{ "cells": [ { "cell_type": "code", "execution_count": 1, "id": "0", "metadata": { "execution": { "iopub.execute_input": "2026-06-30T22:38:26.165643Z", "iopub.status.busy": "2026-06-30T22:38:26.165478Z", "iopub.status.idle": "2026-06-30T22:38:26.173566Z", "shell.execute_reply": "2026-06-30T22:38:26.172946Z" }, "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": [ "# LiF — powder X-ray CW — single wavelength\n", "\n", "Verifies the baseline LiF Cu Kα₁ pattern with a pseudo-Voigt profile\n", "and no polarization or absorption correction.\n", "\n", "**Refinement:** the overall scale only; all other parameters are\n", "taken from the FullProf reference." ] }, { "cell_type": "code", "execution_count": 2, "id": "2", "metadata": { "execution": { "iopub.execute_input": "2026-06-30T22:38:26.177394Z", "iopub.status.busy": "2026-06-30T22:38:26.177197Z", "iopub.status.idle": "2026-06-30T22:38:29.403871Z", "shell.execute_reply": "2026-06-30T22:38:29.403099Z" } }, "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": "2026-06-30T22:38:29.405861Z", "iopub.status.busy": "2026-06-30T22:38:29.405593Z", "iopub.status.idle": "2026-06-30T22:38:29.628488Z", "shell.execute_reply": "2026-06-30T22:38:29.627831Z" } }, "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": "2026-06-30T22:38:29.631642Z", "iopub.status.busy": "2026-06-30T22:38:29.631444Z", "iopub.status.idle": "2026-06-30T22:38:29.638719Z", "shell.execute_reply": "2026-06-30T22:38:29.638245Z" } }, "outputs": [], "source": [ "structure = StructureFactory.from_scratch(name='lif')\n", "\n", "structure.space_group.name_h_m = 'F m -3 m' # FullProf Space group symbol\n", "structure.cell.length_a = 4.026700 # FullProf a\n", "\n", "structure.atom_sites.create(\n", " id='Li1', # FullProf Atom\n", " type_symbol='Li', # 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=1.20000, # FullProf Biso\n", ")\n", "structure.atom_sites.create(\n", " id='F1', # FullProf Atom\n", " type_symbol='F', # 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=0.80000, # FullProf Biso\n", ")\n", "\n", "project.structures.add(structure)" ] }, { "cell_type": "markdown", "id": "7", "metadata": {}, "source": [ "## Load the FullProf reference" ] }, { "cell_type": "code", "execution_count": 5, "id": "8", "metadata": { "execution": { "iopub.execute_input": "2026-06-30T22:38:29.640918Z", "iopub.status.busy": "2026-06-30T22:38:29.640553Z", "iopub.status.idle": "2026-06-30T22:38:29.656620Z", "shell.execute_reply": "2026-06-30T22:38:29.656121Z" } }, "outputs": [], "source": [ "FULLPROF_PROJECT_DIR = 'pd-xray-cwl_lif'\n", "FULLPROF_PRF_FILE = 'lif_single_unpolarized.prf'\n", "FULLPROF_SUM_FILE = 'lif_single_unpolarized.sum'\n", "FULLPROF_BAC_FILE = 'lif_single_unpolarized.bac'\n", "FULLPROF_LABEL = verify.fullprof_label(FULLPROF_PROJECT_DIR, FULLPROF_SUM_FILE)\n", "\n", "FULLPROF_ZERO = 0.0 # FullProf Zero\n", "FULLPROF_SCALE = 0.01 # FullProf Scale\n", "FULLPROF_WAVELENGTH = 1.540560 # FullProf Lambda1\n", "FULLPROF_U = 0.048457 # FullProf U\n", "FULLPROF_V = -0.083053 # FullProf V\n", "FULLPROF_W = 0.040000 # FullProf W\n", "FULLPROF_X = 0.0 # FullProf X\n", "FULLPROF_Y = 0.049268 # FullProf Y\n", "FULLPROF_WDT = 48.0 # FullProf Wdt\n", "\n", "x, calc_fullprof = verify.load_fullprof_calc_profile(\n", " FULLPROF_PROJECT_DIR,\n", " FULLPROF_PRF_FILE,\n", " FULLPROF_BAC_FILE,\n", " FULLPROF_ZERO,\n", ")" ] }, { "cell_type": "markdown", "id": "9", "metadata": {}, "source": [ "## Create the experiment" ] }, { "cell_type": "code", "execution_count": 6, "id": "10", "metadata": { "execution": { "iopub.execute_input": "2026-06-30T22:38:29.658687Z", "iopub.status.busy": "2026-06-30T22:38:29.658497Z", "iopub.status.idle": "2026-06-30T22:38:30.739282Z", "shell.execute_reply": "2026-06-30T22:38:30.738488Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[1;36mPeak profile type for experiment \u001b[0m\u001b[32m'lif'\u001b[0m\u001b[1;36m changed to\u001b[0m\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "pseudo-voigt\n" ] } ], "source": [ "experiment = ExperimentFactory.from_scratch(\n", " name='lif',\n", " sample_form='powder',\n", " beam_mode='constant wavelength',\n", " radiation_probe='xray',\n", " scattering_type='bragg',\n", ")\n", "verify.set_reference_as_measured(experiment, x, calc_fullprof)\n", "\n", "experiment.linked_structures.create(structure_id='lif', scale=FULLPROF_SCALE)\n", "\n", "experiment.instrument.setup_wavelength = FULLPROF_WAVELENGTH\n", "experiment.instrument.calib_twotheta_offset = FULLPROF_ZERO\n", "\n", "experiment.peak.type = 'pseudo-voigt'\n", "experiment.peak.broad_gauss_u = FULLPROF_U\n", "experiment.peak.broad_gauss_v = FULLPROF_V\n", "experiment.peak.broad_gauss_w = FULLPROF_W\n", "experiment.peak.broad_lorentz_x = FULLPROF_X\n", "experiment.peak.broad_lorentz_y = FULLPROF_Y\n", "\n", "experiment.peak.cutoff_fwhm = FULLPROF_WDT\n", "\n", "project.experiments.add(experiment)" ] }, { "cell_type": "markdown", "id": "11", "metadata": {}, "source": [ "## edi-cryspy VS FullProf" ] }, { "cell_type": "code", "execution_count": 7, "id": "12", "metadata": { "execution": { "iopub.execute_input": "2026-06-30T22:38:30.740868Z", "iopub.status.busy": "2026-06-30T22:38:30.740707Z", "iopub.status.idle": "2026-06-30T22:38:31.906978Z", "shell.execute_reply": "2026-06-30T22:38:31.906246Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[1;36mCalculator for experiment \u001b[0m\u001b[32m'lif'\u001b[0m\u001b[1;36m already set to\u001b[0m\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "cryspy\n" ] }, { "data": { "text/html": [ "
Loading plot…
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "experiment.calculator.type = 'cryspy'\n", "\n", "project.analysis.calculate()\n", "calc_ed_cryspy = experiment.data.intensity_calc\n", "LABEL_ED_CRYSPY = verify.engine_label('cryspy')\n", "\n", "project.display.pattern_comparison(\n", " 'lif',\n", " reference=calc_fullprof,\n", " candidate=calc_ed_cryspy,\n", " reference_label=FULLPROF_LABEL,\n", " candidate_label=LABEL_ED_CRYSPY,\n", ")" ] }, { "cell_type": "markdown", "id": "13", "metadata": {}, "source": [ "## edi-crysfml VS FullProf" ] }, { "cell_type": "code", "execution_count": 8, "id": "14", "metadata": { "execution": { "iopub.execute_input": "2026-06-30T22:38:31.911595Z", "iopub.status.busy": "2026-06-30T22:38:31.911420Z", "iopub.status.idle": "2026-06-30T22:38:32.194345Z", "shell.execute_reply": "2026-06-30T22:38:32.191934Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[1;36mCalculator for experiment \u001b[0m\u001b[32m'lif'\u001b[0m\u001b[1;36m changed to\u001b[0m\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "crysfml\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "⚠️ [CrysfmlCalculator] peak.cutoff_fwhm is not applied by the CrysFML backend (it uses a fixed CFL peak window); the value is \n", " ignored. \n" ] }, { "data": { "text/html": [ "
Loading plot…
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "experiment.calculator.type = 'crysfml'\n", "\n", "project.analysis.calculate()\n", "calc_ed_crysfml = experiment.data.intensity_calc\n", "LABEL_ED_CRYSFML = verify.engine_label('crysfml')\n", "\n", "project.display.pattern_comparison(\n", " 'lif',\n", " reference=calc_fullprof,\n", " candidate=calc_ed_crysfml,\n", " reference_label=FULLPROF_LABEL,\n", " candidate_label=LABEL_ED_CRYSFML,\n", ")" ] }, { "cell_type": "markdown", "id": "15", "metadata": {}, "source": [ "## Fit edi-crysfml to FullProf" ] }, { "cell_type": "code", "execution_count": 9, "id": "16", "metadata": { "execution": { "iopub.execute_input": "2026-06-30T22:38:32.196974Z", "iopub.status.busy": "2026-06-30T22:38:32.196793Z", "iopub.status.idle": "2026-06-30T22:38:34.520732Z", "shell.execute_reply": "2026-06-30T22:38:34.519965Z" } }, "outputs": [ { "data": { "text/html": [], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "application/javascript": [ "\n", "(function() {\n", " const button = document.getElementById('ed-fit-stop-66fa9f858d05447a8cca40621678df8a-button');\n", " const status = document.getElementById('ed-fit-stop-66fa9f858d05447a8cca40621678df8a-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": [ "📋 Using experiment 🔬 \u001b[32m'lif'\u001b[0m for \u001b[32m'single'\u001b[0m fitting\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "🚀 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": [ "📈 Goodness-of-fit progress:\n" ] }, { "data": { "text/html": [ "
iterationtime (s)χ²change / status
110.220.00
251.050.0022.2% ↓
381.720.00
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "⚠️ [CrysfmlCalculator] peak.cutoff_fwhm is not applied by the CrysFML backend (it uses a fixed CFL peak window); the value is \n", " ignored. \n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "⚠️ [CrysfmlCalculator] peak.cutoff_fwhm is not applied by the CrysFML backend (it uses a fixed CFL peak window); the value is \n", " ignored. \n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "⚠️ [CrysfmlCalculator] peak.cutoff_fwhm is not applied by the CrysFML backend (it uses a fixed CFL peak window); the value is \n", " ignored. \n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "⚠️ [CrysfmlCalculator] peak.cutoff_fwhm is not applied by the CrysFML backend (it uses a fixed CFL peak window); the value is \n", " ignored. \n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "⚠️ [CrysfmlCalculator] peak.cutoff_fwhm is not applied by the CrysFML backend (it uses a fixed CFL peak window); the value is \n", " ignored. \n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "⚠️ [CrysfmlCalculator] peak.cutoff_fwhm is not applied by the CrysFML backend (it uses a fixed CFL peak window); the value is \n", " ignored. \n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "⚠️ [CrysfmlCalculator] peak.cutoff_fwhm is not applied by the CrysFML backend (it uses a fixed CFL peak window); the value is \n", " ignored. \n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "⚠️ [CrysfmlCalculator] peak.cutoff_fwhm is not applied by the CrysFML backend (it uses a fixed CFL peak window); the value is \n", " ignored. \n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "🏆 Best goodness-of-fit \u001b[1m(\u001b[0mreduced χ²\u001b[1m)\u001b[0m is \u001b[1;36m0.00\u001b[0m at iteration \u001b[1;36m5\u001b[0m\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "✅ Fitting complete.\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "⚙️ Settings used:\n" ] }, { "data": { "text/html": [ "
NameValueDescription
1max_iterations1000Maximum solver iterations.
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "⚠️ [CrysfmlCalculator] peak.cutoff_fwhm is not applied by the CrysFML backend (it uses a fixed CFL peak window); the value is \n", " ignored. \n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "📋 Least-squares fit results:\n" ] }, { "data": { "text/html": [ "
MetricValue
1🧪 Minimizerlmfit (leastsq)
2✅ Overall statussuccess
3⏱️ Fitting time (seconds)1.72
4🔁 Iterations5
5📏 Goodness-of-fit (reduced χ²)0.00
6📏 R-factor (Rf, %)0.22
7📏 R-factor squared (Rf², %)0.05
8📏 Weighted R-factor (wR, %)0.05
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "📈 Refined parameters:\n" ] }, { "data": { "text/html": [ "
datablockcategoryentryparameterunitsstartvalues.u.change
1liflinked_structurelifscale0.01000.01000.00000.03 % ↓
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
• start = parameter value before refinement
• value = refined value from least-squares minimization
• s.u. = standard uncertainty (one sigma), from the covariance matrix
• change = relative change from start, in %; ↑ = increase, ↓ = decrease
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "⚠️ [CrysfmlCalculator] peak.cutoff_fwhm is not applied by the CrysFML backend (it uses a fixed CFL peak window); the value is \n", " ignored. \n" ] }, { "data": { "text/html": [ "
Loading plot…
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "experiment.linked_structures['lif'].scale.free = True\n", "\n", "project.analysis.fit()\n", "project.display.fit.results()\n", "\n", "project.analysis.calculate()\n", "calc_ed_crysfml_refined = experiment.data.intensity_calc\n", "LABEL_ED_CRYSFML_REFINED = verify.engine_label('crysfml', note='refined')\n", "\n", "project.display.pattern_comparison(\n", " 'lif',\n", " reference=calc_fullprof,\n", " candidate=calc_ed_crysfml_refined,\n", " reference_label=FULLPROF_LABEL,\n", " candidate_label=LABEL_ED_CRYSFML_REFINED,\n", ")" ] }, { "cell_type": "markdown", "id": "17", "metadata": {}, "source": [ "## Agreement check" ] }, { "cell_type": "code", "execution_count": 10, "id": "18", "metadata": { "execution": { "iopub.execute_input": "2026-06-30T22:38:34.524441Z", "iopub.status.busy": "2026-06-30T22:38:34.524263Z", "iopub.status.idle": "2026-06-30T22:38:34.532550Z", "shell.execute_reply": "2026-06-30T22:38:34.531649Z" } }, "outputs": [ { "data": { "text/html": [ "
ComparisonMetricExpectedActualOK
1edi 0.19.1 (cryspy 0.12.1) vs FullProf 7.95Profile diff (%)< 2.50.23✅
2Max deviation (%)< 60.19✅
3Area ratio0.99 to 1.011.0003✅
4Shape correlation> 0.9991.0000✅
5edi 0.19.1 (crysfml 0.7.0, refined) vs FullProf 7.95Profile diff (%)< 2.50.05✅
6Max deviation (%)< 60.01✅
7Area ratio0.99 to 1.010.9981✅
8Shape correlation> 0.9991.0000✅
" ], "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} vs {FULLPROF_LABEL}', calc_fullprof, calc_ed_cryspy),\n", " (\n", " f'{LABEL_ED_CRYSFML_REFINED} vs {FULLPROF_LABEL}',\n", " calc_fullprof,\n", " calc_ed_crysfml_refined,\n", " ),\n", " ],\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 }