Adds diffraction analysis for Na2Ca3Al2F14 sample

Author: AndrewSazonov

docs/mkdocs.yml

@@ -58,7 +58,8 @@ nav:
       - Basic Usage:
           - 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-tof 1: tutorials/advanced_single-fit_pd-neut-tof_Si-SEPD.ipynb
+          - SingleFit pd-neut-tof 2: tutorials/advanced_single-fit_pd-neut-tof_NCAF-WISH.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:

tutorials/advanced_single-fit_pd-neut-tof_NCAF-WISH.py

@@ -0,0 +1,355 @@
+# %% [markdown]
+# # Standard diffraction: Na2Ca3Al2F14
+#
+# Standard diffraction analysis of Na2Ca3Al2F14 after the powder neutron
+# time-of-flight diffraction measurement from WISH at ISIS.
+#
+# Only a single dataset from detector banks 5 & 6 is used here.
+
+# %% [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('ncaf')
+
+# %% [markdown]
+# ### Define space group
+
+# %%
+model.space_group.name_h_m = 'I 21 3'
+model.space_group.it_coordinate_system_code = '1'
+
+# %% [markdown]
+# ### Define unit cell
+
+# %%
+model.cell.length_a = 10.250256
+
+# %% [markdown]
+# ### Define atom sites
+
+# %%
+model.atom_sites.add('Ca', 'Ca', 0.4661, 0.0, 0.25, wyckoff_letter="b", b_iso=0.9)
+model.atom_sites.add('Al', 'Al', 0.25171, 0.25171, 0.25171, wyckoff_letter="a", b_iso=0.66)
+model.atom_sites.add('Na', 'Na', 0.08481, 0.08481, 0.08481, wyckoff_letter="a", b_iso=1.9)
+model.atom_sites.add('F1', 'F', 0.1375, 0.3053, 0.1195, wyckoff_letter="c", b_iso=0.9)
+model.atom_sites.add('F2', 'F', 0.3626, 0.3634, 0.1867, wyckoff_letter="c", b_iso=1.28)
+model.atom_sites.add('F3', 'F', 0.4612, 0.4612, 0.4612, wyckoff_letter="a", b_iso=0.79)
+
+# %% [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('wish_ncaf.xye',
+                         branch='docs',
+                         destination='data')
+
+# %% [markdown]
+# ### Create experiment object
+
+# %%
+expt = Experiment('wish',
+                  beam_mode='time-of-flight',
+                  data_path='data/wish_ncaf.xye')
+
+# %% [markdown]
+# ### Define instrument
+
+# %%
+expt.instrument.setup_twotheta_bank = 152.827
+expt.instrument.calib_d_to_tof_offset = 0.0
+expt.instrument.calib_d_to_tof_linear = 20770
+expt.instrument.calib_d_to_tof_quad = -1.08308
+
+# %% [markdown]
+# ### Define peak profile
+
+# %%
+expt.peak_profile_type = 'pseudo-voigt * ikeda-carpenter'
+expt.peak.broad_gauss_sigma_0 = 0.0
+expt.peak.broad_gauss_sigma_1 = 0.0
+expt.peak.broad_gauss_sigma_2 = 5.0
+expt.peak.broad_mix_beta_0 = 0.01
+expt.peak.broad_mix_beta_1 = 0.01
+
+# %% [markdown]
+# ### Define peak asymmetry
+
+# %%
+expt.peak.asym_alpha_0 = 0.0
+expt.peak.asym_alpha_1 = 0.1
+
+# %% [markdown]
+# ### Define background
+
+# %%
+expt.background_type = 'line-segment'
+for x, y in [
+    (9162, 465),
+    (11136, 593),
+    (13313, 497),
+    (14906, 546),
+    (16454, 533),
+    (17352, 496),
+    (18743, 428),
+    (20179, 452),
+    (21368, 397),
+    (22176, 468),
+    (22827, 477),
+    (24644, 380),
+    (26439, 381),
+    (28257, 378),
+    (31196, 343),
+    (34034, 328),
+    (37265, 310),
+    (41214, 323),
+    (44827, 283),
+    (49830, 273),
+    (52905, 257),
+    (58204, 260),
+    (62916, 261),
+    (70186, 262),
+    (74204, 262),
+    (82103, 268),
+    (91958, 268),
+    (102712, 262)
+]:
+    expt.background.add(x, y)
+
+# %% [markdown]
+# ### Select linked phase
+
+# %%
+expt.linked_phases.add('ncaf', 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='wish',
+                          show_residual=True)
+project.plot_meas_vs_calc(expt_name='wish',
+                          x_min=37000, x_max=40000,
+                          show_residual=True)
+
+# %% [markdown]
+# ### Perform Fit 1/5
+#
+# Set parameters to be fitted
+
+# %%
+model.cell.length_a.free = True
+
+expt.instrument.calib_d_to_tof_offset.free = True
+expt.linked_phases['ncaf'].scale.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='wish',
+                          show_residual=True)
+project.plot_meas_vs_calc(expt_name='wish',
+                          x_min=37000, x_max=40000,
+                          show_residual=True)
+
+# %% [markdown]
+# ### Perform Fit 2/5
+#
+# Set parameters to be fitted
+
+# %%
+expt.peak.broad_gauss_sigma_2.free = True
+expt.peak.broad_mix_beta_0.free = True
+expt.peak.broad_mix_beta_1.free = True
+expt.peak.asym_alpha_0.free = True
+expt.peak.asym_alpha_1.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='wish',
+                          show_residual=True)
+project.plot_meas_vs_calc(expt_name='wish',
+                          x_min=37000, x_max=40000,
+                          show_residual=True)
+
+
+# %% [markdown]
+# ### Perform Fit 3/5
+#
+# Set parameters to be fitted
+
+# %%
+model.atom_sites['Ca'].fract_x.free = True
+model.atom_sites['Al'].fract_x.free = True
+model.atom_sites['Na'].fract_x.free = True
+model.atom_sites['F1'].fract_x.free = True
+model.atom_sites['F1'].fract_y.free = True
+model.atom_sites['F1'].fract_z.free = True
+model.atom_sites['F2'].fract_x.free = True
+model.atom_sites['F2'].fract_y.free = True
+model.atom_sites['F2'].fract_z.free = True
+model.atom_sites['F3'].fract_x.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='wish',
+                          show_residual=True)
+project.plot_meas_vs_calc(expt_name='wish',
+                          x_min=37000, x_max=40000,
+                          show_residual=True)
+
+# %% [markdown]
+# ### Perform Fit 4/5
+#
+# Set parameters to be fitted
+
+# %%
+expt.instrument.calib_d_to_tof_linear.free = True
+
+model.atom_sites['Ca'].b_iso.free = True
+model.atom_sites['Al'].b_iso.free = True
+model.atom_sites['Na'].b_iso.free = True
+model.atom_sites['F1'].b_iso.free = True
+model.atom_sites['F2'].b_iso.free = True
+model.atom_sites['F3'].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='wish',
+                          show_residual=True)
+project.plot_meas_vs_calc(expt_name='wish',
+                          x_min=37000, x_max=40000,
+                          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()