Adds draft of the Rietveld refinement for BSFTO

Author: AndrewSazonov

tutorials-drafts/cryst-struct_pd-neut-tof_multiphase-BSFTO-HRPT.py

@@ -0,0 +1,278 @@
+# %% [markdown]
+# # Structure Refinement: BSFTO, HRPT
+#
+# This example demonstrates a Rietveld refinement of Bi1−xSmxFe0.94Ti0.06O3
+# crystal and magnetic structure...
+
+# %% [markdown]
+# ## Import Library
+
+# %%
+from easydiffraction import (
+    Project,
+    SampleModel,
+    Experiment,
+    download_from_repository
+)
+
+# %% [markdown]
+# ## Define Sample Models
+#
+# This section shows how to add sample models and modify their parameters.
+#
+# ### Create Sample Model 1: Orthorhombic phase
+
+# %%
+model_1 = SampleModel('ort')
+
+# %% [markdown]
+# #### Set Space Group
+
+# %%
+model_1.space_group.name_h_m = 'P b a m'
+model_1.space_group.it_coordinate_system_code = 'abc'
+
+# %% [markdown]
+# #### Set Unit Cell
+
+# %%
+model_1.cell.length_a = 5.588
+model_1.cell.length_b = 11.125
+model_1.cell.length_c = 7.876
+
+# %% [markdown]
+# #### Set Atom Sites
+
+# %%
+model_1.atom_sites.add('Bi1', 'Bi', 0.702, 0.114, 0,     wyckoff_letter='g', b_iso=0.0, occupancy=0.88)
+model_1.atom_sites.add('Sm1', 'Sm', 0.702, 0.114, 0,     wyckoff_letter='g', b_iso=0.0, occupancy=0.12)
+model_1.atom_sites.add('Bi2', 'Bi', 0.751, 0.132, 0.5,   wyckoff_letter='h', b_iso=0.0, occupancy=0.88)
+model_1.atom_sites.add('Sm2', 'Sm', 0.751, 0.132, 0.5,   wyckoff_letter='h', b_iso=0.0, occupancy=0.12)
+model_1.atom_sites.add('Fe',  'Fe', 0.236, 0.121, 0.259, wyckoff_letter='i', b_iso=0.0, occupancy=0.94)
+model_1.atom_sites.add('Ti',  'Ti', 0.236, 0.121, 0.259, wyckoff_letter='i', b_iso=0.0, occupancy=0.06)
+model_1.atom_sites.add('O1',  'O',  0.258, 0.151, 0,     wyckoff_letter='g', b_iso=0.0, occupancy=1.0)
+model_1.atom_sites.add('O2',  'O',  0.316, 0.093, 0.5,   wyckoff_letter='h', b_iso=0.0, occupancy=1.0)
+model_1.atom_sites.add('O3',  'O',  0.002, 0.258, 0.299, wyckoff_letter='i', b_iso=0.0, occupancy=1.0)
+model_1.atom_sites.add('O4',  'O',  0,     0.5,   0.264, wyckoff_letter='f', b_iso=0.0, occupancy=1.0)
+model_1.atom_sites.add('O5',  'O',  0,     0,     0.198, wyckoff_letter='e', b_iso=0.0, occupancy=1.0)
+
+# %% [markdown]
+# ### Create Sample Model 2: Rhombohedral phase
+
+# %%
+model_2 = SampleModel('rho')
+
+# %% [markdown]
+# #### Set Space Group
+
+# %%
+model_2.space_group.name_h_m = 'R 3 c'
+model_2.space_group.it_coordinate_system_code = 'h'
+
+# %% [markdown]
+# #### Set Unit Cell
+
+# %%
+model_2.cell.length_a = 5.568
+model_2.cell.length_c = 13.758
+
+# %% [markdown]
+# #### Set Atom Sites
+
+# %%
+model_2.atom_sites.add('Bi',  'Bi', 0,     0,     0,     wyckoff_letter='a', b_iso=0.0, occupancy=0.88)
+model_2.atom_sites.add('Sm',  'Sm', 0,     0,     0,     wyckoff_letter='a', b_iso=0.0, occupancy=0.12)
+model_2.atom_sites.add('Fe',  'Fe', 0,     0,     0.223, wyckoff_letter='a', b_iso=0.0, occupancy=0.94)
+model_2.atom_sites.add('Ti',  'Ti', 0,     0,     0.223, wyckoff_letter='a', b_iso=0.0, occupancy=0.06)
+model_2.atom_sites.add('O',   'O',  0.436, 0.022, 0.958, wyckoff_letter='b', b_iso=0.0, occupancy=1.0)
+
+# %% [markdown]
+# ## Define Experiment
+#
+# This section shows how to add experiments, configure their parameters, and
+# link the sample models defined in the previous step.
+#
+# #### Download Data
+
+# %%
+#download_from_repository('hrpt_n_Bi0p88Sm0p12Fe0p94Ti0p06O3_DW_V_9x8x52_1p49_HI.xye',
+#                         branch='develop',
+#                         destination='data')
+
+# %% [markdown]
+# #### Create Experiment
+
+# %%
+experiment = Experiment('hrpt',
+                        data_path='data/hrpt_n_Bi0p88Sm0p12Fe0p94Ti0p06O3_DW_V_9x8x52_1p49_HI.xye')
+
+# %% [markdown]
+# #### Set Instrument
+
+# %%
+experiment.instrument.setup_wavelength = 1.494
+experiment.instrument.calib_twotheta_offset = 0.14
+
+# %% [markdown]
+# #### Set Peak Profile
+
+# %%
+experiment.peak.broad_gauss_u = 0.7
+experiment.peak.broad_gauss_v = -0.41
+experiment.peak.broad_gauss_w = 0.18
+experiment.peak.broad_lorentz_x = 0
+experiment.peak.broad_lorentz_y = 0.21
+
+# %% [markdown]
+# #### Set Background
+
+# %% [markdown]
+# Select the background type.
+
+# %%
+experiment.background_type = 'line-segment'
+
+# %% [markdown]
+# Add background points.
+
+# %%
+experiment.background.add(x=10, y=865)
+experiment.background.add(x=30, y=888)
+experiment.background.add(x=50, y=893)
+experiment.background.add(x=110, y=874)
+experiment.background.add(x=165, y=702)
+
+# %% [markdown]
+# #### Set Linked Phases
+
+# %%
+experiment.linked_phases.add('ort', scale=0.07)
+experiment.linked_phases.add('rho', scale=0.21)
+
+# %% [markdown]
+# ## Define Project
+#
+# The project object is used to manage sample models, experiments, and analysis.
+#
+# #### Create Project
+
+# %%
+project = Project()
+
+# %% [markdown]
+# #### Set Plotting Engine
+
+# %%
+project.plotter.engine = 'plotly'
+
+# %% [markdown]
+# #### Add Sample Models
+
+# %%
+project.sample_models.add(model_1)
+project.sample_models.add(model_2)
+
+# %% [markdown]
+# #### Show Sample Models
+
+# %%
+project.sample_models.show_names()
+
+# %% [markdown]
+# #### Add Experiments
+
+# %%
+project.experiments.add(experiment)
+
+# %% [markdown]
+# #### Set Excluded Regions
+#
+# Show measured data as loaded from the file.
+
+# %%
+project.plot_meas(expt_name='hrpt')
+
+# %% [markdown]
+# Add excluded regions.
+
+# %%
+experiment.excluded_regions.add(minimum=0, maximum=10)
+experiment.excluded_regions.add(minimum=160, maximum=180)
+
+# %% [markdown]
+# Show excluded regions.
+
+# %%
+experiment.excluded_regions.show()
+
+# %% [markdown]
+# Show measured data after adding excluded regions.
+
+# %%
+project.plot_meas(expt_name='hrpt')
+
+# %% [markdown]
+# Show experiment as CIF.
+
+# %%
+project.experiments['hrpt'].show_as_cif()
+
+# %% [markdown]
+# ## Perform Analysis
+#
+# This section outlines the analysis process, including how to configure
+# calculation and fitting engines.
+#
+# #### Set Calculator
+
+# %%
+project.analysis.current_calculator = 'cryspy'
+
+# %% [markdown]
+# #### Set Minimizer
+
+# %%
+project.analysis.current_minimizer = 'lmfit (leastsq)'
+
+# %% [markdown]
+# #### Set Fitting Parameters
+#
+# Set sample model parameters to be optimized.
+
+# %%
+#model_1.cell.length_a.free = True
+#model_1.atom_sites['Co'].b_iso.free = True
+#model_1.atom_sites['O'].b_iso.free = True
+
+#model_2.cell.length_a.free = True
+
+# %% [markdown]
+# Set experiment parameters to be optimized.
+
+# %%
+experiment.instrument.calib_twotheta_offset.free = True
+
+# %%
+experiment.peak.broad_gauss_u.free = True
+experiment.peak.broad_gauss_v.free = True
+experiment.peak.broad_gauss_w.free = True
+experiment.peak.broad_lorentz_y.free = True
+
+# %%
+experiment.linked_phases['ort'].scale.free = True
+experiment.linked_phases['rho'].scale.free = True
+
+for point in experiment.background:
+    point.y.free = True
+
+# %% [markdown]
+# #### Perform Fit
+
+# %%
+project.analysis.fit()
+
+# %% [markdown]
+# #### Plot Measured vs Calculated
+
+# %%
+project.plot_meas_vs_calc(expt_name='hrpt')