Y2O3 - powder neutron CW - isotropic ADPs¶

Verifies the baseline Y2O3 constant-wavelength neutron powder pattern with isotropic ADPs.

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¶

Occupancies are the crystallographic site fractions (all fully occupied). FullProf's .pcr lists the multiplicity-weighted values (0.5, 0.16667, 1.0 for the 24d, 8b and 48e sites); cryspy derives the site multiplicity from the symmetry, so the fractions are 1.0 here.

In [4]:

structure = StructureFactory.from_scratch(name='y2o3')

structure.space_group.name_h_m = 'I a -3'  # FullProf Space group symbol

structure.cell.length_a = 10.605744  # FullProf a

structure.atom_sites.create(
    id='Y1',  # FullProf Atom
    type_symbol='Y',  # FullProf Typ
    fract_x=-0.03236,  # FullProf X
    fract_y=0.0,  # FullProf Y
    fract_z=0.25,  # FullProf Z
    occupancy=1.0,  # FullProf Occ 0.50000 (24d site)
    adp_type='Biso',  # FullProf N_t = 0
    adp_iso=0.3,  # FullProf Biso
)
structure.atom_sites.create(
    id='Y2',  # FullProf Atom
    type_symbol='Y',  # FullProf Typ
    fract_x=0.25,  # FullProf X
    fract_y=0.25,  # FullProf Y
    fract_z=0.25,  # FullProf Z
    occupancy=1.0,  # FullProf Occ 0.16667 (8b site)
    adp_type='Biso',  # FullProf N_t = 0
    adp_iso=0.3,  # FullProf Biso
)
structure.atom_sites.create(
    id='O1',  # FullProf Atom
    type_symbol='O',  # FullProf Typ
    fract_x=0.39072,  # FullProf X
    fract_y=0.15204,  # FullProf Y
    fract_z=0.38030,  # FullProf Z
    occupancy=1.0,  # FullProf Occ 1.00000 (48e site)
    adp_type='Biso',  # FullProf N_t = 0
    adp_iso=0.5,  # FullProf Biso
)

project.structures.add(structure)

structure = StructureFactory.from_scratch(name='y2o3') structure.space_group.name_h_m = 'I a -3' # FullProf Space group symbol structure.cell.length_a = 10.605744 # FullProf a structure.atom_sites.create( id='Y1', # FullProf Atom type_symbol='Y', # FullProf Typ fract_x=-0.03236, # FullProf X fract_y=0.0, # FullProf Y fract_z=0.25, # FullProf Z occupancy=1.0, # FullProf Occ 0.50000 (24d site) adp_type='Biso', # FullProf N_t = 0 adp_iso=0.3, # FullProf Biso ) structure.atom_sites.create( id='Y2', # FullProf Atom type_symbol='Y', # FullProf Typ fract_x=0.25, # FullProf X fract_y=0.25, # FullProf Y fract_z=0.25, # FullProf Z occupancy=1.0, # FullProf Occ 0.16667 (8b site) adp_type='Biso', # FullProf N_t = 0 adp_iso=0.3, # FullProf Biso ) structure.atom_sites.create( id='O1', # FullProf Atom type_symbol='O', # FullProf Typ fract_x=0.39072, # FullProf X fract_y=0.15204, # FullProf Y fract_z=0.38030, # FullProf Z occupancy=1.0, # FullProf Occ 1.00000 (48e site) adp_type='Biso', # FullProf N_t = 0 adp_iso=0.5, # FullProf Biso ) project.structures.add(structure)

Load the FullProf reference¶

In [5]:

FULLPROF_PROJECT_DIR = 'pd-neut-cwl_y2o3_isotropic-adp'
FULLPROF_PRF_FILE = 'y2o3_isotropic_adp.prf'
FULLPROF_SUM_FILE = 'y2o3_isotropic_adp.sum'
FULLPROF_BAC_FILE = 'y2o3_isotropic_adp.bac'
FULLPROF_LABEL = verify.fullprof_label(FULLPROF_PROJECT_DIR, FULLPROF_SUM_FILE)

FULLPROF_ZERO = -0.01625  # FullProf Zero
FULLPROF_SCALE = 1.0602  # FullProf Scale
FULLPROF_WAVELENGTH = 1.54822  # FullProf Lambda
FULLPROF_U = 0.036631  # FullProf U
FULLPROF_V = -0.068345  # FullProf V
FULLPROF_W = 0.131426  # FullProf W
FULLPROF_WDT = 20.0  # FullProf Wdt

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

FULLPROF_PROJECT_DIR = 'pd-neut-cwl_y2o3_isotropic-adp' FULLPROF_PRF_FILE = 'y2o3_isotropic_adp.prf' FULLPROF_SUM_FILE = 'y2o3_isotropic_adp.sum' FULLPROF_BAC_FILE = 'y2o3_isotropic_adp.bac' FULLPROF_LABEL = verify.fullprof_label(FULLPROF_PROJECT_DIR, FULLPROF_SUM_FILE) FULLPROF_ZERO = -0.01625 # FullProf Zero FULLPROF_SCALE = 1.0602 # FullProf Scale FULLPROF_WAVELENGTH = 1.54822 # FullProf Lambda FULLPROF_U = 0.036631 # FullProf U FULLPROF_V = -0.068345 # FullProf V FULLPROF_W = 0.131426 # FullProf W FULLPROF_WDT = 20.0 # FullProf Wdt 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='y2o3',
    sample_form='powder',
    beam_mode='constant wavelength',
    radiation_probe='neutron',
    scattering_type='bragg',
)
verify.set_reference_as_measured(experiment, x, calc_fullprof)

experiment.linked_structures.create(structure_id='y2o3', 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

# FullProf excluded the 0-12 deg and 137.5-180 deg regions (.pcr).
experiment.excluded_regions.create(id='1', start=0.0, end=12.0)
experiment.excluded_regions.create(id='2', start=137.5, end=180.0)

experiment.peak.cutoff_fwhm = FULLPROF_WDT

project.experiments.add(experiment)

experiment = ExperimentFactory.from_scratch( name='y2o3', sample_form='powder', beam_mode='constant wavelength', radiation_probe='neutron', scattering_type='bragg', ) verify.set_reference_as_measured(experiment, x, calc_fullprof) experiment.linked_structures.create(structure_id='y2o3', 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 # FullProf excluded the 0-12 deg and 137.5-180 deg regions (.pcr). experiment.excluded_regions.create(id='1', start=0.0, end=12.0) experiment.excluded_regions.create(id='2', start=137.5, end=180.0) experiment.peak.cutoff_fwhm = FULLPROF_WDT project.experiments.add(experiment)

Peak profile type for experiment 'y2o3' changed to

pseudo-voigt

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(
    'y2o3',
    reference=verify.restrict_to_included(experiment, 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( 'y2o3', reference=verify.restrict_to_included(experiment, calc_fullprof), candidate=calc_ed_cryspy, reference_label=FULLPROF_LABEL, candidate_label=LABEL_ED_CRYSPY, )

Calculator for experiment 'y2o3' already set to

cryspy

Loading plot…

Agreement check¶

In [8]:

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

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

	Comparison	Metric	Expected	Actual	OK
1	edi 0.19.0 (cryspy 0.12.1) vs FullProf 8.40	Profile diff (%)	< 2.5	0.37	✅
2		Max deviation (%)	< 6	0.29	✅
3		Area ratio	0.99 to 1.01	1.0000	✅
4		Shape correlation	> 0.999	1.0000	✅

Out[8]:

True