Refactors for CIF parsing functionality

Author: AndrewSazonov

tmp/quick_single-fit_pd-neut-cwl_LBCO-HRPT.py renamed to tmp/_read_cif.py

@@ -1,120 +1,121 @@
-# %%
+# %% [markdown]
+# # Structure Refinement: LBCO, HRPT
+#
+# This minimalistic example is designed to be as compact as possible for
+# a Rietveld refinement of a crystal structure using constant-wavelength
+# neutron powder diffraction data for La0.5Ba0.5CoO3 from HRPT at PSI.
+#
+# It does not contain any advanced features or options, and includes no
+# comments or explanations—these can be found in the other tutorials.
+# Default values are used for all parameters if not specified. Only
+# essential and self-explanatory code is provided.
+#
+# The example is intended for users who are already familiar with the
+# EasyDiffraction library and want to quickly get started with a simple
+# refinement. It is also useful for those who want to see what a
+# refinement might look like in code. For a more detailed explanation of
+# the code, please refer to the other tutorials.
+
+# %% [markdown]
 # ## Import Library
+
+# %%
 import easydiffraction as ed
 
 # %%
+from easydiffraction.utils.logging import Logger
+Logger.configure(
+    level=Logger.Level.INFO,
+    mode=Logger.Mode.COMPACT,
+    reaction=Logger.Reaction.WARN,
+)
+
+# %% [markdown]
 # ## Step 1: Define Project
-project = ed.Project()
-#project.tabler.engine = 'rich'
-#project.tabler.engine = 'pandas'
 
 # %%
+project = ed.Project()
+
+# %% [markdown]
 # ## Step 2: Define Sample Model
-project.sample_models.add_minimal(name='lbco')
 
+# %%
+project.sample_models.add_from_cif_path("data/lbco.cif")
+
+# %%
+project.sample_models.show_names()
+
+# %%
 sample_model = project.sample_models['lbco']
-sample_model.space_group.name_h_m = 'P m -3 m'
-sample_model.space_group.it_coordinate_system_code = '1'
-sample_model.cell.length_a = 3.88
-sample_model.atom_sites.add_from_args(
-    label='La',
-    type_symbol='La',
-    fract_x=0,
-    fract_y=0,
-    fract_z=0,
-    wyckoff_letter='a',
-    b_iso=0.5,
-    occupancy=0.5,
-)
-sample_model.atom_sites.add_from_args(
-    label='Ba',
-    type_symbol='Ba',
-    fract_x=0,
-    fract_y=0,
-    fract_z=0,
-    wyckoff_letter='a',
-    b_iso=0.5,
-    occupancy=0.5,
-)
-sample_model.atom_sites.add_from_args(
-    label='Co',
-    type_symbol='Co',
-    fract_x=0.5,
-    fract_y=0.5,
-    fract_z=0.5,
-    wyckoff_letter='b',
-    b_iso=0.5,
-)
-sample_model.atom_sites.add_from_args(
-    label='O', type_symbol='O', fract_x=0, fract_y=0.5, fract_z=0.5, wyckoff_letter='c', b_iso=0.5
-)
 
 # %%
+sample_model.show_as_cif()
+
+# %% [markdown]
 # ## Step 3: Define Experiment
-ed.download_from_repository('hrpt_lbco.xye', destination='data')
-
-project.experiments.add_from_data_path(
-    name='hrpt',
-    data_path='data/hrpt_lbco.xye',
-    sample_form='powder',
-    beam_mode='constant wavelength',
-    radiation_probe='neutron',
-)
 
+# %%
+project.experiments.add_from_cif_path("data/hrpt.cif")
+
+# %%
 experiment = project.experiments['hrpt']
+
+# %%
+project.experiments.show_names()
+
+# %%
 experiment.instrument.setup_wavelength = 1.494
 experiment.instrument.calib_twotheta_offset = 0.6
+
+# %%
 experiment.peak.broad_gauss_u = 0.1
 experiment.peak.broad_gauss_v = -0.1
 experiment.peak.broad_gauss_w = 0.1
 experiment.peak.broad_lorentz_y = 0.1
+
+# %%
 experiment.background.add_from_args(x=10, y=170)
 experiment.background.add_from_args(x=30, y=170)
 experiment.background.add_from_args(x=50, y=170)
 experiment.background.add_from_args(x=110, y=170)
 experiment.background.add_from_args(x=165, y=170)
+
+# %%
 experiment.excluded_regions.add_from_args(start=0, end=5)
 experiment.excluded_regions.add_from_args(start=165, end=180)
-experiment.linked_phases.add_from_args(id='lbco', scale=10.0)
 
 # %%
+experiment.linked_phases.add_from_args(id='lbco', scale=10.0)
+
+# %% [markdown]
 # ## Step 4: Perform Analysis
+
+# %%
 sample_model.cell.length_a.free = True
+
 sample_model.atom_sites['La'].b_iso.free = True
 sample_model.atom_sites['Ba'].b_iso.free = True
 sample_model.atom_sites['Co'].b_iso.free = True
 sample_model.atom_sites['O'].b_iso.free = True
 
+# %%
 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.background['10'].y.free = True
 experiment.background['30'].y.free = True
 experiment.background['50'].y.free = True
 experiment.background['110'].y.free = True
 experiment.background['165'].y.free = True
+
 experiment.linked_phases['lbco'].scale.free = True
 
 # %%
-sample_model.cell.length_a = 3.88
 project.analysis.fit()
 
 # %%
-#project.plot_meas_vs_calc(expt_name='hrpt', show_residual=True)
-
-# %%
-project.analysis.show_all_params()
-
-# %%
-project.analysis.show_fittable_params()
-
-# %%
-project.analysis.show_free_params()
-
-# %%
-project.analysis.how_to_access_parameters()
-
-# %%
-project.analysis.show_parameter_cif_uids()
+project.plot_meas_vs_calc(expt_name='hrpt', show_residual=True)