NaCl - powder X-ray CW total - gaussian-damped sinc¶

Verifies the total-scattering gaussian-damped sinc profile by comparing EasyDiffraction's pdffit calculator with a direct diffpy.pdffit2 calculation on the same synthetic r-grid.

Refinement: none — every parameter is taken from the direct diffpy.pdffit2 reference; only the calculated patterns are compared.

In [2]:

from importlib import metadata

import numpy as np
from diffpy.pdffit2 import PdfFit
from diffpy.structure.parsers.p_cif import P_cif as pdffit_cif_parser

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

from importlib import metadata import numpy as np from diffpy.pdffit2 import PdfFit from diffpy.structure.parsers.p_cif import P_cif as pdffit_cif_parser import easydiffraction as edi from easydiffraction import ExperimentFactory from easydiffraction.analysis import verification as verify

Build the project¶

In [3]:

project = edi.Project()

project = edi.Project()

Define the structure¶

In [4]:

project.structures.create(name='nacl')
structure = project.structures['nacl']

structure.space_group.name_h_m = 'F m -3 m'
structure.space_group.coord_system_code = '1'
structure.cell.length_a = 5.6018

structure.atom_sites.create(
    id='Na',
    type_symbol='Na',
    fract_x=0.0,
    fract_y=0.0,
    fract_z=0.0,
    adp_type='Biso',
    adp_iso=1.1053,
)
structure.atom_sites.create(
    id='Cl',
    type_symbol='Cl',
    fract_x=0.5,
    fract_y=0.5,
    fract_z=0.5,
    adp_type='Biso',
    adp_iso=0.5708,
)

project.structures.create(name='nacl') structure = project.structures['nacl'] structure.space_group.name_h_m = 'F m -3 m' structure.space_group.coord_system_code = '1' structure.cell.length_a = 5.6018 structure.atom_sites.create( id='Na', type_symbol='Na', fract_x=0.0, fract_y=0.0, fract_z=0.0, adp_type='Biso', adp_iso=1.1053, ) structure.atom_sites.create( id='Cl', type_symbol='Cl', fract_x=0.5, fract_y=0.5, fract_z=0.5, adp_type='Biso', adp_iso=0.5708, )

Create the experiment¶

In [5]:

experiment = ExperimentFactory.from_scratch(
    name='nacl_pdf',
    sample_form='powder',
    beam_mode='constant wavelength',
    radiation_probe='xray',
    scattering_type='total',
)

R_GRID = np.arange(1.0, 30.05, 0.05)
PDF_SCALE = 0.4254
PDF_QDAMP = 0.0606
PDF_QBROAD = 0.0
PDF_QMAX = 21.0
PDF_DELTA_1 = 0.0
PDF_DELTA_2 = 3.5041
PDF_PARTICLE_DIAMETER = 0.0

experiment.data._create_items_set_xcoord_and_id(R_GRID)
experiment.data._set_g_r_meas(np.zeros_like(R_GRID))
experiment.data._set_g_r_meas_su(np.ones_like(R_GRID))

experiment.peak.type = 'gaussian-damped-sinc'
experiment.peak.damp_q = PDF_QDAMP
experiment.peak.broad_q = PDF_QBROAD
experiment.peak.cutoff_q = PDF_QMAX
experiment.peak.sharp_delta_1 = PDF_DELTA_1
experiment.peak.sharp_delta_2 = PDF_DELTA_2
experiment.peak.damp_particle_diameter = PDF_PARTICLE_DIAMETER

experiment.linked_structures.create(structure_id='nacl', scale=PDF_SCALE)

project.experiments.add(experiment)

experiment = ExperimentFactory.from_scratch( name='nacl_pdf', sample_form='powder', beam_mode='constant wavelength', radiation_probe='xray', scattering_type='total', ) R_GRID = np.arange(1.0, 30.05, 0.05) PDF_SCALE = 0.4254 PDF_QDAMP = 0.0606 PDF_QBROAD = 0.0 PDF_QMAX = 21.0 PDF_DELTA_1 = 0.0 PDF_DELTA_2 = 3.5041 PDF_PARTICLE_DIAMETER = 0.0 experiment.data._create_items_set_xcoord_and_id(R_GRID) experiment.data._set_g_r_meas(np.zeros_like(R_GRID)) experiment.data._set_g_r_meas_su(np.ones_like(R_GRID)) experiment.peak.type = 'gaussian-damped-sinc' experiment.peak.damp_q = PDF_QDAMP experiment.peak.broad_q = PDF_QBROAD experiment.peak.cutoff_q = PDF_QMAX experiment.peak.sharp_delta_1 = PDF_DELTA_1 experiment.peak.sharp_delta_2 = PDF_DELTA_2 experiment.peak.damp_particle_diameter = PDF_PARTICLE_DIAMETER experiment.linked_structures.create(structure_id='nacl', scale=PDF_SCALE) project.experiments.add(experiment)

Peak profile type for experiment 'nacl_pdf' changed to

gaussian-damped-sinc

Direct pdffit2 reference¶

In [6]:

B_TO_U_FACTOR = 8.0 * np.pi**2
NACL_CIF_FOR_PDFFIT2 = f"""
data_nacl
_space_group_name_H-M_alt 'F m -3 m'
_space_group_IT_coordinate_system_code 1
_cell_length_a 5.6018
_cell_length_b 5.6018
_cell_length_c 5.6018
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_U_iso_or_equiv
Na Na 0.0 0.0 0.0 {1.1053 / B_TO_U_FACTOR:.12f}
Cl Cl 0.5 0.5 0.5 {0.5708 / B_TO_U_FACTOR:.12f}
"""

pdffit2 = PdfFit()
pdffit2.add_structure(pdffit_cif_parser().parse(NACL_CIF_FOR_PDFFIT2))
pdffit2.setvar('pscale', PDF_SCALE)
pdffit2.setvar('delta1', PDF_DELTA_1)
pdffit2.setvar('delta2', PDF_DELTA_2)
pdffit2.setvar('spdiameter', PDF_PARTICLE_DIAMETER)
pdffit2.read_data_lists(
    stype='X',
    qmax=PDF_QMAX,
    qdamp=PDF_QDAMP,
    r_data=list(R_GRID),
    Gr_data=list(np.zeros_like(R_GRID)),
)
pdffit2.setvar('qbroad', PDF_QBROAD)
pdffit2.calc()

calc_direct_pdffit2 = np.array(pdffit2.getpdf_fit())
LABEL_DIRECT_PDFFIT2 = f'diffpy.pdffit2 {metadata.version("diffpy.pdffit2")}'

B_TO_U_FACTOR = 8.0 * np.pi**2 NACL_CIF_FOR_PDFFIT2 = f""" data_nacl _space_group_name_H-M_alt 'F m -3 m' _space_group_IT_coordinate_system_code 1 _cell_length_a 5.6018 _cell_length_b 5.6018 _cell_length_c 5.6018 _cell_angle_alpha 90 _cell_angle_beta 90 _cell_angle_gamma 90 loop_ _atom_site_label _atom_site_type_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_U_iso_or_equiv Na Na 0.0 0.0 0.0 {1.1053 / B_TO_U_FACTOR:.12f} Cl Cl 0.5 0.5 0.5 {0.5708 / B_TO_U_FACTOR:.12f} """ pdffit2 = PdfFit() pdffit2.add_structure(pdffit_cif_parser().parse(NACL_CIF_FOR_PDFFIT2)) pdffit2.setvar('pscale', PDF_SCALE) pdffit2.setvar('delta1', PDF_DELTA_1) pdffit2.setvar('delta2', PDF_DELTA_2) pdffit2.setvar('spdiameter', PDF_PARTICLE_DIAMETER) pdffit2.read_data_lists( stype='X', qmax=PDF_QMAX, qdamp=PDF_QDAMP, r_data=list(R_GRID), Gr_data=list(np.zeros_like(R_GRID)), ) pdffit2.setvar('qbroad', PDF_QBROAD) pdffit2.calc() calc_direct_pdffit2 = np.array(pdffit2.getpdf_fit()) LABEL_DIRECT_PDFFIT2 = f'diffpy.pdffit2 {metadata.version("diffpy.pdffit2")}'

edi-pdffit VS direct pdffit2¶

In [7]:

experiment.calculator.type = 'pdffit'

project.analysis.calculate()
calc_ed_pdffit = experiment.data.intensity_calc
LABEL_ED_PDFFIT = verify.engine_label('pdffit')

project.display.pattern_comparison(
    'nacl_pdf',
    reference=calc_direct_pdffit2,
    candidate=calc_ed_pdffit,
    reference_label=LABEL_DIRECT_PDFFIT2,
    candidate_label=LABEL_ED_PDFFIT,
)

experiment.calculator.type = 'pdffit' project.analysis.calculate() calc_ed_pdffit = experiment.data.intensity_calc LABEL_ED_PDFFIT = verify.engine_label('pdffit') project.display.pattern_comparison( 'nacl_pdf', reference=calc_direct_pdffit2, candidate=calc_ed_pdffit, reference_label=LABEL_DIRECT_PDFFIT2, candidate_label=LABEL_ED_PDFFIT, )

Calculator for experiment 'nacl_pdf' already set to

pdffit

Loading plot…

Agreement check¶

In [8]:

verify.assert_patterns_agree(
    [
        (
            f'{LABEL_ED_PDFFIT} vs {LABEL_DIRECT_PDFFIT2}',
            calc_direct_pdffit2,
            calc_ed_pdffit,
        ),
    ],
)

verify.assert_patterns_agree( [ ( f'{LABEL_ED_PDFFIT} vs {LABEL_DIRECT_PDFFIT2}', calc_direct_pdffit2, calc_ed_pdffit, ), ], )

	Comparison	Metric	Expected	Actual	OK
1	edi 0.19.0 (pdffit 1.6.0) vs diffpy.pdffit2 1.6.0	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[8]:

True

In [ ]: