Refactor terminology from "sample" to "structure" in documentation and code comments

AndrewSazonov · AndrewSazonov · commit 58ab4a78e5c8 · 2026-03-16T13:38:41.000+01:00
diff --git a/docs/user-guide/analysis-workflow/analysis.md b/docs/user-guide/analysis-workflow/analysis.md
@@ -20,7 +20,7 @@ EasyDiffraction relies on third-party crystallographic libraries, referred to as
 **calculation engines** or just **calculators**, to perform the calculations.
 
 The calculation engines are used to calculate the diffraction pattern for the
-defined model of the studied sample using the instrumental and other required
+defined model of the studied structure using the instrumental and other required
 experiment-related parameters, such as the wavelength, resolution, etc.
 
 You do not necessarily need the measured data to perform the calculations, but
diff --git a/docs/user-guide/analysis-workflow/project.md b/docs/user-guide/analysis-workflow/project.md
@@ -127,7 +127,7 @@ hrpt.cif
 
 ### 2. structures / <span class="orange">lbco.cif</span>
 
-This file contains crystallographic information associated with the sample
+This file contains crystallographic information associated with the structure
 model, including **space group**, **unit cell parameters**, and **atomic
 positions**.
 
diff --git a/docs/user-guide/concept.md b/docs/user-guide/concept.md
@@ -58,8 +58,8 @@ Credits: DOI 10.1126/science.1238932
 ## Data Analysis
 
 Data analysis uses the reduced data to extract meaningful information about the
-sample. This may include determining the crystal or magnetic structure,
-identifying phases, performing quantitative analysis, etc.
+crystallographic structure. This may include determining the crystal or magnetic
+structure, identifying phases, performing quantitative analysis, etc.
 
 Analysis often involves comparing experimental data with data calculated from a
 crystallographic model to validate and interpret the results. For powder
diff --git a/docs/user-guide/first-steps.md b/docs/user-guide/first-steps.md
@@ -66,7 +66,7 @@ workflow. One of them is the `download_from_repository` function, which allows
 you to download data files from our remote repository, making it easy to access
 and use them while experimenting with EasyDiffraction.
 
-For example, you can download a sample data file like this:
+For example, you can download a data file like this:
 
 ```python
 import easydiffraction as ed
diff --git a/tutorials/ed-13.py b/tutorials/ed-13.py
@@ -52,11 +52,11 @@
 #
 # In EasyDiffraction, a project serves as a container for all
 # information related to the analysis of a specific experiment or set of
-# experiments. It enables you to organize your data, experiments, sample
-# models, and fitting parameters in a structured manner. You can think
-# of it as a folder containing all the essential details about your
-# analysis. The project also allows us to visualize both the measured
-# and calculated diffraction patterns, among other things.
+# experiments. It enables you to organize your data, experiments,
+# crystal structures, and fitting parameters in an organized manner. You
+# can think of it as a folder containing all the essential details about
+# your analysis. The project also allows us to visualize both the
+# measured and calculated diffraction patterns, among other things.
 
 # %% [markdown] tags=["doc-link"]
 # 📖 See
@@ -440,7 +440,7 @@
 
 # %% [markdown] tags=["doc-link"]
 # 📖 See
-# [documentation](https://docs.easydiffraction.org/lib/user-guide/analysis-workflow/model/)
+# [documentation](https://docs.easydiffraction.org/lib/user-guide/analysis-workflow/structure/)
 # for more details about structures and their purpose in the data
 # analysis workflow.
 
@@ -455,7 +455,7 @@
 
 # %% [markdown] tags=["doc-link"]
 # 📖 See
-# [documentation](https://docs.easydiffraction.org/lib/user-guide/analysis-workflow/model/#space-group-category)
+# [documentation](https://docs.easydiffraction.org/lib/user-guide/analysis-workflow/structure/#space-group-category)
 # for more details about the space group.
 
 # %%
@@ -467,7 +467,7 @@
 
 # %% [markdown] tags=["doc-link"]
 # 📖 See
-# [documentation](https://docs.easydiffraction.org/lib/user-guide/analysis-workflow/model/#cell-category)
+# [documentation](https://docs.easydiffraction.org/lib/user-guide/analysis-workflow/structure/#cell-category)
 # for more details about the unit cell parameters.
 
 # %%
@@ -478,7 +478,7 @@
 
 # %% [markdown] tags=["doc-link"]
 # 📖 See
-# [documentation](https://docs.easydiffraction.org/lib/user-guide/analysis-workflow/model/#atom-sites-category)
+# [documentation](https://docs.easydiffraction.org/lib/user-guide/analysis-workflow/structure/#atom-sites-category)
 # for more details about the atom sites category.
 
 # %%
@@ -528,12 +528,12 @@
 # %% [markdown] **Reminder:**
 #
 # The fitting process involves comparing the measured diffraction
-# pattern with the calculated diffraction pattern based on the sample
-# model and instrument parameters. The goal is to adjust the parameters
-# of the structure and the experiment to minimize the difference
-# between the measured and calculated diffraction patterns. This is done
-# by refining the parameters of the structure and the instrument
-# settings to achieve a better fit.
+# pattern with the calculated diffraction pattern based on the crystal
+# structure and instrument parameters. The goal is to adjust the
+# parameters of the structure and the experiment to minimize the
+# difference between the measured and calculated diffraction patterns.
+# This is done by refining the parameters of the structure and the
+# instrument settings to achieve a better fit.
 
 # %% [markdown] tags=["doc-link"]
 # 📖 See
@@ -872,7 +872,7 @@
 # %% [markdown]
 # ### 🧩 Exercise 3: Define a Structure – LBCO
 #
-# The LBSO structure is not as simple as the Si model, as it contains
+# The LBSO structure is not as simple as the Si one, as it contains
 # multiple atoms in the unit cell. It is not in COD, so we give you the
 # structural parameters in CIF format to create the structure.
 #
@@ -946,7 +946,7 @@
 
 # %% [markdown] tags=["dmsc-school-hint"]
 # You can use the same approach as in the previous part of the notebook,
-# but this time you need to use the model name corresponding to the LBCO
+# but this time you need to use the name corresponding to the LBCO
 # structure, e.g. 'lbco'.
 
 # %% [markdown]
@@ -1055,8 +1055,8 @@
 # **Hint:**
 
 # %% [markdown] tags=["dmsc-school-hint"]
-# Use the `linked_phases` attribute of the experiment to link the sample
-# model.
+# Use the `linked_phases` attribute of the experiment to link the
+# crystal structure.
 
 # %% [markdown]
 # **Solution:**
diff --git a/tutorials/ed-14.py b/tutorials/ed-14.py
@@ -22,10 +22,10 @@
 
 # %%
 # Download CIF file from repository
-model_path = ed.download_data(id=20, destination='data')
+structure_path = ed.download_data(id=20, destination='data')
 
 # %%
-project.structures.add(cif_path=model_path)
+project.structures.add(cif_path=structure_path)
 
 # %%
 project.structures.show_names()
diff --git a/tutorials/ed-15.py b/tutorials/ed-15.py
@@ -22,10 +22,10 @@
 
 # %%
 # Download CIF file from repository
-model_path = ed.download_data(id=21, destination='data')
+structure_path = ed.download_data(id=21, destination='data')
 
 # %%
-project.structures.add(cif_path=model_path)
+project.structures.add(cif_path=structure_path)
 
 # %%
 project.structures.show_names()
diff --git a/tutorials/ed-2.py b/tutorials/ed-2.py
@@ -2,9 +2,9 @@
 # # Structure Refinement: LBCO, HRPT
 #
 # This minimalistic example is designed to show how Rietveld refinement
-# of a crystal structure can be performed when both the structure and
-# experiment are defined directly in code. Only the experimentally
-# measured data is loaded from an external file.
+# can be performed when both the crystal structure and experiment are
+# defined directly in code. Only the experimentally measured data is
+# loaded from an external file.
 #
 # For this example, constant-wavelength neutron powder diffraction data
 # for La0.5Ba0.5CoO3 from HRPT at PSI is used.
diff --git a/tutorials/ed-3.py b/tutorials/ed-3.py
@@ -8,8 +8,9 @@
 #
 # It is intended for users with minimal programming experience who want
 # to learn how to perform standard crystal structure fitting using
-# diffraction data. This script covers creating a project, adding sample
-# models and experiments, performing analysis, and refining parameters.
+# diffraction data. This script covers creating a project, adding
+# crystal structures and experiments, performing analysis, and refining
+# parameters.
 #
 # Only a single import of `easydiffraction` is required, and all
 # operations are performed through high-level components of the
@@ -98,9 +99,10 @@
 # %% [markdown]
 # #### Show Defined Structures
 #
-# Show the names of the models added. These names are used to access the
-# model using the syntax: `project.structures['model_name']`. All
-# model parameters can be accessed via the `project` object.
+# Show the names of the crystal structures added. These names are used
+# to access the structure using the syntax:
+# `project.structures[name]`. All structure parameters can be accessed
+# via the `project` object.
 
 # %%
 project.structures.show_names()
diff --git a/tutorials/ed-4.py b/tutorials/ed-4.py
@@ -29,27 +29,27 @@
 # #### Create Structure
 
 # %%
-model = StructureFactory.create(name='pbso4')
+structure = StructureFactory.create(name='pbso4')
 
 # %% [markdown]
 # #### Set Space Group
 
 # %%
-model.space_group.name_h_m = 'P n m a'
+structure.space_group.name_h_m = 'P n m a'
 
 # %% [markdown]
 # #### Set Unit Cell
 
 # %%
-model.cell.length_a = 8.47
-model.cell.length_b = 5.39
-model.cell.length_c = 6.95
+structure.cell.length_a = 8.47
+structure.cell.length_b = 5.39
+structure.cell.length_c = 6.95
 
 # %% [markdown]
 # #### Set Atom Sites
 
 # %%
-model.atom_sites.add(
+structure.atom_sites.add(
     label='Pb',
     type_symbol='Pb',
     fract_x=0.1876,
@@ -58,7 +58,7 @@
     wyckoff_letter='c',
     b_iso=1.37,
 )
-model.atom_sites.add(
+structure.atom_sites.add(
     label='S',
     type_symbol='S',
     fract_x=0.0654,
@@ -67,7 +67,7 @@
     wyckoff_letter='c',
     b_iso=0.3777,
 )
-model.atom_sites.add(
+structure.atom_sites.add(
     label='O1',
     type_symbol='O',
     fract_x=0.9082,
@@ -76,7 +76,7 @@
     wyckoff_letter='c',
     b_iso=1.9764,
 )
-model.atom_sites.add(
+structure.atom_sites.add(
     label='O2',
     type_symbol='O',
     fract_x=0.1935,
@@ -85,7 +85,7 @@
     wyckoff_letter='c',
     b_iso=1.4456,
 )
-model.atom_sites.add(
+structure.atom_sites.add(
     label='O3',
     type_symbol='O',
     fract_x=0.0811,
@@ -246,7 +246,7 @@
 # #### Add Structure
 
 # %%
-project.structures.add(structure=model)
+project.structures.add(structure=structure)
 
 # %% [markdown]
 # #### Add Experiments
@@ -284,9 +284,9 @@
 # Set structure parameters to be optimized.
 
 # %%
-model.cell.length_a.free = True
-model.cell.length_b.free = True
-model.cell.length_c.free = True
+structure.cell.length_a.free = True
+structure.cell.length_b.free = True
+structure.cell.length_c.free = True
 
 # %% [markdown]
 # Set experiment parameters to be optimized.
diff --git a/tutorials/ed-5.py b/tutorials/ed-5.py
diff --git a/tutorials/ed-6.py b/tutorials/ed-6.py
diff --git a/tutorials/ed-7.py b/tutorials/ed-7.py
diff --git a/tutorials/ed-8.py b/tutorials/ed-8.py
diff --git a/tutorials/ed-9.py b/tutorials/ed-9.py

Original file line number	Diff line number	Diff line change
`@@ -2,9 +2,9 @@`
`2`	`2`	`# # Structure Refinement: LBCO, HRPT`
`3`	`3`	`#`
`4`	`4`	`# This minimalistic example is designed to show how Rietveld refinement`
`5`		`-# of a crystal structure can be performed when both the structure and`
`6`		`-# experiment are defined directly in code. Only the experimentally`
`7`		`-# measured data is loaded from an external file.`
	`5`	`+# can be performed when both the crystal structure and experiment are`
	`6`	`+# defined directly in code. Only the experimentally measured data is`
	`7`	`+# loaded from an external file.`
`8`	`8`	`#`
`9`	`9`	`# For this example, constant-wavelength neutron powder diffraction data`
`10`	`10`	`# for La0.5Ba0.5CoO3 from HRPT at PSI is used.`