{ "cells": [ { "cell_type": "code", "execution_count": 1, "id": "0", "metadata": { "execution": { "iopub.execute_input": "2026-06-30T22:37:22.939389Z", "iopub.status.busy": "2026-06-30T22:37:22.939206Z", "iopub.status.idle": "2026-06-30T22:37:22.943505Z", "shell.execute_reply": "2026-06-30T22:37:22.942601Z" }, "tags": [ "hide-in-docs" ] }, "outputs": [], "source": [ "# Check whether easydiffraction is installed; install it if needed.\n", "# Required for remote environments such as Google Colab.\n", "import importlib.util\n", "\n", "if importlib.util.find_spec('easydiffraction') is None:\n", " %pip install easydiffraction==0.19.1" ] }, { "cell_type": "markdown", "id": "1", "metadata": {}, "source": [ "# Tb2Ti2O7 - single-crystal neutron CW - isotropic extinction\n", "\n", "Verifies the cryspy isotropic extinction model against a FullProf\n", "single-crystal reference with isotropic ADPs.\n", "\n", "**Refinement:** the overall scale and the extinction radius. Known\n", "difference: cryspy and FullProf use different extinction conventions." ] }, { "cell_type": "code", "execution_count": 2, "id": "2", "metadata": { "execution": { "iopub.execute_input": "2026-06-30T22:37:22.945263Z", "iopub.status.busy": "2026-06-30T22:37:22.945050Z", "iopub.status.idle": "2026-06-30T22:37:25.796615Z", "shell.execute_reply": "2026-06-30T22:37:25.795699Z" } }, "outputs": [], "source": [ "import easydiffraction as edi\n", "from easydiffraction import ExperimentFactory\n", "from easydiffraction import StructureFactory\n", "from easydiffraction.analysis import verification as verify" ] }, { "cell_type": "markdown", "id": "3", "metadata": {}, "source": [ "## Build the project" ] }, { "cell_type": "code", "execution_count": 3, "id": "4", "metadata": { "execution": { "iopub.execute_input": "2026-06-30T22:37:25.798298Z", "iopub.status.busy": "2026-06-30T22:37:25.798023Z", "iopub.status.idle": "2026-06-30T22:37:26.006832Z", "shell.execute_reply": "2026-06-30T22:37:26.006132Z" } }, "outputs": [], "source": [ "project = edi.Project()" ] }, { "cell_type": "markdown", "id": "5", "metadata": {}, "source": [ "## Define the structure" ] }, { "cell_type": "code", "execution_count": 4, "id": "6", "metadata": { "execution": { "iopub.execute_input": "2026-06-30T22:37:26.008940Z", "iopub.status.busy": "2026-06-30T22:37:26.008765Z", "iopub.status.idle": "2026-06-30T22:37:26.016753Z", "shell.execute_reply": "2026-06-30T22:37:26.015977Z" } }, "outputs": [], "source": [ "structure = StructureFactory.from_scratch(name='tbti')\n", "\n", "structure.space_group.name_h_m = 'F d -3 m' # FullProf Space group symbol\n", "\n", "structure.cell.length_a = 10.130 # FullProf a\n", "\n", "structure.atom_sites.create(\n", " id='Tb', # FullProf Atom\n", " type_symbol='Tb', # FullProf Typ\n", " fract_x=0.5, # FullProf X\n", " fract_y=0.5, # FullProf Y\n", " fract_z=0.5, # FullProf Z\n", " adp_type='Biso', # FullProf Biso\n", " adp_iso=0.0, # FullProf Biso\n", ")\n", "structure.atom_sites.create(\n", " id='Ti', # FullProf Atom\n", " type_symbol='Ti', # FullProf Typ\n", " fract_x=0.0, # FullProf X\n", " fract_y=0.0, # FullProf Y\n", " fract_z=0.0, # FullProf Z\n", " adp_type='Biso', # FullProf Biso\n", " adp_iso=0.0, # FullProf Biso\n", ")\n", "structure.atom_sites.create(\n", " id='O1', # FullProf Atom\n", " type_symbol='O', # FullProf Typ\n", " fract_x=0.32804, # FullProf X\n", " fract_y=0.125, # FullProf Y\n", " fract_z=0.125, # FullProf Z\n", " adp_type='Biso', # FullProf Biso\n", " adp_iso=0.0, # FullProf Biso\n", ")\n", "structure.atom_sites.create(\n", " id='O2', # FullProf Atom\n", " type_symbol='O', # FullProf Typ\n", " fract_x=0.375, # FullProf X\n", " fract_y=0.375, # FullProf Y\n", " fract_z=0.375, # FullProf Z\n", " adp_type='Biso', # FullProf Biso\n", " adp_iso=0.0, # FullProf Biso\n", ")\n", "\n", "project.structures.add(structure)" ] }, { "cell_type": "code", "execution_count": 5, "id": "7", "metadata": { "execution": { "iopub.execute_input": "2026-06-30T22:37:26.018343Z", "iopub.status.busy": "2026-06-30T22:37:26.018029Z", "iopub.status.idle": "2026-06-30T22:37:27.082791Z", "shell.execute_reply": "2026-06-30T22:37:27.081989Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[1;36mStructure ๐Ÿงฉ \u001b[0m\u001b[32m'tbti'\u001b[0m\u001b[1;36m as text\u001b[0m\n" ] }, { "data": { "text/html": [ "
Edi
1data_tbti
2
3_cell.length_a 10.13
4_cell.length_b 10.13
5_cell.length_c 10.13
6_cell.angle_alpha 90.
7_cell.angle_beta 90.
8_cell.angle_gamma 90.
9
10_space_group.name_h_m "F d -3 m"
11_space_group.coord_system_code 2
12
13_geom.min_bond_distance_cutoff 0.
14_geom.bond_distance_inc 0.25
15
16loop_
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
27Tb Tb 0.5 0.5 0.5 d 16 1. 0. Biso
28Ti Ti 0. 0. 0. c 16 1. 0. Biso
29O1 O 0.32804 0.125 0.125 f 48 1. 0. Biso
30O2 O 0.375 0.375 0.375 b 8 1. 0. Biso
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "structure.show_as_text()" ] }, { "cell_type": "markdown", "id": "8", "metadata": {}, "source": [ "## Load the FullProf reference" ] }, { "cell_type": "code", "execution_count": 6, "id": "9", "metadata": { "execution": { "iopub.execute_input": "2026-06-30T22:37:27.084667Z", "iopub.status.busy": "2026-06-30T22:37:27.084500Z", "iopub.status.idle": "2026-06-30T22:37:27.088855Z", "shell.execute_reply": "2026-06-30T22:37:27.088257Z" } }, "outputs": [], "source": [ "FULLPROF_PROJECT_DIR = 'sc-neut-cwl_tbti_isotropic-extinction'\n", "FULLPROF_OUT_FILE = 'tbti.out'\n", "FULLPROF_SCALE = 0.2609 # FullProf Scale\n", "FULLPROF_WAVELENGTH = 0.7930 # FullProf Lambda\n", "# cryspy uses Becker-Coppens isotropic extinction, not the one from\n", "# FullProf.\n", "EXTINCTION_RADIUS = 10.0\n", "EXTINCTION_MOSAICITY = 35000.0\n", "\n", "f2calc = verify.load_fullprof_sc_f2calc(FULLPROF_PROJECT_DIR, FULLPROF_OUT_FILE)\n", "FULLPROF_LABEL = verify.fullprof_label(FULLPROF_PROJECT_DIR, FULLPROF_OUT_FILE)" ] }, { "cell_type": "markdown", "id": "10", "metadata": {}, "source": [ "## Create the experiment" ] }, { "cell_type": "code", "execution_count": 7, "id": "11", "metadata": { "execution": { "iopub.execute_input": "2026-06-30T22:37:27.090752Z", "iopub.status.busy": "2026-06-30T22:37:27.090592Z", "iopub.status.idle": "2026-06-30T22:37:27.164151Z", "shell.execute_reply": "2026-06-30T22:37:27.162928Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[1;36mExtinction type changed to\u001b[0m\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "becker-coppens\n" ] } ], "source": [ "experiment = ExperimentFactory.from_scratch(\n", " name='tbti',\n", " sample_form='single crystal',\n", " beam_mode='constant wavelength',\n", " radiation_probe='neutron',\n", " scattering_type='bragg',\n", ")\n", "experiment.linked_structure.structure_id = 'tbti'\n", "experiment.linked_structure.scale = FULLPROF_SCALE\n", "experiment.instrument.setup_wavelength = FULLPROF_WAVELENGTH\n", "experiment.extinction.type = 'becker-coppens'\n", "experiment.extinction.model = 'gauss'\n", "experiment.extinction.radius.value = EXTINCTION_RADIUS\n", "experiment.extinction.mosaicity.value = EXTINCTION_MOSAICITY\n", "\n", "verify.set_reference_reflections(experiment, f2calc)\n", "\n", "project.experiments.add(experiment)" ] }, { "cell_type": "markdown", "id": "12", "metadata": {}, "source": [ "## edi-cryspy VS FullProf" ] }, { "cell_type": "code", "execution_count": 8, "id": "13", "metadata": { "execution": { "iopub.execute_input": "2026-06-30T22:37:27.166395Z", "iopub.status.busy": "2026-06-30T22:37:27.165723Z", "iopub.status.idle": "2026-06-30T22:37:27.469524Z", "shell.execute_reply": "2026-06-30T22:37:27.468566Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[1;36mCalculator for experiment \u001b[0m\u001b[32m'tbti'\u001b[0m\u001b[1;36m already set to\u001b[0m\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "cryspy\n" ] }, { "data": { "text/html": [ "
Loading plotโ€ฆ
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "calc_ed_cryspy = verify.calculate_reflections(project, experiment, 'cryspy')\n", "LABEL_ED_CRYSPY = verify.engine_label('cryspy')\n", "reference, candidate = verify.align_reflections(f2calc, calc_ed_cryspy)\n", "\n", "project.display.reflection_comparison(\n", " 'tbti',\n", " reference=reference,\n", " candidate=candidate,\n", " reference_label=FULLPROF_LABEL,\n", " candidate_label=LABEL_ED_CRYSPY,\n", ")" ] }, { "cell_type": "markdown", "id": "14", "metadata": {}, "source": [ "## Fit edi-cryspy to FullProf" ] }, { "cell_type": "code", "execution_count": 9, "id": "15", "metadata": { "execution": { "iopub.execute_input": "2026-06-30T22:37:27.471106Z", "iopub.status.busy": "2026-06-30T22:37:27.470919Z", "iopub.status.idle": "2026-06-30T22:37:28.026861Z", "shell.execute_reply": "2026-06-30T22:37:28.026042Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[1;36mCalculator for experiment \u001b[0m\u001b[32m'tbti'\u001b[0m\u001b[1;36m already set to\u001b[0m\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "cryspy\n" ] }, { "data": { "text/html": [], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "\n", "(function() {\n", " const button = document.getElementById('ed-fit-stop-6b237d5b96af49debcd96966a5197b49-button');\n", " const status = document.getElementById('ed-fit-stop-6b237d5b96af49debcd96966a5197b49-status');\n", " const kernelId = '';\n", " if (!button) {\n", " return;\n", " }\n", "\n", " function setStatus(text) {\n", " if (status) {\n", " status.textContent = text;\n", " }\n", " }\n", "\n", " function pageConfig() {\n", " const element = document.getElementById('jupyter-config-data');\n", " if (!element || !element.textContent) {\n", " return {};\n", " }\n", " try {\n", " return JSON.parse(element.textContent);\n", " } catch (error) {\n", " return {};\n", " }\n", " }\n", "\n", " function baseUrl(config) {\n", " const configured = config.baseUrl || config.base_url ||\n", " (window.Jupyter && Jupyter.notebook && Jupyter.notebook.base_url);\n", " if (configured) {\n", " return configured.endsWith('/') ? configured : configured + '/';\n", " }\n", " const markers = ['/lab/', '/notebooks/', '/tree/'];\n", " for (const marker of markers) {\n", " const index = window.location.pathname.indexOf(marker);\n", " if (index >= 0) {\n", " return window.location.pathname.slice(0, index + 1);\n", " }\n", " }\n", " return '/';\n", " }\n", "\n", " function token(config) {\n", " return config.token || new URLSearchParams(window.location.search).get('token') || '';\n", " }\n", "\n", " function cookie(name) {\n", " const prefix = name + '=';\n", " for (const part of document.cookie.split(';')) {\n", " const trimmed = part.trim();\n", " if (trimmed.startsWith(prefix)) {\n", " return decodeURIComponent(trimmed.slice(prefix.length));\n", " }\n", " }\n", " return '';\n", " }\n", "\n", " function notebookPath() {\n", " const decoded = decodeURIComponent(window.location.pathname);\n", " const markers = ['/lab/tree/', '/notebooks/', '/tree/'];\n", " for (const marker of markers) {\n", " const index = decoded.indexOf(marker);\n", " if (index >= 0) {\n", " return decoded.slice(index + marker.length);\n", " }\n", " }\n", " return '';\n", " }\n", "\n", " async function kernelFromSessions(config) {\n", " const url = new URL(baseUrl(config) + 'api/sessions', window.location.origin);\n", " const authToken = token(config);\n", " if (authToken) {\n", " url.searchParams.set('token', authToken);\n", " }\n", " const response = await fetch(url, {credentials: 'same-origin'});\n", " if (!response.ok) {\n", " return '';\n", " }\n", " const sessions = await response.json();\n", " const path = notebookPath();\n", " const session = sessions.find((item) => item.path === path) || sessions[0];\n", " return session && session.kernel ? session.kernel.id : '';\n", " }\n", "\n", " async function interruptKernel(config, resolvedKernelId) {\n", " const url = new URL(\n", " baseUrl(config) + 'api/kernels/' + resolvedKernelId + '/interrupt',\n", " window.location.origin\n", " );\n", " const authToken = token(config);\n", " if (authToken) {\n", " url.searchParams.set('token', authToken);\n", " }\n", " const xsrfToken = cookie('_xsrf');\n", " const headers = {};\n", " if (xsrfToken) {\n", " headers['X-XSRFToken'] = xsrfToken;\n", " }\n", " const response = await fetch(url, {\n", " method: 'POST',\n", " credentials: 'same-origin',\n", " headers: headers\n", " });\n", " return response.ok;\n", " }\n", "\n", " button.addEventListener('click', async function() {\n", " button.disabled = true;\n", " setStatus('Stopping...');\n", " const config = pageConfig();\n", " try {\n", " const resolvedKernelId = kernelId || await kernelFromSessions(config);\n", " if (!resolvedKernelId) {\n", " throw new Error('Could not resolve the current kernel id.');\n", " }\n", " const interrupted = await interruptKernel(config, resolvedKernelId);\n", " if (!interrupted) {\n", " throw new Error('Jupyter Server rejected the interrupt request.');\n", " }\n", " setStatus('Interrupt sent...');\n", " } catch (error) {\n", " button.disabled = false;\n", " setStatus('Use Kernel > Interrupt to stop this fit.');\n", " }\n", " });\n", "})();\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "\u001b[1;36mStandard fitting\u001b[0m\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "๐Ÿ“‹ Using experiment ๐Ÿ”ฌ \u001b[32m'tbti'\u001b[0m for \u001b[32m'single'\u001b[0m fitting\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "๐Ÿš€ Starting fit process with \u001b[32m'lmfit \u001b[0m\u001b[32m(\u001b[0m\u001b[32mleastsq\u001b[0m\u001b[32m)\u001b[0m\u001b[32m'\u001b[0m\u001b[33m...\u001b[0m\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "๐Ÿ“ˆ Goodness-of-fit progress:\n" ] }, { "data": { "text/html": [ "
iterationtime (s)ฯ‡ยฒchange / status
110.01559733.19
260.05227010.0559.4% โ†“
3100.08123452.7645.6% โ†“
4130.104334.8596.5% โ†“
5160.121422.0267.2% โ†“
6260.191416.64
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "๐Ÿ† Best goodness-of-fit \u001b[1m(\u001b[0mreduced ฯ‡ยฒ\u001b[1m)\u001b[0m is \u001b[1;36m1416.64\u001b[0m at iteration \u001b[1;36m25\u001b[0m\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "โœ… Fitting complete.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "โš™๏ธ Settings used:\n" ] }, { "data": { "text/html": [ "
NameValueDescription
1max_iterations1000Maximum solver iterations.
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "๐Ÿ“‹ Least-squares fit results:\n" ] }, { "data": { "text/html": [ "
MetricValue
1๐Ÿงช Minimizerlmfit (leastsq)
2โœ… Overall statussuccess
3โฑ๏ธ Fitting time (seconds)0.19
4๐Ÿ” Iterations23
5๐Ÿ“ Goodness-of-fit (reduced ฯ‡ยฒ)1416.64
6๐Ÿ“ R-factor (Rf, %)2.52
7๐Ÿ“ R-factor squared (Rfยฒ, %)4.34
8๐Ÿ“ Weighted R-factor (wR, %)4.34
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "๐Ÿ“ˆ Refined parameters:\n" ] }, { "data": { "text/html": [ "
datablockcategoryentryparameterunitsstartvalues.u.change
1tbtiextinctionradiusฮผm10.0000-20.04620.5414300.46 % โ†“
2tbtilinked_structurescale0.26092.05980.0174689.51 % โ†‘
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
โ€ข start = parameter value before refinement
โ€ข value = refined value from least-squares minimization
โ€ข s.u. = standard uncertainty (one sigma), from the covariance matrix
โ€ข change = relative change from start, in %; โ†‘ = increase, โ†“ = decrease
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "\u001b[1;36mCalculator for experiment \u001b[0m\u001b[32m'tbti'\u001b[0m\u001b[1;36m already set to\u001b[0m\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "cryspy\n" ] }, { "data": { "text/html": [ "
Loading plotโ€ฆ
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
MetricBeforeAfter
1Profile diff (%)86.184.34
2Max deviation (%)85.739.92
3Area ratio0.13510.9985
4Shape correlation0.99820.9985
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "experiment.calculator.type = 'cryspy'\n", "\n", "experiment.linked_structure.scale.free = True\n", "experiment.extinction.radius.free = True\n", "\n", "project.analysis.fit()\n", "project.display.fit.results()\n", "\n", "calc_ed_cryspy_refined = verify.calculate_reflections(project, experiment, 'cryspy')\n", "LABEL_ED_CRYSPY_REFINED = verify.engine_label('cryspy', note='scale + ext radius')\n", "reference_refined, candidate_refined = verify.align_reflections(f2calc, calc_ed_cryspy_refined)\n", "\n", "project.display.reflection_comparison(\n", " 'tbti',\n", " reference=reference_refined,\n", " candidate=candidate_refined,\n", " reference_label=FULLPROF_LABEL,\n", " candidate_label=LABEL_ED_CRYSPY_REFINED,\n", ")\n", "\n", "verify.report_refinement_closeness(\n", " reference,\n", " candidate,\n", " candidate_refined,\n", ")" ] }, { "cell_type": "markdown", "id": "16", "metadata": {}, "source": [ "## Agreement check" ] }, { "cell_type": "code", "execution_count": 10, "id": "17", "metadata": { "execution": { "iopub.execute_input": "2026-06-30T22:37:28.028628Z", "iopub.status.busy": "2026-06-30T22:37:28.028457Z", "iopub.status.idle": "2026-06-30T22:37:28.036821Z", "shell.execute_reply": "2026-06-30T22:37:28.035912Z" } }, "outputs": [ { "data": { "text/html": [ "
ComparisonMetricExpectedActualOK
1edi 0.19.1 (cryspy 0.12.1, scale + ext radius) vs FullProf 8.40Profile diff (%)< 2.54.34โŒ
2Max deviation (%)< 69.92โŒ
3Area ratio0.99 to 1.010.9985โœ…
4Shape correlation> 0.9990.9985โŒ
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
โ€ข Known discrepancy = cryspy and FullProf use different extinction conventions.
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "True" ] }, "execution_count": 10, "metadata": {}, "output_type": "execute_result" } ], "source": [ "verify.assert_patterns_agree(\n", " [\n", " (f'{LABEL_ED_CRYSPY_REFINED} vs {FULLPROF_LABEL}', reference_refined, candidate_refined),\n", " ],\n", " known_discrepancy=True,\n", " reason='cryspy and FullProf use different extinction conventions.',\n", ")" ] } ], "metadata": { "jupytext": { "cell_metadata_filter": "-all", "main_language": "python", "notebook_metadata_filter": "-all" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.14.5" } }, "nbformat": 4, "nbformat_minor": 5 }