LiF — powder X-ray CW — absorption¶

Verifies the Debye-Scherrer cylindrical absorption correction on the same single-wavelength LiF reference.

Refinement: none — every parameter is taken from the FullProf reference; only the calculated patterns are compared.

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='lif')

structure.space_group.name_h_m = 'F m -3 m'  # FullProf Space group symbol
structure.cell.length_a = 4.026700  # FullProf a

structure.atom_sites.create(
    id='Li1',  # FullProf Atom
    type_symbol='Li',  # FullProf Typ
    fract_x=0.0,  # FullProf X
    fract_y=0.0,  # FullProf Y
    fract_z=0.0,  # FullProf Z
    adp_type='Biso',  # FullProf Biso
    adp_iso=1.20000,  # FullProf Biso
)
structure.atom_sites.create(
    id='F1',  # FullProf Atom
    type_symbol='F',  # FullProf Typ
    fract_x=0.5,  # FullProf X
    fract_y=0.5,  # FullProf Y
    fract_z=0.5,  # FullProf Z
    adp_type='Biso',  # FullProf Biso
    adp_iso=0.80000,  # FullProf Biso
)

project.structures.add(structure)

structure = StructureFactory.from_scratch(name='lif') structure.space_group.name_h_m = 'F m -3 m' # FullProf Space group symbol structure.cell.length_a = 4.026700 # FullProf a structure.atom_sites.create( id='Li1', # FullProf Atom type_symbol='Li', # FullProf Typ fract_x=0.0, # FullProf X fract_y=0.0, # FullProf Y fract_z=0.0, # FullProf Z adp_type='Biso', # FullProf Biso adp_iso=1.20000, # FullProf Biso ) structure.atom_sites.create( id='F1', # FullProf Atom type_symbol='F', # FullProf Typ fract_x=0.5, # FullProf X fract_y=0.5, # FullProf Y fract_z=0.5, # FullProf Z adp_type='Biso', # FullProf Biso adp_iso=0.80000, # FullProf Biso ) project.structures.add(structure)

Load the FullProf reference¶

In [5]:

FULLPROF_PROJECT_DIR = 'pd-xray-cwl_lif'
FULLPROF_PRF_FILE = 'lif_single_absorption.prf'
FULLPROF_SUM_FILE = 'lif_single_absorption.sum'
FULLPROF_BAC_FILE = 'lif_single_absorption.bac'
FULLPROF_LABEL = verify.fullprof_label(FULLPROF_PROJECT_DIR, FULLPROF_SUM_FILE)

FULLPROF_ZERO = 0.0  # FullProf Zero
FULLPROF_SCALE = 0.01  # FullProf Scale
FULLPROF_WAVELENGTH = 1.540560  # FullProf Lambda1
FULLPROF_U = 0.048457  # FullProf U
FULLPROF_V = -0.083053  # FullProf V
FULLPROF_W = 0.040000  # FullProf W
FULLPROF_X = 0.0  # FullProf X
FULLPROF_Y = 0.049268  # FullProf Y
FULLPROF_WDT = 48.0  # FullProf Wdt
FULLPROF_MU_R = 0.9  # FullProf muR

x, calc_fullprof = verify.load_fullprof_calc_profile(
    FULLPROF_PROJECT_DIR,
    FULLPROF_PRF_FILE,
    FULLPROF_BAC_FILE,
    FULLPROF_ZERO,
)

FULLPROF_PROJECT_DIR = 'pd-xray-cwl_lif' FULLPROF_PRF_FILE = 'lif_single_absorption.prf' FULLPROF_SUM_FILE = 'lif_single_absorption.sum' FULLPROF_BAC_FILE = 'lif_single_absorption.bac' FULLPROF_LABEL = verify.fullprof_label(FULLPROF_PROJECT_DIR, FULLPROF_SUM_FILE) FULLPROF_ZERO = 0.0 # FullProf Zero FULLPROF_SCALE = 0.01 # FullProf Scale FULLPROF_WAVELENGTH = 1.540560 # FullProf Lambda1 FULLPROF_U = 0.048457 # FullProf U FULLPROF_V = -0.083053 # FullProf V FULLPROF_W = 0.040000 # FullProf W FULLPROF_X = 0.0 # FullProf X FULLPROF_Y = 0.049268 # FullProf Y FULLPROF_WDT = 48.0 # FullProf Wdt FULLPROF_MU_R = 0.9 # FullProf muR x, calc_fullprof = verify.load_fullprof_calc_profile( FULLPROF_PROJECT_DIR, FULLPROF_PRF_FILE, FULLPROF_BAC_FILE, FULLPROF_ZERO, )

Create the experiment¶

In [6]:

experiment = ExperimentFactory.from_scratch(
    name='lif',
    sample_form='powder',
    beam_mode='constant wavelength',
    radiation_probe='xray',
    scattering_type='bragg',
)
verify.set_reference_as_measured(experiment, x, calc_fullprof)

experiment.linked_structures.create(structure_id='lif', scale=FULLPROF_SCALE)

experiment.instrument.setup_wavelength = FULLPROF_WAVELENGTH
experiment.instrument.calib_twotheta_offset = FULLPROF_ZERO

experiment.peak.type = 'pseudo-voigt'
experiment.peak.broad_gauss_u = FULLPROF_U
experiment.peak.broad_gauss_v = FULLPROF_V
experiment.peak.broad_gauss_w = FULLPROF_W
experiment.peak.broad_lorentz_x = FULLPROF_X
experiment.peak.broad_lorentz_y = FULLPROF_Y

experiment.absorption.type = 'cylinder-hewat'
experiment.absorption.mu_r = FULLPROF_MU_R

experiment.peak.cutoff_fwhm = FULLPROF_WDT

project.experiments.add(experiment)

experiment = ExperimentFactory.from_scratch( name='lif', sample_form='powder', beam_mode='constant wavelength', radiation_probe='xray', scattering_type='bragg', ) verify.set_reference_as_measured(experiment, x, calc_fullprof) experiment.linked_structures.create(structure_id='lif', scale=FULLPROF_SCALE) experiment.instrument.setup_wavelength = FULLPROF_WAVELENGTH experiment.instrument.calib_twotheta_offset = FULLPROF_ZERO experiment.peak.type = 'pseudo-voigt' experiment.peak.broad_gauss_u = FULLPROF_U experiment.peak.broad_gauss_v = FULLPROF_V experiment.peak.broad_gauss_w = FULLPROF_W experiment.peak.broad_lorentz_x = FULLPROF_X experiment.peak.broad_lorentz_y = FULLPROF_Y experiment.absorption.type = 'cylinder-hewat' experiment.absorption.mu_r = FULLPROF_MU_R experiment.peak.cutoff_fwhm = FULLPROF_WDT project.experiments.add(experiment)

Peak profile type for experiment 'lif' changed to

pseudo-voigt

Absorption type changed to

cylinder-hewat

edi-cryspy VS FullProf¶

In [7]:

experiment.calculator.type = 'cryspy'

project.analysis.calculate()
calc_ed_cryspy = experiment.data.intensity_calc
LABEL_ED_CRYSPY = verify.engine_label('cryspy')

project.display.pattern_comparison(
    'lif',
    reference=calc_fullprof,
    candidate=calc_ed_cryspy,
    reference_label=FULLPROF_LABEL,
    candidate_label=LABEL_ED_CRYSPY,
)

experiment.calculator.type = 'cryspy' project.analysis.calculate() calc_ed_cryspy = experiment.data.intensity_calc LABEL_ED_CRYSPY = verify.engine_label('cryspy') project.display.pattern_comparison( 'lif', reference=calc_fullprof, candidate=calc_ed_cryspy, reference_label=FULLPROF_LABEL, candidate_label=LABEL_ED_CRYSPY, )

Calculator for experiment 'lif' already set to

cryspy

Loading plot…

Agreement check¶

In [8]:

verify.assert_patterns_agree(
    [
        (f'{LABEL_ED_CRYSPY} vs {FULLPROF_LABEL}', calc_fullprof, calc_ed_cryspy),
    ],
)

verify.assert_patterns_agree( [ (f'{LABEL_ED_CRYSPY} vs {FULLPROF_LABEL}', calc_fullprof, calc_ed_cryspy), ], )

	Comparison	Metric	Expected	Actual	OK
1	edi 0.19.0 (cryspy 0.12.1) vs FullProf 7.95	Profile diff (%)	< 2.5	0.23	✅
2		Max deviation (%)	< 6	0.18	✅
3		Area ratio	0.99 to 1.01	1.0002	✅
4		Shape correlation	> 0.999	1.0000	✅

Out[8]:

True