Taurine - single-crystal neutron TOF - basic¶

Verifies calculated F2 values for a no-extinction neutron single-crystal time-of-flight baseline with isotropic ADPs.

Refinement: the overall scale only; all other parameters are taken from the FullProf reference. Extinction is set to zero in the FullProf model so the comparison focuses on the structure-factor physics shared by cryspy and FullProf.

In [2]:

import easydiffraction as edi
from easydiffraction import ExperimentFactory
from easydiffraction import StructureFactory
from easydiffraction.analysis import verification as verify

import easydiffraction as edi from easydiffraction import ExperimentFactory from easydiffraction import StructureFactory from easydiffraction.analysis import verification as verify

Build the project¶

In [3]:

project = edi.Project()

project = edi.Project()

Define the structure¶

In [4]:

structure = StructureFactory.from_scratch(name='taurine')

structure.space_group.name_h_m = 'P 21/c'  # FullProf Space group symbol

structure.cell.length_a = 5.272901  # FullProf a
structure.cell.length_b = 11.656488  # FullProf b
structure.cell.length_c = 7.838297  # FullProf c
structure.cell.angle_beta = 94.010994  # FullProf beta

# fmt: off
_ATOMS = [
    ('S1', 'S', 0.19448, 0.35173, 0.34730, 1.37018),
    ('O1', 'O', 0.31207, 0.23951, 0.35143, 2.68011),
    ('O2', 'O', -0.05909, 0.33563, 0.29636, 3.50515),
    ('O3', 'O', 0.22105, 0.41215, 0.50573, 1.83513),
    ('N1', 'N', 0.26340, 0.62808, 0.33048, 2.07364),
    ('H1', 'H', 0.12861, 0.58669, 0.41769, 3.31527),
    ('H2', 'H', 0.18953, 0.71385, 0.31124, 4.46988),
    ('H3', 'H', 0.43970, 0.62023, 0.34592, 4.34151),
    ('C1', 'C', 0.34384, 0.44116, 0.20155, 1.73667),
    ('H11', 'H', 0.55246, 0.43345, 0.24304, 3.32279),
    ('H12', 'H', 0.32537, 0.38970, 0.08264, 3.05746),
    ('C2', 'C', 0.20029, 0.55716, 0.18272, 1.66017),
    ('H21', 'H', 0.27650, 0.60004, 0.07688, 2.15403),
    ('H22', 'H', -0.00383, 0.54767, 0.15762, 4.71303),
]
# fmt: on

for _id, _type, _x, _y, _z, _biso in _ATOMS:
    structure.atom_sites.create(
        id=_id,  # FullProf Atom
        type_symbol=_type,  # FullProf Typ
        fract_x=_x,  # FullProf X
        fract_y=_y,  # FullProf Y
        fract_z=_z,  # FullProf Z
        adp_type='Biso',  # FullProf Biso
        adp_iso=_biso,  # FullProf Biso
    )

project.structures.add(structure)

structure = StructureFactory.from_scratch(name='taurine') structure.space_group.name_h_m = 'P 21/c' # FullProf Space group symbol structure.cell.length_a = 5.272901 # FullProf a structure.cell.length_b = 11.656488 # FullProf b structure.cell.length_c = 7.838297 # FullProf c structure.cell.angle_beta = 94.010994 # FullProf beta # fmt: off _ATOMS = [ ('S1', 'S', 0.19448, 0.35173, 0.34730, 1.37018), ('O1', 'O', 0.31207, 0.23951, 0.35143, 2.68011), ('O2', 'O', -0.05909, 0.33563, 0.29636, 3.50515), ('O3', 'O', 0.22105, 0.41215, 0.50573, 1.83513), ('N1', 'N', 0.26340, 0.62808, 0.33048, 2.07364), ('H1', 'H', 0.12861, 0.58669, 0.41769, 3.31527), ('H2', 'H', 0.18953, 0.71385, 0.31124, 4.46988), ('H3', 'H', 0.43970, 0.62023, 0.34592, 4.34151), ('C1', 'C', 0.34384, 0.44116, 0.20155, 1.73667), ('H11', 'H', 0.55246, 0.43345, 0.24304, 3.32279), ('H12', 'H', 0.32537, 0.38970, 0.08264, 3.05746), ('C2', 'C', 0.20029, 0.55716, 0.18272, 1.66017), ('H21', 'H', 0.27650, 0.60004, 0.07688, 2.15403), ('H22', 'H', -0.00383, 0.54767, 0.15762, 4.71303), ] # fmt: on for _id, _type, _x, _y, _z, _biso in _ATOMS: structure.atom_sites.create( id=_id, # FullProf Atom type_symbol=_type, # FullProf Typ fract_x=_x, # FullProf X fract_y=_y, # FullProf Y fract_z=_z, # FullProf Z adp_type='Biso', # FullProf Biso adp_iso=_biso, # FullProf Biso ) project.structures.add(structure)

In [5]:

structure.show_as_text()

structure.show_as_text()

Structure 🧩 'taurine' as text

	Edi
1	data_taurine
2
3	_cell.length_a 5.272901
4	_cell.length_b 11.656488
5	_cell.length_c 7.838297
6	_cell.angle_alpha 90.
7	_cell.angle_beta 94.010994
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 0.19448 0.35173 0.3473 e 4 1. 1.37018 Biso
28	O1 O 0.31207 0.23951 0.35143 e 4 1. 2.68011 Biso
29	O2 O -0.05909 0.33563 0.29636 e 4 1. 3.50515 Biso
30	O3 O 0.22105 0.41215 0.50573 e 4 1. 1.83513 Biso
31	N1 N 0.2634 0.62808 0.33048 e 4 1. 2.07364 Biso
32	H1 H 0.12861 0.58669 0.41769 e 4 1. 3.31527 Biso
33	H2 H 0.18953 0.71385 0.31124 e 4 1. 4.46988 Biso
34	H3 H 0.4397 0.62023 0.34592 e 4 1. 4.34151 Biso
35	C1 C 0.34384 0.44116 0.20155 e 4 1. 1.73667 Biso
36	H11 H 0.55246 0.43345 0.24304 e 4 1. 3.32279 Biso
37	H12 H 0.32537 0.3897 0.08264 e 4 1. 3.05746 Biso
38	C2 C 0.20029 0.55716 0.18272 e 4 1. 1.66017 Biso
39	H21 H 0.2765 0.60004 0.07688 e 4 1. 2.15403 Biso
40	H22 H -0.00383 0.54767 0.15762 e 4 1. 4.71303 Biso

Load the FullProf reference¶

In [6]:

FULLPROF_PROJECT_DIR = 'sc-neut-tof_taurine_basic'
FULLPROF_OUT_FILE = 'taurine.out'
FULLPROF_SCALE = 2.711  # FullProf Scale

f2calc = verify.load_fullprof_sc_f2calc(FULLPROF_PROJECT_DIR, FULLPROF_OUT_FILE)
FULLPROF_LABEL = verify.fullprof_label(FULLPROF_PROJECT_DIR, FULLPROF_OUT_FILE)

FULLPROF_PROJECT_DIR = 'sc-neut-tof_taurine_basic' FULLPROF_OUT_FILE = 'taurine.out' FULLPROF_SCALE = 2.711 # FullProf Scale f2calc = verify.load_fullprof_sc_f2calc(FULLPROF_PROJECT_DIR, FULLPROF_OUT_FILE) FULLPROF_LABEL = verify.fullprof_label(FULLPROF_PROJECT_DIR, FULLPROF_OUT_FILE)

Create the experiment¶

In [7]:

experiment = ExperimentFactory.from_scratch(
    name='taurine',
    sample_form='single crystal',
    beam_mode='time-of-flight',
    radiation_probe='neutron',
    scattering_type='bragg',
)

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

verify.set_reference_reflections(experiment, f2calc)

project.experiments.add(experiment)

experiment = ExperimentFactory.from_scratch( name='taurine', sample_form='single crystal', beam_mode='time-of-flight', radiation_probe='neutron', scattering_type='bragg', ) experiment.linked_structure.structure_id = 'taurine' experiment.linked_structure.scale = FULLPROF_SCALE verify.set_reference_reflections(experiment, f2calc) project.experiments.add(experiment)

edi-cryspy VS FullProf¶

In [8]:

calc_ed_cryspy = verify.calculate_reflections(project, experiment, 'cryspy')
LABEL_ED_CRYSPY = verify.engine_label('cryspy')
reference, candidate = verify.align_reflections(f2calc, calc_ed_cryspy)

project.display.reflection_comparison(
    'taurine',
    reference=reference,
    candidate=candidate,
    reference_label=FULLPROF_LABEL,
    candidate_label=LABEL_ED_CRYSPY,
)

calc_ed_cryspy = verify.calculate_reflections(project, experiment, 'cryspy') LABEL_ED_CRYSPY = verify.engine_label('cryspy') reference, candidate = verify.align_reflections(f2calc, calc_ed_cryspy) project.display.reflection_comparison( 'taurine', reference=reference, candidate=candidate, reference_label=FULLPROF_LABEL, candidate_label=LABEL_ED_CRYSPY, )

Calculator for experiment 'taurine' already set to

cryspy

Loading plot…

Fit edi-cryspy to FullProf¶

In [9]:

experiment.calculator.type = 'cryspy'

experiment.linked_structure.scale.free = True

project.analysis.fit()
project.display.fit.results()

calc_ed_cryspy_refined = verify.calculate_reflections(project, experiment, 'cryspy')
LABEL_ED_CRYSPY_REFINED = verify.engine_label('cryspy', note='scale only')
reference_refined, candidate_refined = verify.align_reflections(f2calc, calc_ed_cryspy_refined)

project.display.reflection_comparison(
    'taurine',
    reference=reference_refined,
    candidate=candidate_refined,
    reference_label=FULLPROF_LABEL,
    candidate_label=LABEL_ED_CRYSPY_REFINED,
)

verify.report_refinement_closeness(
    reference,
    candidate,
    candidate_refined,
)

experiment.calculator.type = 'cryspy' experiment.linked_structure.scale.free = True project.analysis.fit() project.display.fit.results() calc_ed_cryspy_refined = verify.calculate_reflections(project, experiment, 'cryspy') LABEL_ED_CRYSPY_REFINED = verify.engine_label('cryspy', note='scale only') reference_refined, candidate_refined = verify.align_reflections(f2calc, calc_ed_cryspy_refined) project.display.reflection_comparison( 'taurine', reference=reference_refined, candidate=candidate_refined, reference_label=FULLPROF_LABEL, candidate_label=LABEL_ED_CRYSPY_REFINED, ) verify.report_refinement_closeness( reference, candidate, candidate_refined, )

Calculator for experiment 'taurine' already set to

cryspy

Standard fitting

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

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

📈 Goodness-of-fit progress:

	iteration	time (s)	χ²	change / status
1	1	0.01	764.53
2	5	0.04	0.00	100.0% ↓
3	8	0.08	0.00

🏆 Best goodness-of-fit (reduced χ²) is 0.00 at iteration 7

✅ Fitting complete.

⚙️ Settings used:

	Name	Value	Description
1	max_iterations	1000	Maximum solver iterations.

📋 Least-squares fit results:

	Metric	Value
1	🧪 Minimizer	lmfit (leastsq)
2	✅ Overall status	success
3	⏱️ Fitting time (seconds)	0.08
4	🔁 Iterations	5
5	📏 Goodness-of-fit (reduced χ²)	0.00
6	📏 R-factor (Rf, %)	0.00
7	📏 R-factor squared (Rf², %)	0.00
8	📏 Weighted R-factor (wR, %)	0.00

📈 Refined parameters:

	datablock	category	entry	parameter	units	start	value	s.u.	change
1	taurine	linked_structure		scale		2.7110	1.3555	0.0000	50.00 % ↓

• 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

Calculator for experiment 'taurine' already set to

cryspy

Loading plot…

	Metric	Before	After
1	Profile diff (%)	100.00	0.00
2	Max deviation (%)	100.00	0.00
3	Area ratio	2.0000	1.0000
4	Shape correlation	1.0000	1.0000

Agreement check¶

In [10]:

verify.assert_patterns_agree([
    (f'{LABEL_ED_CRYSPY_REFINED} vs {FULLPROF_LABEL}', reference_refined, candidate_refined),
])

verify.assert_patterns_agree([ (f'{LABEL_ED_CRYSPY_REFINED} vs {FULLPROF_LABEL}', reference_refined, candidate_refined), ])

	Comparison	Metric	Expected	Actual	OK
1	edi 0.19.0 (cryspy 0.12.1, scale only) vs FullProf 8.40	Profile diff (%)	< 2.5	0.00	✅
2		Max deviation (%)	< 6	0.00	✅
3		Area ratio	0.99 to 1.01	1.0000	✅
4		Shape correlation	> 0.999	1.0000	✅

Out[10]:

True