Adds one more single-fit tutorial for pd-neut-cwl analysis

Author: AndrewSazonov

docs/mkdocs.yml

@@ -59,6 +59,7 @@ nav:
           - SingleFit pd-neut-cwl: tutorials/basic_single-fit_pd-neut-cwl_LBCO-HRPT.ipynb
       - Advanced Usage:
           - SingleFit pd-neut-tof: tutorials/advanced_single-fit_pd-neut-tof_Si-SEPD.ipynb
+          - SingleFit pd-neut-cwl: tutorials/advanced_single-fit_pd-neut-cwl_HS-HRPT.ipynb
           - JointFit pd-neut-xray-cwl: tutorials/advanced_joint-fit_pd-neut-xray-cwl_PbSO4.ipynb
       - Pair Distribution Function:
           - SingleFit pd-neut-tof: tutorials/pdf_pd-neut-tof_Si-NOMAD.ipynb

tutorials/advanced_single-fit_pd-neut-cwl_HS-HRPT.py

@@ -0,0 +1,332 @@
+# %% [markdown]
+# # Standard diffraction: HS
+#
+# Standard diffraction analysis of HS after the powder neutron constant wavelength
+# diffraction measurement from HRPT at PSI.
+
+# %% [markdown]
+# ## Import EasyDiffraction
+
+# %%
+from easydiffraction import (
+    Project,
+    SampleModel,
+    Experiment,
+    download_from_repository
+)
+
+# %% [markdown]
+# ## Define Sample Model
+#
+# This section covers how to add sample models and modify their parameters.
+#
+# ### Create sample model object
+
+# %%
+model = SampleModel('hs')
+
+# %% [markdown]
+# ### Define space group
+
+# %%
+model.space_group.name_h_m = 'R -3 m'
+model.space_group.it_coordinate_system_code = 'h'
+
+# %% [markdown]
+# ### Define unit cell
+
+# %%
+model.cell.length_a = 6.9
+model.cell.length_c = 14.1
+
+# %% [markdown]
+# ### Define atom sites
+
+# %%
+model.atom_sites.add('Zn', 'Zn', 0, 0, 0.5, wyckoff_letter='b', b_iso=0.5)
+model.atom_sites.add('Cu', 'Cu', 0.5, 0, 0, wyckoff_letter='e', b_iso=0.5)
+model.atom_sites.add('O', 'O', 0.21, -0.21, 0.06, wyckoff_letter='h', b_iso=0.5)
+model.atom_sites.add('Cl', 'Cl', 0, 0, 0.197, wyckoff_letter='c', b_iso=0.5)
+model.atom_sites.add('H', '2H', 0.13, -0.13, 0.08, wyckoff_letter='h', b_iso=0.5)
+
+# %% [markdown]
+# ### Symmetry constraints
+#
+# Model as CIF before applying symmetry constraints
+
+# %%
+model.show_as_cif()
+
+# %% [markdown]
+# Apply symmetry constraints
+
+# %%
+model.apply_symmetry_constraints()
+
+# Model as CIF after applying symmetry constraints
+
+# %%
+model.show_as_cif()
+
+# %% [markdown]
+# ## Define Experiment
+#
+# This section teaches how to add experiments, configure their parameters, and
+# link to them the sample models defined in the previous step.
+#
+# ### Download measured data
+
+# %%
+download_from_repository('hrpt_hs.xye',
+                         branch='docs',
+                         destination='data')
+
+# %% [markdown]
+# ### Create experiment object
+
+# %%
+expt = Experiment(name='hrpt',
+                  data_path='data/hrpt_hs.xye')
+
+# %% [markdown]
+# ### Define instrument
+
+# %%
+expt.instrument.setup_wavelength = 1.89
+expt.instrument.calib_twotheta_offset = 0.0
+
+# %% [markdown]
+# ### Define peak profile
+
+# %%
+expt.peak.broad_gauss_u = 0.1
+expt.peak.broad_gauss_v = -0.2
+expt.peak.broad_gauss_w = 0.2
+expt.peak.broad_lorentz_x = 0.0
+expt.peak.broad_lorentz_y = 0
+
+# %% [markdown]
+# ### Define background
+
+# %%
+expt.background.add(x=4.4196, y=500)
+expt.background.add(x=6.6207, y=500)
+expt.background.add(x=10.4918, y=500)
+expt.background.add(x=15.4634, y=500)
+expt.background.add(x=45.6041, y=500)
+expt.background.add(x=74.6844, y=500)
+expt.background.add(x=103.4187, y=500)
+expt.background.add(x=121.6311, y=500)
+expt.background.add(x=159.4116, y=500)
+
+# %% [markdown]
+# ### Select linked phase
+
+# %%
+expt.linked_phases.add('hs', scale=0.5)
+
+# %% [markdown]
+# ## Define Project
+#
+# The project object is used to manage the sample model, experiments, and
+# analysis
+#
+# ### Create project object
+
+# %%
+project = Project()
+
+# %% [markdown]
+# ### Configure Plotting Engine
+
+# %%
+project.plotter.engine = 'plotly'
+
+# %% [markdown]
+# ### Add sample model
+
+# %%
+project.sample_models.add(model)
+
+# %% [markdown]
+# ### Add experiment
+
+# %%
+project.experiments.add(expt)
+
+# %% [markdown]
+# ## Analysis
+#
+# This section will guide you through the analysis process, including setting
+# up calculators and fitting models.
+#
+# ### Set calculation engine
+
+# %%
+project.analysis.current_calculator = 'cryspy'
+
+# %% [markdown]
+# ### Set fitting engine
+
+# %%
+project.analysis.current_minimizer = 'lmfit (leastsq)'
+
+# %% [markdown]
+# ### Show measured vs calculated
+
+# %%
+project.plot_meas_vs_calc(expt_name='hrpt',
+                          show_residual=True)
+project.plot_meas_vs_calc(expt_name='hrpt',
+                          x_min=48, x_max=51,
+                          show_residual=True)
+
+# %% [markdown]
+# ### Perform Fit 1/5
+#
+# Set parameters to be fitted
+
+# %%
+model.cell.length_a.free = True
+model.cell.length_c.free = True
+
+expt.linked_phases['hs'].scale.free = True
+expt.instrument.calib_twotheta_offset.free = True
+
+# %% [markdown]
+# Show free parameters after selection
+
+# %%
+project.analysis.show_free_params()
+
+# %% [markdown]
+# #### Start fitting
+
+# %%
+project.analysis.fit()
+
+# %% [markdown]
+# #### Show fitting results
+
+# %%
+project.plot_meas_vs_calc(expt_name='hrpt',
+                          show_residual=True)
+project.plot_meas_vs_calc(expt_name='hrpt',
+                          x_min=48, x_max=51,
+                          show_residual=True)
+
+# %% [markdown]
+# ### Perform Fit 2/5
+#
+# Set parameters to be fitted
+
+# %%
+expt.peak.broad_gauss_u.free = True
+expt.peak.broad_gauss_v.free = True
+expt.peak.broad_gauss_w.free = True
+expt.peak.broad_lorentz_x.free = True
+
+for point in expt.background:
+    point.y.free = True
+
+# %% [markdown]
+# Show free parameters after selection
+
+# %%
+project.analysis.show_free_params()
+
+# %% [markdown]
+# #### Start fitting
+
+# %%
+project.analysis.fit()
+
+# %% [markdown]
+# #### Show fitting results
+
+# %%
+project.plot_meas_vs_calc(expt_name='hrpt',
+                          show_residual=True)
+project.plot_meas_vs_calc(expt_name='hrpt',
+                          x_min=48, x_max=51,
+                          show_residual=True)
+
+# %% [markdown]
+# ### Perform Fit 3/5
+#
+# Set parameters to be fitted
+
+# %%
+model.atom_sites['O'].fract_x.free = True
+model.atom_sites['O'].fract_z.free = True
+model.atom_sites['Cl'].fract_z.free = True
+model.atom_sites['H'].fract_x.free = True
+model.atom_sites['H'].fract_z.free = True
+
+# %% [markdown]
+# Show free parameters after selection
+
+# %%
+project.analysis.show_free_params()
+
+# %% [markdown]
+# #### Start fitting
+
+# %%
+project.analysis.fit()
+
+# %% [markdown]
+# #### Show fitting results
+
+# %%
+project.plot_meas_vs_calc(expt_name='hrpt',
+                          show_residual=True)
+project.plot_meas_vs_calc(expt_name='hrpt',
+                          x_min=48, x_max=51,
+                          show_residual=True)
+
+# %% [markdown]
+# ### Perform Fit 4/5
+#
+# Set parameters to be fitted
+
+# %%
+model.atom_sites['Zn'].b_iso.free = True
+model.atom_sites['Cu'].b_iso.free = True
+model.atom_sites['O'].b_iso.free = True
+model.atom_sites['Cl'].b_iso.free = True
+model.atom_sites['H'].b_iso.free = True
+
+# %% [markdown]
+# Show free parameters after selection
+
+# %%
+project.analysis.show_free_params()
+
+# %% [markdown]
+# #### Start fitting
+
+# %%
+project.analysis.fit()
+
+# %% [markdown]
+# #### Show fitting results
+
+# %%
+project.plot_meas_vs_calc(expt_name='hrpt',
+                          show_residual=True)
+project.plot_meas_vs_calc(expt_name='hrpt',
+                          x_min=48, x_max=51,
+                          show_residual=True)
+
+# %% [markdown]
+# ## Summary
+#
+# In this final section, you will learn how to review the results of the
+# analysis
+
+# %% [markdown]
+# ### Show project summary report
+
+# %%
+project.summary.show_report()