009	N/A	N/A
101	taurine	atom_site_aniso	H11	adp_13	Ų	0.0000	0.0233	N/A	N/A
102	taurine	atom_site_aniso	H11	adp_23	Ų	0.0000	0.0024	N/A	N/A
103	taurine	atom_site_aniso	H12	adp_11	Ų	0.0424	0.0818	N/A	92.75 % ↑
104	taurine	atom_site_aniso	H12	adp_22	Ų	0.0424	0.0451	N/A	6.25 % ↑
105	taurine	atom_site_aniso	H12	adp_33	Ų	0.0424	0.0397	N/A	6.35 % ↓
106	taurine	atom_site_aniso	H12	adp_12	Ų	0.0000	0.0346	N/A	N/A
107	taurine	atom_site_aniso	H12	adp_13	Ų	0.0000	0.0236	N/A	N/A
108	taurine	atom_site_aniso	H12	adp_23	Ų	0.0000	0.0030	N/A	N/A
109	taurine	atom_site_aniso	C2	adp_11	Ų	0.0232	-0.0044	N/A	118.88 % ↓
110	taurine	atom_site_aniso	C2	adp_22	Ų	0.0232	0.0453	N/A	95.35 % ↑
111	taurine	atom_site_aniso	C2	adp_33	Ų	0.0232	0.0259	N/A	11.45 % ↑
112	taurine	atom_site_aniso	C2	adp_12	Ų	0.0000	-0.0039	N/A	N/A
113	taurine	atom_site_aniso	C2	adp_13	Ų	0.0000	-0.0015	N/A	N/A
114	taurine	atom_site_aniso	C2	adp_23	Ų	0.0000	0.0040	N/A	N/A
115	taurine	atom_site_aniso	H21	adp_11	Ų	0.0301	0.0450	N/A	49.48 % ↑
116	taurine	atom_site_aniso	H21	adp_22	Ų	0.0301	0.0480	N/A	59.54 % ↑
117	taurine	atom_site_aniso	H21	adp_33	Ų	0.0301	0.0327	N/A	8.82 % ↑
118	taurine	atom_site_aniso	H21	adp_12	Ų	0.0000	-0.0258	N/A	N/A
119	taurine	atom_site_aniso	H21	adp_13	Ų	0.0000	0.0064	N/A	N/A
120	taurine	atom_site_aniso	H21	adp_23	Ų	0.0000	-0.0015	N/A	N/A
121	taurine	atom_site_aniso	H22	adp_11	Ų	0.0593	0.0047	N/A	92.02 % ↓
122	taurine	atom_site_aniso	H22	adp_22	Ų	0.0593	0.0377	N/A	36.52 % ↓
123	taurine	atom_site_aniso	H22	adp_33	Ų	0.0593	0.0655	N/A	10.41 % ↑
124	taurine	atom_site_aniso	H22	adp_12	Ų	0.0000	0.0085	N/A	N/A
125	taurine	atom_site_aniso	H22	adp_13	Ų	0.0000	-0.0214	N/A	N/A
126	taurine	atom_site_aniso	H22	adp_23	Ų	0.0000	0.0079	N/A	N/A
127	senju	extinction		radius	μm	0.2304	3.6178	N/A	1469.91 % ↑
128	senju	linked_structure		scale		1.3466	1.3597	N/A	0.97 % ↑

• start = parameter value before refinement
• value = refined value from least-squares minimization
• s.u. = standard uncertainty (one sigma), from the covariance matrix
• change = relative change from start, in %; ↑ = increase, ↓ = decrease

⚠️ Red value: outside expected physical limits (consider adding constraints)

In [32]:

project.display.fit.correlations()

project.display.fit.correlations()

⚠️ Correlation matrix is unavailable for this fit. This can happen if the minimization failed, if some parameters are too strongly correlated or poorly determined, or if the selected minimizer does not return covariance information.

In [33]:

project.display.pattern(expt_name='senju')

project.display.pattern(expt_name='senju')

Loading plot…

In [34]:

structure.show_as_text()

structure.show_as_text()

Structure 🧩 'taurine' as text

	Edi
1	data_taurine
2
3	_cell.length_a 5.2729
4	_cell.length_b 11.6565
5	_cell.length_c 7.8383
6	_cell.angle_alpha 90.
7	_cell.angle_beta 94.011
8	_cell.angle_gamma 90.
9
10	_space_group.name_h_m "P 21/c"
11	_space_group.coord_system_code b1
12
13	_geom.min_bond_distance_cutoff 0.
14	_geom.bond_distance_inc 0.25
15
16	loop_
17	_atom_site.id
18	_atom_site.type_symbol
19	_atom_site.fract_x
20	_atom_site.fract_y
21	_atom_site.fract_z
22	_atom_site.wyckoff_letter
23	_atom_site.multiplicity
24	_atom_site.occupancy
25	_atom_site.adp_iso
26	_atom_site.adp_type
27	S1 S 0.2031755() 0.35057473() 0.34906359() e 4 1. 0.00401494 Uani
28	O1 O 0.32086822() 0.24065466() 0.35030831() e 4 1. 0.03558451 Uani
29	O2 O 0.9422186() 0.33553543() 0.2943315() e 4 1. 0.02941716 Uani
30	O3 O 0.22604795() 0.41246962() 0.50887095() e 4 1. 0.02952104 Uani
31	N1 N 0.26100544() 0.62759294() 0.33245102() e 4 1. 0.02518271 Uani
32	H1 H 0.13555896() 0.59395698() 0.42130547() e 4 1. 0.03715471 Uani
33	H2 H 0.18433696() 0.70527363() 0.30417188() e 4 1. 0.06321393 Uani
34	H3 H 0.44176081() 0.63400275() 0.35554231() e 4 1. 0.05756825 Uani
35	C1 C 0.3504733() 0.43932984() 0.20371258() e 4 1. 0.02107854 Uani
36	H11 H 0.54033064() 0.44159352() 0.24052714() e 4 1. 0.04200888 Uani
37	H12 H 0.33140208() 0.38609867() 0.08605386() e 4 1. 0.05554352 Uani
38	C2 C 0.20626418() 0.55564967() 0.18063121() e 4 1. 0.02227774 Uani
39	H21 H 0.27378775() 0.60158819() 0.07716259() e 4 1. 0.04191537 Uani
40	H22 H 0.99481548() 0.55579558() 0.16430428() e 4 1. 0.0359701 Uani
41
42	loop_
43	_atom_site_aniso.id
44	_atom_site_aniso.adp_11
45	_atom_site_aniso.adp_22
46	_atom_site_aniso.adp_33
47	_atom_site_aniso.adp_12
48	_atom_site_aniso.adp_13
49	_atom_site_aniso.adp_23
50	S1 -0.02049645() 0.00280086() 0.0297404() -0.01928384() 0.00158068() -0.00002913()
51	O1 0.03753137() 0.02626999() 0.04295216() -0.00265574() 0.01197014() -0.01170016()
52	O2 0.03166587() 0.00219754() 0.05438807() -0.00188539() 0.01870859() -0.00793643()
53	O3 0.0408599() 0.03053501() 0.01716822() 0.01038486() 0.00019991() 0.00086291()
54	N1 0.01438727() 0.03483324() 0.02632762() -0.00516777() 0.00324174() -0.00181414()
55	H1 0.04498022() 0.02753397() 0.03894993() -0.00465784() 0.01276985() -0.01104185()
56	H2 0.06450102() 0.09585856() 0.0292822() 0.04411927() -0.00869109() 0.01028107()
57	H3 0.01908915() 0.07725996() 0.07635565() 0.00551452() -0.0065522() -0.017712()
58	C1 0.03521991() 0.0093205() 0.0186952() 0.01472301() 0.00555376() -0.00533095()
59	H11 0.06620726() 0.00556669() 0.05425269() 0.00091732() 0.02329037() 0.0023716()
60	H12 0.08179805() 0.04508835() 0.03974417() 0.03464255() 0.02361103() 0.00299542()
61	C2 -0.00438188() 0.04534467() 0.02587042() -0.00390863() -0.00150789() 0.00399456()
62	H21 0.04498601() 0.04801285() 0.03274724() -0.02581675() 0.00636336() -0.00151917()
63	H22 0.00473233() 0.03766364() 0.06551433() 0.00848636() -0.02136492() 0.00789778()

💾 Save Project¶

In [35]:

project.save_as(dir_path='projects/refine-taurine-senju')

project.save_as(dir_path='projects/refine-taurine-senju')

Saving project 📦 'taurine_senju' to '../../../projects/refine-taurine-senju'

├── 📄 project.edi
├── 📁 structures/
│   └── 📄 taurine.edi
├── 📁 experiments/
│   └── 📄 senju.edi
├── 📁 analysis/
│   └── 📄 analysis.edi
└── 📁 reports/
    └── 📄 taurine_senju.html