{ "cells": [ { "cell_type": "code", "execution_count": 1, "id": "0", "metadata": { "execution": { "iopub.execute_input": "2026-08-18T18:18:21.257731Z", "iopub.status.busy": "2026-08-18T18:18:21.257549Z", "iopub.status.idle": "2026-08-18T18:18:21.261805Z", "shell.execute_reply": "2026-08-18T18:18:21.261060Z" }, "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==0.20.1" ] }, { "cell_type": "markdown", "id": "1", "metadata": {}, "source": [ "# LaB6 - powder neutron CW - FCJ asymmetry\n", "\n", "Verifies the LaB6 baseline with only the Finger-Cox-Jephcoat\n", "axial-divergence asymmetry enabled.\n", "\n", "**Refinement:** none. The cryspy CW profile has no Finger-Cox-Jephcoat\n", "term, so it cannot reproduce the FullProf FCJ reference. The CrysFML\n", "Thompson-Cox-Hastings profile supports the corresponding FCJ terms and\n", "is compared directly with FullProf." ] }, { "cell_type": "code", "execution_count": 2, "id": "2", "metadata": { "execution": { "iopub.execute_input": "2026-08-18T18:18:21.263584Z", "iopub.status.busy": "2026-08-18T18:18:21.263406Z", "iopub.status.idle": "2026-08-18T18:18:24.177944Z", "shell.execute_reply": "2026-08-18T18:18:24.177069Z" } }, "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": "2026-08-18T18:18:24.180042Z", "iopub.status.busy": "2026-08-18T18:18:24.179725Z", "iopub.status.idle": "2026-08-18T18:18:24.488932Z", "shell.execute_reply": "2026-08-18T18:18:24.488033Z" } }, "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": "2026-08-18T18:18:24.490673Z", "iopub.status.busy": "2026-08-18T18:18:24.490476Z", "iopub.status.idle": "2026-08-18T18:18:24.497648Z", "shell.execute_reply": "2026-08-18T18:18:24.496959Z" } }, "outputs": [], "source": [ "structure = StructureFactory.from_scratch(name='lab6')\n", "structure.space_group.name_h_m = 'P m -3 m' # FullProf Space group symbol\n", "structure.cell.length_a = 4.156885 # FullProf a\n", "structure.atom_sites.create(\n", " id='La', # FullProf Atom\n", " type_symbol='La', # 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=0.25812, # FullProf Biso\n", ")\n", "structure.atom_sites.create(\n", " id='B', # FullProf Atom\n", " type_symbol='B', # FullProf Typ\n", " fract_x=0.19972, # 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=0.11925, # 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": "2026-08-18T18:18:24.499491Z", "iopub.status.busy": "2026-08-18T18:18:24.499285Z", "iopub.status.idle": "2026-08-18T18:18:24.509978Z", "shell.execute_reply": "2026-08-18T18:18:24.509357Z" } }, "outputs": [], "source": [ "FULLPROF_PROJECT_DIR = 'pd-neut-cwl_lab6'\n", "FULLPROF_PRF_FILE = 'ECH0030684_LaB6_1p622A_fcj.prf'\n", "FULLPROF_SUM_FILE = 'ECH0030684_LaB6_1p622A_fcj.sum'\n", "FULLPROF_BAC_FILE = 'ECH0030684_LaB6_1p622A_fcj.bac'\n", "FULLPROF_LABEL = verify.fullprof_label(FULLPROF_PROJECT_DIR, FULLPROF_SUM_FILE)\n", "\n", "FULLPROF_ZERO = -0.45778 # FullProf Zero\n", "FULLPROF_SCALE = 42.98374 # FullProf Scale\n", "FULLPROF_WAVELENGTH = 1.623899 # FullProf Lambda\n", "FULLPROF_U = 0.143431 # FullProf U\n", "FULLPROF_V = -0.523140 # FullProf V\n", "FULLPROF_W = 0.590412 # FullProf W\n", "FULLPROF_X = 0.0 # FullProf X\n", "FULLPROF_Y = 0.054515 # FullProf Y\n", "FULLPROF_WDT = 12.0 # FullProf Wdt\n", "FULLPROF_S_L = 0.08000 # FullProf S_L\n", "FULLPROF_D_L = 0.08000 # FullProf D_L\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": "2026-08-18T18:18:24.511754Z", "iopub.status.busy": "2026-08-18T18:18:24.511578Z", "iopub.status.idle": "2026-08-18T18:18:25.015656Z", "shell.execute_reply": "2026-08-18T18:18:25.014834Z" } }, "outputs": [], "source": [ "experiment = ExperimentFactory.from_scratch(\n", " name='lab6',\n", " sample_form='powder',\n", " beam_mode='constant wavelength',\n", " radiation_probe='neutron',\n", " scattering_type='bragg',\n", ")\n", "verify.set_reference_as_measured(experiment, x, calc_fullprof)\n", "\n", "experiment.linked_structures.create(structure_id='lab6', scale=FULLPROF_SCALE)\n", "\n", "experiment.instrument.setup_wavelength = FULLPROF_WAVELENGTH\n", "experiment.instrument.calib_twotheta_offset = FULLPROF_ZERO\n", "\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": "2026-08-18T18:18:25.017718Z", "iopub.status.busy": "2026-08-18T18:18:25.017556Z", "iopub.status.idle": "2026-08-18T18:18:25.476770Z", "shell.execute_reply": "2026-08-18T18:18:25.475966Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[1;36mCalculator for experiment \u001b[0m\u001b[32m'lab6'\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", " 'lab6',\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": [ "## Agreement check (cryspy)" ] }, { "cell_type": "code", "execution_count": 8, "id": "14", "metadata": { "execution": { "iopub.execute_input": "2026-08-18T18:18:25.480147Z", "iopub.status.busy": "2026-08-18T18:18:25.479961Z", "iopub.status.idle": "2026-08-18T18:18:25.488404Z", "shell.execute_reply": "2026-08-18T18:18:25.487728Z" } }, "outputs": [ { "data": { "text/html": [ "
ComparisonMetricExpectedActualOK
1edi 0.20.1 (cryspy 0.13.0) vs FullProf 8.40Profile diff (%)< 2.521.05❌
2Max deviation (%)< 616.34❌
3Area ratio0.99 to 1.010.9963✅
4Shape correlation> 0.9990.9774❌
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "
• Known discrepancy = FCJ asymmetry is not implemented in cryspy.
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [ "True" ] }, "execution_count": 8, "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", " known_discrepancy=True,\n", " reason='FCJ asymmetry is not implemented in cryspy.',\n", ")" ] }, { "cell_type": "markdown", "id": "15", "metadata": {}, "source": [ "## edi-crysfml VS FullProf" ] }, { "cell_type": "code", "execution_count": 9, "id": "16", "metadata": { "execution": { "iopub.execute_input": "2026-08-18T18:18:25.490445Z", "iopub.status.busy": "2026-08-18T18:18:25.490288Z", "iopub.status.idle": "2026-08-18T18:18:25.757969Z", "shell.execute_reply": "2026-08-18T18:18:25.757248Z" } }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\u001b[1;36mCalculator for experiment \u001b[0m\u001b[32m'lab6'\u001b[0m\u001b[1;36m changed to\u001b[0m\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "crysfml\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "⚠️ Switching peak profile type adds these settings with defaults: \n", " • asym_fcj_1=0.0 \n", " • asym_fcj_2=0.0 \n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "⚠️ Switching peak profile type resets these settings to defaults: \n", " • broad_gauss_u: 0.143431 -> 0.01 \n", " • broad_gauss_v: -0.52314 -> -0.01 \n", " • broad_gauss_w: 0.590412 -> 0.02 \n", " • broad_lorentz_y: 0.054515 -> 0.0 \n", " • cutoff_fwhm: 12.0 -> 0.0 \n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "\u001b[1;36mPeak profile type for experiment \u001b[0m\u001b[32m'lab6'\u001b[0m\u001b[1;36m changed to\u001b[0m\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "thompson-cox-hastings\n" ] }, { "data": { "text/html": [ "
Loading plot…
" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "experiment.calculator.type = 'crysfml'\n", "\n", "# Switching profile types resets shared profile parameters to defaults,\n", "# so restore the FullProf values after selecting TCH with FCJ asymmetry.\n", "experiment.peak.type = 'thompson-cox-hastings'\n", "\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", "experiment.peak.asym_fcj_1 = FULLPROF_S_L\n", "experiment.peak.asym_fcj_2 = FULLPROF_D_L\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", " 'lab6',\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": "17", "metadata": {}, "source": [ "## Agreement check (crysfml)" ] }, { "cell_type": "code", "execution_count": 10, "id": "18", "metadata": { "execution": { "iopub.execute_input": "2026-08-18T18:18:25.760490Z", "iopub.status.busy": "2026-08-18T18:18:25.760305Z", "iopub.status.idle": "2026-08-18T18:18:25.767285Z", "shell.execute_reply": "2026-08-18T18:18:25.766733Z" } }, "outputs": [ { "data": { "text/html": [ "
ComparisonMetricExpectedActualOK
1edi 0.20.1 (crysfml 0.8.0) vs FullProf 8.40Profile diff (%)< 2.50.44✅
2Max deviation (%)< 60.37✅
3Area ratio0.99 to 1.011.0039✅
4Shape 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_CRYSFML} vs {FULLPROF_LABEL}', calc_fullprof, calc_ed_crysfml),\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": "3.14.6" } }, "nbformat": 4, "nbformat_minor": 5 }