Fe - powder neutron TOF - pseudo-Voigt profile¶

Verifies the simple non-convoluted pseudo-Voigt time-of-flight peak profile.

Refinement: none. The calculation uses parameters from the FullProf reference directly.

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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¶

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project = edi.Project()
project = edi.Project()

Define the structure¶

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structure = StructureFactory.from_scratch(name='fe')
structure.space_group.name_h_m = 'I m -3 m'  # FullProf Space group symbol
structure.cell.length_a = 2.886  # FullProf a
structure.atom_sites.create(
    id='Fe',  # FullProf Atom
    type_symbol='Fe',  # 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=1.71513,  # FullProf Biso
)

project.structures.add(structure)
structure = StructureFactory.from_scratch(name='fe')
structure.space_group.name_h_m = 'I m -3 m'  # FullProf Space group symbol
structure.cell.length_a = 2.886  # FullProf a
structure.atom_sites.create(
    id='Fe',  # FullProf Atom
    type_symbol='Fe',  # 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=1.71513,  # FullProf Biso
)

project.structures.add(structure)

Load the FullProf reference¶

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FULLPROF_PROJECT_DIR = 'pd-neut-tof_fe_pseudo-voigt'
FULLPROF_PRF_FILE = 'fe_1.prf'
FULLPROF_SUM_FILE = 'fe.sum'
FULLPROF_BAC_FILE = 'fe_1.bac'
FULLPROF_LABEL = verify.fullprof_label(FULLPROF_PROJECT_DIR, FULLPROF_SUM_FILE)

FULLPROF_ZERO = -10.29183  # FullProf Zero
FULLPROF_SCALE = 401.4629  # FullProf Scale
FULLPROF_TWOTHETA_BANK = 90.0  # FullProf 2ThetaBank
FULLPROF_DTT1 = 54902.18750  # FullProf Dtt1
FULLPROF_DTT2 = 0.0  # FullProf Dtt2
FULLPROF_SIGMA_0 = 893.6397  # FullProf Sigma-0
FULLPROF_SIGMA_1 = 1283.6387  # FullProf Sigma-1
FULLPROF_SIGMA_2 = 311.7041  # FullProf Sigma-2
FULLPROF_GAMMA_0 = 5.0330  # FullProf Gamma-0
FULLPROF_GAMMA_1 = 0.0  # FullProf Gamma-1
FULLPROF_GAMMA_2 = 0.0  # FullProf Gamma-2
FULLPROF_WDT = 12.0  # 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-tof_fe_pseudo-voigt'
FULLPROF_PRF_FILE = 'fe_1.prf'
FULLPROF_SUM_FILE = 'fe.sum'
FULLPROF_BAC_FILE = 'fe_1.bac'
FULLPROF_LABEL = verify.fullprof_label(FULLPROF_PROJECT_DIR, FULLPROF_SUM_FILE)

FULLPROF_ZERO = -10.29183  # FullProf Zero
FULLPROF_SCALE = 401.4629  # FullProf Scale
FULLPROF_TWOTHETA_BANK = 90.0  # FullProf 2ThetaBank
FULLPROF_DTT1 = 54902.18750  # FullProf Dtt1
FULLPROF_DTT2 = 0.0  # FullProf Dtt2
FULLPROF_SIGMA_0 = 893.6397  # FullProf Sigma-0
FULLPROF_SIGMA_1 = 1283.6387  # FullProf Sigma-1
FULLPROF_SIGMA_2 = 311.7041  # FullProf Sigma-2
FULLPROF_GAMMA_0 = 5.0330  # FullProf Gamma-0
FULLPROF_GAMMA_1 = 0.0  # FullProf Gamma-1
FULLPROF_GAMMA_2 = 0.0  # FullProf Gamma-2
FULLPROF_WDT = 12.0  # FullProf Wdt

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

Create the experiment¶

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experiment = ExperimentFactory.from_scratch(
    name='fe',
    sample_form='powder',
    beam_mode='time-of-flight',
    radiation_probe='neutron',
    scattering_type='bragg',
)
verify.set_reference_as_measured(experiment, x, calc_fullprof)

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

experiment.instrument.setup_twotheta_bank = FULLPROF_TWOTHETA_BANK
experiment.instrument.calib_d_to_tof_offset = FULLPROF_ZERO
experiment.instrument.calib_d_to_tof_linear = FULLPROF_DTT1
experiment.instrument.calib_d_to_tof_quadratic = FULLPROF_DTT2

experiment.peak.type = 'pseudo-voigt'
experiment.peak.broad_gauss_sigma_0 = FULLPROF_SIGMA_0
experiment.peak.broad_gauss_sigma_1 = FULLPROF_SIGMA_1
experiment.peak.broad_gauss_sigma_2 = FULLPROF_SIGMA_2
experiment.peak.broad_lorentz_gamma_0 = FULLPROF_GAMMA_0
experiment.peak.broad_lorentz_gamma_1 = FULLPROF_GAMMA_1
experiment.peak.broad_lorentz_gamma_2 = FULLPROF_GAMMA_2

experiment.excluded_regions.create(id='1', start=0.0, end=40000.0)
experiment.excluded_regions.create(id='2', start=130000.0, end=180000.0)

experiment.peak.cutoff_fwhm = FULLPROF_WDT

project.experiments.add(experiment)
experiment = ExperimentFactory.from_scratch(
    name='fe',
    sample_form='powder',
    beam_mode='time-of-flight',
    radiation_probe='neutron',
    scattering_type='bragg',
)
verify.set_reference_as_measured(experiment, x, calc_fullprof)

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

experiment.instrument.setup_twotheta_bank = FULLPROF_TWOTHETA_BANK
experiment.instrument.calib_d_to_tof_offset = FULLPROF_ZERO
experiment.instrument.calib_d_to_tof_linear = FULLPROF_DTT1
experiment.instrument.calib_d_to_tof_quadratic = FULLPROF_DTT2

experiment.peak.type = 'pseudo-voigt'
experiment.peak.broad_gauss_sigma_0 = FULLPROF_SIGMA_0
experiment.peak.broad_gauss_sigma_1 = FULLPROF_SIGMA_1
experiment.peak.broad_gauss_sigma_2 = FULLPROF_SIGMA_2
experiment.peak.broad_lorentz_gamma_0 = FULLPROF_GAMMA_0
experiment.peak.broad_lorentz_gamma_1 = FULLPROF_GAMMA_1
experiment.peak.broad_lorentz_gamma_2 = FULLPROF_GAMMA_2

experiment.excluded_regions.create(id='1', start=0.0, end=40000.0)
experiment.excluded_regions.create(id='2', start=130000.0, end=180000.0)

experiment.peak.cutoff_fwhm = FULLPROF_WDT

project.experiments.add(experiment)

⚠️ Switching peak profile type removes these settings:                                                                            
   • decay_beta_0                                                                                                                 
   • decay_beta_1                                                                                                                 
   • rise_alpha_0                                                                                                                 
   • rise_alpha_1

⚠️ Switching peak profile type adds these settings with defaults:                                                                 
   • broad_lorentz_gamma_0=0.0                                                                                                    
   • broad_lorentz_gamma_1=0.0                                                                                                    
   • broad_lorentz_gamma_2=0.0                                                                                                    
   • broad_lorentz_size=0.0                                                                                                       
   • broad_lorentz_strain=0.0

Peak profile type for experiment 'fe' changed to

pseudo-voigt

edi-cryspy VS FullProf¶

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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(
    'fe',
    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(
    'fe',
    reference=calc_fullprof,
    candidate=calc_ed_cryspy,
    reference_label=FULLPROF_LABEL,
    candidate_label=LABEL_ED_CRYSPY,
)

Calculator for experiment 'fe' already set to

cryspy

Loading plot…

Agreement check¶

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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 0.20.0 (cryspy 0.13.0) vs FullProf 8.40	Profile diff (%)	< 2.5	0.12	✅
2		Max deviation (%)	< 6	0.11	✅
3		Area ratio	0.99 to 1.01	1.0002	✅
4		Shape correlation	> 0.999	1.0000	✅

Out[8]:

True