diff --git a/.github/workflows/pypi-test.yml b/.github/workflows/pypi-test.yml index 46097a1d..46a8a905 100644 --- a/.github/workflows/pypi-test.yml +++ b/.github/workflows/pypi-test.yml @@ -48,6 +48,9 @@ jobs: - name: Init pixi project run: pixi init easydiffraction + - name: Set the minimum system requirements + run: pixi project system-requirements add macos 14.0 + - name: Add Python 3.14 from Conda working-directory: easydiffraction run: pixi add "python=3.14" @@ -58,22 +61,25 @@ jobs: pixi add gsl pixi add --platform osx-arm64 libcxx - - name: Add easydiffraction from PyPI - working-directory: easydiffraction - run: pixi add --pypi "easydiffraction" - - - name: Add dev dependencies from PyPI + - name: Add pycrysfml calculator from custom PyPI index working-directory: easydiffraction - run: pixi add --pypi pytest pytest-xdist + run: | + echo '' >> pixi.toml + echo '[pypi-dependencies]' >> pixi.toml + echo 'pycrysfml = { version = ">=0.2.1", index = "https://easyscience.github.io/pypi/" }' >> pixi.toml - - name: Add Pixi task as a shortcut + - name: Add easydiffraction (with dev dependencies) from PyPI working-directory: easydiffraction - run: pixi task add easydiffraction "python -m easydiffraction" + run: pixi add --pypi "easydiffraction[dev]" - name: Run unit tests to verify the installation working-directory: easydiffraction run: pixi run python -m pytest ../tests/unit/ --color=yes -v + - name: Run functional tests to verify the installation + working-directory: easydiffraction + run: pixi run python -m pytest ../tests/functional/ --color=yes -v + - name: Run integration tests to verify the installation working-directory: easydiffraction run: pixi run python -m pytest ../tests/integration/ --color=yes -n auto diff --git a/docs/docs/cli/index.md b/docs/docs/cli/index.md new file mode 100644 index 00000000..5fc13c77 --- /dev/null +++ b/docs/docs/cli/index.md @@ -0,0 +1,90 @@ +--- +icon: material/console +--- + +# :material-console: Command-Line Interface + +In addition to the Python API and Jupyter Notebooks, EasyDiffraction +provides a **command-line interface (CLI)**. This is useful for basic +operations without writing Python code. + +## Running the CLI + +The CLI is invoked as a Python module: + +```bash +python -m easydiffraction [COMMAND] [OPTIONS] +``` + +If you use **Pixi** and have defined the `easydiffraction` task (see +[Installation & Setup](../installation-and-setup/index.md)), you can +use: + +```bash +pixi run easydiffraction [COMMAND] [OPTIONS] +``` + +To see all available commands and options: + +```bash +python -m easydiffraction --help +``` + +## Available Commands + +### Show Version + +Display the installed EasyDiffraction version: + +```bash +python -m easydiffraction --version +``` + +### List Tutorials + +List all available tutorial notebooks: + +```bash +python -m easydiffraction list-tutorials +``` + +### Download Tutorials + +Download a specific tutorial by ID: + +```bash +python -m easydiffraction download-tutorial 1 +``` + +Download all available tutorials: + +```bash +python -m easydiffraction download-all-tutorials +``` + +Both commands accept `--destination` (`-d`) to specify the output +directory (default: `tutorials/`) and `--overwrite` (`-o`) to replace +existing files. + +### Fit a Project + +Load a saved project and run structural refinement: + +```bash +python -m easydiffraction fit PROJECT_DIR +``` + +`PROJECT_DIR` is the path to a project directory previously created by +`project.save_as()`. It must contain a `project.cif` file along with the +`structures/`, `experiments/`, and `analysis/` subdirectories. + +After fitting, the command displays the fit results and a project +summary. By default, updated parameter values are **saved back** to the +project directory. + +Use the `--dry` flag to run the fit **without overwriting** the project +files: + +```bash +python -m easydiffraction fit PROJECT_DIR --dry +``` diff --git a/docs/docs/index.md b/docs/docs/index.md index 73c35423..cc8b5cb0 100644 --- a/docs/docs/index.md +++ b/docs/docs/index.md @@ -1,11 +1,11 @@ ![](assets/images/logo_dark.svg#gh-dark-mode-only)![](assets/images/logo_light.svg#gh-light-mode-only) -# Diffraction data analysis library +# Diffraction data analysis Here is a brief overview of the main documentation sections: - [:material-information-slab-circle: Introduction](introduction/index.md) - – Provides an overview of EasyDiffraction, including its purpose, + – Provides a description of EasyDiffraction, including its purpose, licensing, latest release details, and contact information. - [:material-cog-box: Installation & Setup](installation-and-setup/index.md) – Guides users through system requirements, environment configuration, @@ -19,3 +19,6 @@ Here is a brief overview of the main documentation sections: - [:material-code-braces-box: API Reference](api-reference/index.md) – An auto-generated reference detailing the available functions and modules in EasyDiffraction. +- [:material-console: Command-Line Interface](cli/index.md) – Describes + how to use EasyDiffraction from the terminal for batch fitting and + other tasks. diff --git a/docs/docs/installation-and-setup/index.md b/docs/docs/installation-and-setup/index.md index f08fd3ae..fdea87bf 100644 --- a/docs/docs/installation-and-setup/index.md +++ b/docs/docs/installation-and-setup/index.md @@ -7,12 +7,11 @@ icon: material/cog-box **EasyDiffraction** is a cross-platform Python library compatible with **Python 3.12** through **3.14**. -EasyDiffraction is a cross-platform Python library compatible with -**Python 3.11 through 3.13**. -Make sure Python is installed on your system before proceeding with the -installation. +To install and set up EasyDiffraction, we recommend using +[**Pixi**](https://pixi.prefix.dev), a modern package manager for +Windows, macOS, and Linux. -## Environment Setup optional { #environment-setup data-toc-label="Environment Setup" } +??? note "Main benefits of using Pixi" - **Ease of use**: Pixi simplifies the installation process, making it accessible even for users with limited experience in package management. @@ -63,10 +62,22 @@ This section describes the simplest way to set up EasyDiffraction using pixi init easydiffraction cd easydiffraction ``` +- If you are on macOS, set the minimum system requirements: + ```txt + pixi project system-requirements add macos 14.0 + ``` - Set the Python version for the Pixi environment (e.g., 3.14): ```txt pixi add python=3.14 ``` +- Add GNU Scientific Library (required for PDF calculations): + ```txt + pixi add gsl + ``` +- If you are on macOS, add libc++ (required for PDF calculations): + ```txt + pixi add --platform osx-arm64 libcxx + ``` - Add EasyDiffraction to the Pixi environment from PyPI: ```txt pixi add --pypi easydiffraction @@ -110,21 +121,21 @@ simply delete and recreate the environment. - Create a new virtual environment: - ```bash + ```txt python3 -m venv venv ``` - Activate the environment: === ":material-apple: macOS" - ```bash + ```txt . venv/bin/activate ``` === ":material-linux: Linux" - ```bash + ```txt . venv/bin/activate ``` === ":fontawesome-brands-windows: Windows" - ```bash + ```txt . venv/Scripts/activate # Windows with Unix-like shells .\venv\Scripts\activate.bat # Windows with CMD .\venv\Scripts\activate.ps1 # Windows with PowerShell @@ -140,198 +151,147 @@ simply delete and recreate the environment. - Exit the environment: - ```bash + ```txt deactivate ``` - If this environment is no longer needed, delete it: === ":material-apple: macOS" - ```bash + ```txt rm -rf venv ``` === ":material-linux: Linux" - ```bash + ```txt rm -rf venv ``` === ":fontawesome-brands-windows: Windows" - ```bash + ```txt rmdir /s /q venv ``` -## Installation Guide - -### Installing from PyPI recommended { #from-pypi data-toc-label="Installing from PyPI" } +### Installing from PyPI { #from-pypi } EasyDiffraction is available on **PyPI (Python Package Index)** and can -be installed using `pip`. We strongly recommend installing it within a -virtual environment, as described in the -[Environment Setup](#environment-setup) section. - -We recommend installing the latest release of EasyDiffraction with the -`visualization` extras, which include optional dependencies used for -simplified visualization of charts and tables. This can be especially -useful for running the Jupyter Notebook examples. To do so, use the -following command: - -```bash -pip install 'easydiffraction[visualization]' -``` - -If only the core functionality is needed, the library can be installed -simply with: +be installed using `pip`. To do so, use the following command: -```bash +```txt pip install easydiffraction ``` To install a specific version of EasyDiffraction, e.g., 1.0.3: -```bash +```txt pip install 'easydiffraction==1.0.3' ``` To upgrade to the latest version: -```bash +```txt +pip install --upgrade easydiffraction +``` + +To upgrade to the latest version and force reinstallation of all +dependencies (useful if files are corrupted): + +```txt pip install --upgrade --force-reinstall easydiffraction ``` To check the installed version: -```bash +```txt pip show easydiffraction ``` -### Installing from GitHub +### Installing from GitHub alternative { #from-github data-toc-label="Installing from GitHub" } Installing unreleased versions is generally not recommended but may be useful for testing. -To install EasyDiffraction from, e.g., the `develop` branch of GitHub: +To install EasyDiffraction from the `develop` branch of GitHub, for +example: -```bash +```txt pip install git+https://github.com/easyscience/diffraction-lib@develop ``` -To include extra dependencies (e.g., visualization): +To include extra dependencies (e.g., dev): -```bash -pip install 'easydiffraction[visualization] @ git+https://github.com/easyscience/diffraction-lib@develop' +```txt +pip install 'easydiffraction[dev] @ git+https://github.com/easyscience/diffraction-lib@develop' ``` ## How to Run Tutorials EasyDiffraction includes a collection of **Jupyter Notebook examples** that demonstrate key functionality. These tutorials serve as -**step-by-step guides** to help users understand the diffraction data -analysis workflow. - -They are available as **static HTML pages** in the -[:material-school: Tutorials](../tutorials/index.md) section. You can -also run them interactively in two ways: +**step-by-step guides** to help users understand the data analysis +workflow. They are available as **static HTML pages** in the +[:material-school: Tutorials](../tutorials/index.md) section. -- **Run Locally** – Download the notebook via the :material-download: - **Download** button and run it on your computer. -- **Run Online** – Use the :google-colab: **Open in Google Colab** - button to run the tutorial directly in your browser (no setup - required). +In the next sections, we explain how to set up Jupyter and run the +tutorials interactively in two different ways: locally or online via +Google Colab. -!!! note +If you decide to run the tutorials locally, you need to download them +first. This can be done individually via the :material-download: +**Download Notebook** button available on each tutorial page, or all at +once using the command line, as shown below. - You can also download all Jupyter notebooks at once as a zip archive from the - [EasyDiffraction Releases](https://github.com/easyscience/diffraction-lib/releases/latest). +### Run Tutorials Locally with Pixi recommended { #running-with-pixi data-toc-label="Run Tutorials Locally with Pixi" } -### Run Tutorials Locally +- Navigate to your existing Pixi project, created as described in the + [Installing with Pixi](#installing-with-pixi) section. +- Add JupyterLab and the Pixi kernel for Jupyter: + ```txt + pixi add --pypi jupyterlab pixi-kernel + ``` +- Download all the EasyDiffraction tutorials to the `tutorials/` + directory: + ```txt + pixi run easydiffraction download-all-tutorials + ``` +- Start JupyterLab in the `tutorials/` directory to access the + notebooks: + ```txt + pixi run jupyter lab tutorials/ + ``` +- Your web browser should open automatically. Click on one of the + `*.ipynb` files and select the `Python (Pixi)` kernel to get started. -To run tutorials locally, install **Jupyter Notebook** or -**JupyterLab**. Here are the steps to follow in the case of **Jupyter -Notebook**: +### Classical Run Tutorials Locally - Install Jupyter Notebook and IPython kernel: - ```bash + ```txt pip install notebook ipykernel ``` -- Add the virtual environment as a Jupyter kernel - ```bash +- Add the virtual environment as a Jupyter kernel: + ```txt python -m ipykernel install --user --name=venv --display-name "EasyDiffraction Python kernel" ``` -- Download the EasyDiffraction tutorials from GitHub Releases: - ```bash - python -m easydiffraction fetch-tutorials +- Download all the EasyDiffraction tutorials to the `tutorials/` + directory: + ```txt + python -m easydiffraction download-all-tutorials ``` -- Launch the Jupyter Notebook server in the `examples/` directory: - ```bash +- Launch the Jupyter Notebook server (opens browser automatically at + `http://localhost:8888/`): + ```txt jupyter notebook tutorials/ ``` -- In your web browser, go to: - ```bash - http://localhost:8888/ - ``` - Open one of the `*.ipynb` files and select the `EasyDiffraction Python kernel` to get started. ### Run Tutorials via Google Colab **Google Colab** lets you run Jupyter Notebooks in the cloud without any -local installation. - -To use Google Colab: +local installation. This is the fastest way to start experimenting with +EasyDiffraction. - Ensure you have a **Google account**. - Go to the **[:material-school: Tutorials](../tutorials/index.md)** section. - Click the :google-colab: **Open in Google Colab** button on any tutorial. - -This is the fastest way to start experimenting with EasyDiffraction, -without setting up Python on your system. - -## Installing with Pixi alternative { #installing-with-pixi data-toc-label="Installing with Pixi" } - -[Pixi](https://pixi.sh) is a modern package and environment manager for -Python and Conda-compatible packages. It simplifies dependency -management, environment isolation, and reproducibility. - -The following simple steps provide an alternative setup method for -EasyDiffraction using Pixi, replacing the traditional virtual -environment approach. - - - -- Install Pixi by following the instructions on the - [official Pixi Installation Guide](https://pixi.sh/latest/installation). -- Create a dedicated directory for the EasyDiffraction and navigate into it: - ```bash - mkdir easydiffraction - cd easydiffraction - ``` -- Download the pixi configuration file for EasyDiffraction: - - === "curl" - ```bash - curl -LO https://raw.githubusercontent.com/easyscience/diffraction-lib/master/pixi.toml - ``` - === "wget" - ```bash - wget https://raw.githubusercontent.com/easyscience/diffraction-lib/master/pixi.toml - ``` - -- Create the environment defined in `pixi.toml` and install all necessary - dependencies: - ```bash - pixi install - ``` -- Fetch the EasyDiffraction tutorials to the `tutorials/` directory: - ```bash - pixi run easydiffraction fetch-tutorials - ``` -- Start JupyterLab in the `tutorials/` directory to access the notebooks: - ```bash - pixi run jupyter lab tutorials/ - ``` -- Your web browser should open automatically. Click on one of the `*.ipynb` - files and select the `Python (Pixi)` kernel to get started. - - diff --git a/docs/docs/introduction/index.md b/docs/docs/introduction/index.md index a2b42b59..ee1d2159 100644 --- a/docs/docs/introduction/index.md +++ b/docs/docs/introduction/index.md @@ -6,34 +6,30 @@ icon: material/information-slab-circle ## Description -**EasyDiffraction** is scientific software for calculating diffraction -patterns -based on structural models and refining model parameters against -experimental data. +**EasyDiffraction** is a software for calculating neutron powder +diffraction patterns based on a structural model and refining its +parameters against experimental data. -It is available as both a cross-platform desktop application and a -Python library. +**EasyDiffraction** is developed both as a Python library and as a +cross-platform desktop application. -This documentation covers the usage of the EasyDiffraction Python -library. -For the graphical user interface (GUI) version, refer to the -[GUI documentation](https://docs.easydiffraction.org/app). +Here, we focus on the Python library. For the graphical user interface +(GUI), please see the corresponding +[GUI resources](https://easyscience.github.io/diffraction-app). -## EasyScience - -EasyDiffraction is developed using the -[EasyScience framework](https://easyscience.software), which provides -tools for -building modular and flexible scientific libraries and applications. + ## License -EasyDiffraction is released under the +**EasyDiffraction** library is released under the [BSD 3-Clause License](https://raw.githubusercontent.com/easyscience/diffraction-lib/master/LICENSE). ## Releases -The latest version of the EasyDiffraction Python library is +The latest version of the **EasyDiffraction** library is [{{ vars.release_version }}](https://github.com/easyscience/diffraction-lib/releases/latest). For a complete list of new features, bug fixes, and improvements, see @@ -42,10 +38,10 @@ the ## Citation -If you use EasyDiffraction in your work, please cite the specific -version you used. +If you use **EasyDiffraction** library in your work, please cite the +specific version you used. -All official releases of the EasyDiffraction library are archived on +All official releases of the **EasyDiffraction** library are archived on Zenodo, each with a version-specific Digital Object Identifier (DOI). Citation details in various styles (e.g., APA, MLA) and formats (e.g., @@ -55,22 +51,24 @@ are available on the ## Contributing -We welcome contributions from the community! EasyDiffraction is intended -to be a community-driven, open-source project supported by a diverse -group of contributors. +We welcome contributions of any kind! + +**EasyDiffraction** is intended to be a community-driven, open-source +project supported by a diverse group of contributors. The project is maintained by the [European Spallation Source (ESS)](https://ess.eu). -To contribute, see our +If you would like to report a bug or request a new feature, please use +the +[GitHub Issue Tracker](https://github.com/easyscience/diffraction-lib/issues) +(A free GitHub account is required.) + +To contribute code, documentation, or tests, please see our [:material-account-plus: Contributing Guidelines](https://github.com/easyscience/diffraction-lib/blob/master/CONTRIBUTING.md) -on GitHub. +for detailed development instructions. ## Get in Touch -For general questions or feedback, contact us at +For general questions or feedback, please contact us at [support@easydiffraction.org](mailto:support@easydiffraction.org). - -To report bugs or request features, please use the -[GitHub Issue Tracker](https://github.com/easyscience/diffraction-lib/issues) -(free registration required). diff --git a/docs/docs/tutorials/ed-1.ipynb b/docs/docs/tutorials/ed-1.ipynb index 15b9f634..740e2c02 100644 --- a/docs/docs/tutorials/ed-1.ipynb +++ b/docs/docs/tutorials/ed-1.ipynb @@ -3,7 +3,7 @@ { "cell_type": "code", "execution_count": null, - "id": "9cc849f9", + "id": "b1e6b328", "metadata": { "tags": [ "hide-in-docs" @@ -156,6 +156,27 @@ "id": "12", "metadata": {}, "outputs": [], + "source": [ + "# Define aliases and constraints for refinement. This is necessary to\n", + "# properly refine the isotropic displacement parameters of La and Ba,\n", + "# which are correlated due to their shared Wyckoff position.\n", + "project.analysis.aliases.create(\n", + " label='biso_La',\n", + " param=project.structures['lbco'].atom_sites['La'].b_iso,\n", + ")\n", + "project.analysis.aliases.create(\n", + " label='biso_Ba',\n", + " param=project.structures['lbco'].atom_sites['Ba'].b_iso,\n", + ")\n", + "project.analysis.constraints.create(expression='biso_Ba = biso_La')" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "13", + "metadata": {}, + "outputs": [], "source": [ "# Start refinement. All parameters, which have standard uncertainties\n", "# in the input CIF files, are refined by default.\n", @@ -165,7 +186,7 @@ { "cell_type": "code", "execution_count": null, - "id": "13", + "id": "14", "metadata": {}, "outputs": [], "source": [ @@ -176,7 +197,7 @@ { "cell_type": "code", "execution_count": null, - "id": "14", + "id": "15", "metadata": {}, "outputs": [], "source": [ @@ -187,7 +208,7 @@ { "cell_type": "code", "execution_count": null, - "id": "15", + "id": "16", "metadata": {}, "outputs": [], "source": [ @@ -197,7 +218,7 @@ }, { "cell_type": "markdown", - "id": "16", + "id": "17", "metadata": {}, "source": [ "## Step 5: Perform Analysis (crysfml)" @@ -206,7 +227,7 @@ { "cell_type": "code", "execution_count": null, - "id": "17", + "id": "18", "metadata": {}, "outputs": [], "source": [ @@ -218,7 +239,7 @@ { "cell_type": "code", "execution_count": null, - "id": "18", + "id": "19", "metadata": {}, "outputs": [], "source": [ @@ -229,7 +250,7 @@ { "cell_type": "code", "execution_count": null, - "id": "19", + "id": "20", "metadata": {}, "outputs": [], "source": [ @@ -240,7 +261,7 @@ { "cell_type": "code", "execution_count": null, - "id": "20", + "id": "21", "metadata": {}, "outputs": [], "source": [ diff --git a/docs/docs/tutorials/ed-1.py b/docs/docs/tutorials/ed-1.py index 92b98ecd..d74c7eea 100644 --- a/docs/docs/tutorials/ed-1.py +++ b/docs/docs/tutorials/ed-1.py @@ -57,6 +57,20 @@ # %% [markdown] # ## Step 4: Perform Analysis (cryspy) +# %% +# Define aliases and constraints for refinement. This is necessary to +# properly refine the isotropic displacement parameters of La and Ba, +# which are correlated due to their shared Wyckoff position. +project.analysis.aliases.create( + label='biso_La', + param=project.structures['lbco'].atom_sites['La'].b_iso, +) +project.analysis.aliases.create( + label='biso_Ba', + param=project.structures['lbco'].atom_sites['Ba'].b_iso, +) +project.analysis.constraints.create(expression='biso_Ba = biso_La') + # %% # Start refinement. All parameters, which have standard uncertainties # in the input CIF files, are refined by default. diff --git a/docs/docs/tutorials/ed-10.ipynb b/docs/docs/tutorials/ed-10.ipynb index 67524351..46489bd6 100644 --- a/docs/docs/tutorials/ed-10.ipynb +++ b/docs/docs/tutorials/ed-10.ipynb @@ -3,7 +3,7 @@ { "cell_type": "code", "execution_count": null, - "id": "0bc5d509", + "id": "307e00fa", "metadata": { "tags": [ "hide-in-docs" diff --git a/docs/docs/tutorials/ed-11.ipynb b/docs/docs/tutorials/ed-11.ipynb index fe700f34..c0bbdd68 100644 --- a/docs/docs/tutorials/ed-11.ipynb +++ b/docs/docs/tutorials/ed-11.ipynb @@ -3,7 +3,7 @@ { "cell_type": "code", "execution_count": null, - "id": "0fe3d93b", + "id": "2ab104e6", "metadata": { "tags": [ "hide-in-docs" diff --git a/docs/docs/tutorials/ed-12.ipynb b/docs/docs/tutorials/ed-12.ipynb index a411eb82..d0913cae 100644 --- a/docs/docs/tutorials/ed-12.ipynb +++ b/docs/docs/tutorials/ed-12.ipynb @@ -3,7 +3,7 @@ { "cell_type": "code", "execution_count": null, - "id": "214aa62c", + "id": "f188a46a", "metadata": { "tags": [ "hide-in-docs" diff --git a/docs/docs/tutorials/ed-13.ipynb b/docs/docs/tutorials/ed-13.ipynb index 0fa6f966..549d9167 100644 --- a/docs/docs/tutorials/ed-13.ipynb +++ b/docs/docs/tutorials/ed-13.ipynb @@ -3,7 +3,7 @@ { "cell_type": "code", "execution_count": null, - "id": "4116731d", + "id": "be0cfa00", "metadata": { "tags": [ "hide-in-docs" @@ -969,7 +969,7 @@ "#### Show Free Parameters\n", "\n", "We can check which parameters are free to be refined by calling the\n", - "`show_free_params` method of the `analysis` object of the project." + "`free_params` method of the `analysis.display` object of the project." ] }, { @@ -2647,7 +2647,7 @@ ], "metadata": { "jupytext": { - "cell_metadata_filter": "tags,title,-all", + "cell_metadata_filter": "title,tags,-all", "main_language": "python", "notebook_metadata_filter": "-all" } diff --git a/docs/docs/tutorials/ed-14.ipynb b/docs/docs/tutorials/ed-14.ipynb index 6bf611fa..88c2077f 100644 --- a/docs/docs/tutorials/ed-14.ipynb +++ b/docs/docs/tutorials/ed-14.ipynb @@ -3,7 +3,7 @@ { "cell_type": "code", "execution_count": null, - "id": "bcfac86e", + "id": "f6f4b6a6", "metadata": { "tags": [ "hide-in-docs" diff --git a/docs/docs/tutorials/ed-15.ipynb b/docs/docs/tutorials/ed-15.ipynb index d4e97853..a6e4e7a0 100644 --- a/docs/docs/tutorials/ed-15.ipynb +++ b/docs/docs/tutorials/ed-15.ipynb @@ -3,7 +3,7 @@ { "cell_type": "code", "execution_count": null, - "id": "2e11e786", + "id": "ceaaff89", "metadata": { "tags": [ "hide-in-docs" diff --git a/docs/docs/tutorials/ed-16.ipynb b/docs/docs/tutorials/ed-16.ipynb index d3cd28f7..2fa0dd21 100644 --- a/docs/docs/tutorials/ed-16.ipynb +++ b/docs/docs/tutorials/ed-16.ipynb @@ -3,7 +3,7 @@ { "cell_type": "code", "execution_count": null, - "id": "2cfb7f0c", + "id": "c342992c", "metadata": { "tags": [ "hide-in-docs" @@ -613,21 +613,11 @@ "cell_type": "code", "execution_count": null, "id": "56", - "metadata": { - "lines_to_next_cell": 2 - }, + "metadata": {}, "outputs": [], "source": [ "project.plotter.plot_meas_vs_calc(expt_name='nomad', show_residual=False)" ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "57", - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { diff --git a/docs/docs/tutorials/ed-16.py b/docs/docs/tutorials/ed-16.py index 214dfe25..4c224f9f 100644 --- a/docs/docs/tutorials/ed-16.py +++ b/docs/docs/tutorials/ed-16.py @@ -254,6 +254,3 @@ # %% project.plotter.plot_meas_vs_calc(expt_name='nomad', show_residual=False) - - -# %% diff --git a/docs/docs/tutorials/ed-17.ipynb b/docs/docs/tutorials/ed-17.ipynb index 189f93fe..3844add8 100644 --- a/docs/docs/tutorials/ed-17.ipynb +++ b/docs/docs/tutorials/ed-17.ipynb @@ -3,7 +3,7 @@ { "cell_type": "code", "execution_count": null, - "id": "9ec0f5a7", + "id": "47b804b0", "metadata": { "tags": [ "hide-in-docs" @@ -540,6 +540,24 @@ "cell_type": "markdown", "id": "41", "metadata": {}, + "source": [ + "#### Compare measured and calculated patterns for the first fit." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "42", + "metadata": {}, + "outputs": [], + "source": [ + "project.plotter.plot_meas_vs_calc(expt_name='d20', show_residual=True)" + ] + }, + { + "cell_type": "markdown", + "id": "43", + "metadata": {}, "source": [ "#### Run Sequential Fitting\n", "\n", @@ -550,7 +568,7 @@ { "cell_type": "code", "execution_count": null, - "id": "42", + "id": "44", "metadata": {}, "outputs": [], "source": [ @@ -559,7 +577,7 @@ }, { "cell_type": "markdown", - "id": "43", + "id": "45", "metadata": { "lines_to_next_cell": 2 }, @@ -571,7 +589,7 @@ { "cell_type": "code", "execution_count": null, - "id": "44", + "id": "46", "metadata": {}, "outputs": [], "source": [ @@ -585,7 +603,7 @@ }, { "cell_type": "markdown", - "id": "45", + "id": "47", "metadata": {}, "source": [ "Run the sequential fit over all data files in the scan directory." @@ -594,7 +612,7 @@ { "cell_type": "code", "execution_count": null, - "id": "46", + "id": "48", "metadata": {}, "outputs": [], "source": [ @@ -602,15 +620,36 @@ " data_dir=data_dir,\n", " extract_diffrn=extract_diffrn,\n", " max_workers='auto',\n", + " reverse=True,\n", ")" ] }, { "cell_type": "markdown", - "id": "47", + "id": "49", "metadata": {}, "source": [ "#### Replay a Dataset\n", + "\n", + "Apply fitted parameters from the first CSV row and plot the result." + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "50", + "metadata": {}, + "outputs": [], + "source": [ + "project.apply_params_from_csv(row_index=0)\n", + "project.plotter.plot_meas_vs_calc(expt_name='d20', show_residual=True)" + ] + }, + { + "cell_type": "markdown", + "id": "51", + "metadata": {}, + "source": [ "\n", "Apply fitted parameters from the last CSV row and plot the result." ] @@ -618,7 +657,7 @@ { "cell_type": "code", "execution_count": null, - "id": "48", + "id": "52", "metadata": {}, "outputs": [], "source": [ @@ -628,7 +667,7 @@ }, { "cell_type": "markdown", - "id": "49", + "id": "53", "metadata": {}, "source": [ "#### Plot Parameter Evolution\n", @@ -639,7 +678,7 @@ { "cell_type": "code", "execution_count": null, - "id": "50", + "id": "54", "metadata": {}, "outputs": [], "source": [ @@ -648,7 +687,7 @@ }, { "cell_type": "markdown", - "id": "51", + "id": "55", "metadata": {}, "source": [ "Plot unit cell parameters vs. temperature." @@ -657,7 +696,7 @@ { "cell_type": "code", "execution_count": null, - "id": "52", + "id": "56", "metadata": {}, "outputs": [], "source": [ @@ -668,7 +707,7 @@ }, { "cell_type": "markdown", - "id": "53", + "id": "57", "metadata": {}, "source": [ "Plot isotropic displacement parameters vs. temperature." @@ -677,7 +716,7 @@ { "cell_type": "code", "execution_count": null, - "id": "54", + "id": "58", "metadata": {}, "outputs": [], "source": [ @@ -690,7 +729,7 @@ }, { "cell_type": "markdown", - "id": "55", + "id": "59", "metadata": {}, "source": [ "Plot selected fractional coordinates vs. temperature." @@ -699,7 +738,7 @@ { "cell_type": "code", "execution_count": null, - "id": "56", + "id": "60", "metadata": {}, "outputs": [], "source": [ diff --git a/docs/docs/tutorials/ed-18.ipynb b/docs/docs/tutorials/ed-18.ipynb index 6285d966..082ab9ef 100644 --- a/docs/docs/tutorials/ed-18.ipynb +++ b/docs/docs/tutorials/ed-18.ipynb @@ -3,7 +3,7 @@ { "cell_type": "code", "execution_count": null, - "id": "2fec19b9", + "id": "15fcf6ce", "metadata": { "tags": [ "hide-in-docs" @@ -161,24 +161,6 @@ "source": [ "project.plotter.plot_meas_vs_calc(expt_name='hrpt', show_residual=True)" ] - }, - { - "cell_type": "markdown", - "id": "15", - "metadata": {}, - "source": [ - "## Save Project" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "16", - "metadata": {}, - "outputs": [], - "source": [ - "project.save()" - ] } ], "metadata": { diff --git a/docs/docs/tutorials/ed-18.py b/docs/docs/tutorials/ed-18.py index ee07a708..5b2c4b67 100644 --- a/docs/docs/tutorials/ed-18.py +++ b/docs/docs/tutorials/ed-18.py @@ -51,9 +51,3 @@ # %% project.plotter.plot_meas_vs_calc(expt_name='hrpt', show_residual=True) - -# %% [markdown] -# ## Save Project - -# %% -project.save() diff --git a/docs/docs/tutorials/ed-2.ipynb b/docs/docs/tutorials/ed-2.ipynb index 11105e3c..0357de4a 100644 --- a/docs/docs/tutorials/ed-2.ipynb +++ b/docs/docs/tutorials/ed-2.ipynb @@ -3,7 +3,7 @@ { "cell_type": "code", "execution_count": null, - "id": "657acf7d", + "id": "15c2d211", "metadata": { "tags": [ "hide-in-docs" diff --git a/docs/docs/tutorials/ed-3.ipynb b/docs/docs/tutorials/ed-3.ipynb index 5d501391..8eade20f 100644 --- a/docs/docs/tutorials/ed-3.ipynb +++ b/docs/docs/tutorials/ed-3.ipynb @@ -3,7 +3,7 @@ { "cell_type": "code", "execution_count": null, - "id": "b7a584f7", + "id": "7be48772", "metadata": { "tags": [ "hide-in-docs" diff --git a/docs/docs/tutorials/ed-4.ipynb b/docs/docs/tutorials/ed-4.ipynb index c1bf91b3..e331438e 100644 --- a/docs/docs/tutorials/ed-4.ipynb +++ b/docs/docs/tutorials/ed-4.ipynb @@ -3,7 +3,7 @@ { "cell_type": "code", "execution_count": null, - "id": "902026e1", + "id": "05436c40", "metadata": { "tags": [ "hide-in-docs" diff --git a/docs/docs/tutorials/ed-5.ipynb b/docs/docs/tutorials/ed-5.ipynb index 7fc07c61..8c524eaf 100644 --- a/docs/docs/tutorials/ed-5.ipynb +++ b/docs/docs/tutorials/ed-5.ipynb @@ -3,7 +3,7 @@ { "cell_type": "code", "execution_count": null, - "id": "3169869f", + "id": "8ce91035", "metadata": { "tags": [ "hide-in-docs" diff --git a/docs/docs/tutorials/ed-6.ipynb b/docs/docs/tutorials/ed-6.ipynb index 4da37be2..f1b7ad5d 100644 --- a/docs/docs/tutorials/ed-6.ipynb +++ b/docs/docs/tutorials/ed-6.ipynb @@ -3,7 +3,7 @@ { "cell_type": "code", "execution_count": null, - "id": "bd23b3c8", + "id": "e53f4485", "metadata": { "tags": [ "hide-in-docs" diff --git a/docs/docs/tutorials/ed-7.ipynb b/docs/docs/tutorials/ed-7.ipynb index 3979677e..57e2d726 100644 --- a/docs/docs/tutorials/ed-7.ipynb +++ b/docs/docs/tutorials/ed-7.ipynb @@ -3,7 +3,7 @@ { "cell_type": "code", "execution_count": null, - "id": "521c03c7", + "id": "788753a7", "metadata": { "tags": [ "hide-in-docs" diff --git a/docs/docs/tutorials/ed-8.ipynb b/docs/docs/tutorials/ed-8.ipynb index 9012becf..7b9cf378 100644 --- a/docs/docs/tutorials/ed-8.ipynb +++ b/docs/docs/tutorials/ed-8.ipynb @@ -3,7 +3,7 @@ { "cell_type": "code", "execution_count": null, - "id": "0cd7ade3", + "id": "9e6c622d", "metadata": { "tags": [ "hide-in-docs" diff --git a/docs/docs/tutorials/ed-9.ipynb b/docs/docs/tutorials/ed-9.ipynb index f49fc4e5..2de9787f 100644 --- a/docs/docs/tutorials/ed-9.ipynb +++ b/docs/docs/tutorials/ed-9.ipynb @@ -3,7 +3,7 @@ { "cell_type": "code", "execution_count": null, - "id": "bd91997f", + "id": "336ce5f0", "metadata": { "tags": [ "hide-in-docs" diff --git a/docs/docs/tutorials/index.md b/docs/docs/tutorials/index.md index 06a9c69e..914bb859 100644 --- a/docs/docs/tutorials/index.md +++ b/docs/docs/tutorials/index.md @@ -7,13 +7,13 @@ icon: material/school This section presents a collection of **Jupyter Notebook** tutorials that demonstrate how to use EasyDiffraction for various tasks. These tutorials serve as self-contained, step-by-step **guides** to help users -grasp the workflow of diffraction data analysis using EasyDiffraction. +grasp the workflow of data analysis using EasyDiffraction. Instructions on how to run the tutorials are provided in the [:material-cog-box: Installation & Setup](../installation-and-setup/index.md#how-to-run-tutorials) section of the documentation. -The tutorials are organized into the following categories. +The tutorials are organized into the following categories: ## Getting Started diff --git a/docs/docs/user-guide/index.md b/docs/docs/user-guide/index.md index 2ddc28b9..72978518 100644 --- a/docs/docs/user-guide/index.md +++ b/docs/docs/user-guide/index.md @@ -10,15 +10,15 @@ effectively. Here is a brief overview of the User Guide sections: -- [Glossary](glossary.md) – Defines common terms and labels used - throughout the documentation. -- [Concept](concept.md) – Introduces the overall idea behind diffraction - data processing and where EasyDiffraction fits. -- [Data Format](data-format.md) – Explains the Crystallographic - Information File (CIF) and how it's used in EasyDiffraction. -- [Parameters](parameters.md) – Describes how parameters are structured, - named, and accessed within the EasyDiffraction library. -- [First Steps](first-steps.md) – Shows how to begin using - EasyDiffraction in Python or Jupyter notebooks. -- [Analysis Workflow](analysis-workflow/index.md) – Breaks down the data - analysis pipeline into practical, sequential steps. +- [Glossary](#) – Defines common terms and labels used throughout the + documentation. +- [Concept](#) – Introduces the overall idea behind data analysis in + EasyDiffraction. +- [Data Format](#) – Explains the data structures and file formats used + by EasyDiffraction. +- [Parameters](#) – Describes how parameters are structured, named, and + accessed within the EasyDiffraction. +- [First Steps](#) – Shows how to begin using EasyDiffraction in Python + or Jupyter notebooks. +- [Analysis Workflow](#) – Breaks down the data analysis pipeline into + practical, sequential steps. diff --git a/docs/mkdocs.yml b/docs/mkdocs.yml index 5f2415c3..66265029 100644 --- a/docs/mkdocs.yml +++ b/docs/mkdocs.yml @@ -228,3 +228,5 @@ nav: - project: api-reference/project.md - summary: api-reference/summary.md - utils: api-reference/utils.md + - Command-Line Interface: + - Command-Line Interface: cli/index.md diff --git a/pixi.lock b/pixi.lock index 0282155e..15c4b18e 100644 --- a/pixi.lock +++ b/pixi.lock @@ -33,7 +33,7 @@ environments: - conda: https://conda.anaconda.org/conda-forge/linux-64/cffi-2.0.0-py314h4a8dc5f_1.conda - conda: https://conda.anaconda.org/conda-forge/noarch/charset-normalizer-3.4.7-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/comm-0.2.3-pyhe01879c_0.conda - - conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.3-py314hd8ed1ab_101.conda + - conda: https://conda.anaconda.org/conda-forge/noarch/cpython-3.14.4-py314hd8ed1ab_100.conda - conda: https://conda.anaconda.org/conda-forge/linux-64/debugpy-1.8.20-py314h42812f9_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/decorator-5.2.1-pyhd8ed1ab_0.conda - conda: https://conda.anaconda.org/conda-forge/noarch/defusedxml-0.7.1-pyhd8ed1ab_0.tar.bz2 @@ -104,13 +104,13 @@ environments: - 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- cpython 3.14.3.* + - cpython 3.14.4.* - python_abi * *_cp314 license: Python-2.0 purls: [] - size: 50062 - timestamp: 1770674497152 + size: 49806 + timestamp: 1775614307464 - conda: https://conda.anaconda.org/conda-forge/noarch/python-json-logger-2.0.7-pyhd8ed1ab_0.conda sha256: 4790787fe1f4e8da616edca4acf6a4f8ed4e7c6967aa31b920208fc8f95efcca md5: a61bf9ec79426938ff785eb69dbb1960 diff --git a/src/easydiffraction/__main__.py b/src/easydiffraction/__main__.py index a15b66ca..f0b5ab12 100644 --- a/src/easydiffraction/__main__.py +++ b/src/easydiffraction/__main__.py @@ -82,5 +82,26 @@ def download_all_tutorials( ed.download_all_tutorials(destination=destination, overwrite=overwrite) +@app.command('fit') +def fit( + project_dir: str = typer.Argument( + ..., + help='Path to the project directory (must contain project.cif).', + ), + dry: bool = typer.Option( + False, + '--dry', + help='Run fitting without saving results back to the project directory.', + ), +) -> None: + """Fit a saved project: easydiffraction fit PROJECT_DIR [--dry].""" + project = ed.Project.load(project_dir) + if dry: + project.info._path = None + project.analysis.fit() + project.analysis.display.fit_results() + project.summary.show_report() + + if __name__ == '__main__': app() diff --git a/src/easydiffraction/analysis/calculators/crysfml.py b/src/easydiffraction/analysis/calculators/crysfml.py index 3454ce28..aaaa537e 100644 --- a/src/easydiffraction/analysis/calculators/crysfml.py +++ b/src/easydiffraction/analysis/calculators/crysfml.py @@ -98,7 +98,7 @@ def calculate_pattern( except KeyError: print('[CrysfmlCalculator] Error: No calculated data') y = [] - return y + return np.asarray(y) def _adjust_pattern_length( # noqa: PLR6301 self, @@ -122,8 +122,14 @@ def _adjust_pattern_length( # noqa: PLR6301 """ # TODO: Check the origin of this discrepancy coming from # PyCrysFML + # Safety guard: with the correct step formula (max-min)/(N-1+ε), + # pycrysfml should return exactly target_length points. Truncate + # if over-length; pad with the last value if under-length. if len(pattern) > target_length: return pattern[:target_length] + if len(pattern) < target_length: + pad = target_length - len(pattern) + return list(pattern) + [pattern[-1]] * pad return pattern def _crysfml_dict( @@ -243,7 +249,13 @@ def _convert_experiment_to_dict( # noqa: PLR6301 else 0.0, '_pd_meas_2theta_range_min': twotheta_min, '_pd_meas_2theta_range_max': twotheta_max, - '_pd_meas_2theta_range_inc': (twotheta_max - twotheta_min) / len(x_data), + # TODO: Check the origin of this discrepancy coming from + # PyCrysFML + # Divide by (N-1+ε) instead of (N-1) so that pycrysfml's + # internal floor((max-min)/step) is robustly N-1 despite + # floating-point rounding, producing exactly N points. + '_pd_meas_2theta_range_inc': (twotheta_max - twotheta_min) + / (len(x_data) - 1 + 1e-9), } } diff --git a/tests/integration/fitting/test_switch-calculator.py b/tests/integration/fitting/test_switch-calculator.py index 4ce7c18a..a195ac18 100644 --- a/tests/integration/fitting/test_switch-calculator.py +++ b/tests/integration/fitting/test_switch-calculator.py @@ -6,7 +6,6 @@ import pytest from numpy.testing import assert_almost_equal - TEMP_DIR = tempfile.gettempdir() diff --git a/tests/unit/easydiffraction/test___main__.py b/tests/unit/easydiffraction/test___main__.py index 76ba7cec..88f08198 100644 --- a/tests/unit/easydiffraction/test___main__.py +++ b/tests/unit/easydiffraction/test___main__.py @@ -64,3 +64,90 @@ def test_cli_subcommands_call_utils(monkeypatch): assert res2.exit_code == 0 assert res3.exit_code == 0 assert logs == ['LIST', 'DOWNLOAD_ALL', 'DOWNLOAD_1'] + + +def test_cli_fit_loads_and_fits(monkeypatch, tmp_path): + import easydiffraction.__main__ as main_mod + from easydiffraction.project.project import Project + + calls = [] + + class FakeInfo: + _path = '/some/path' + + class FakeProject: + info = FakeInfo() + + class _analysis: + @staticmethod + def fit(): + calls.append('FIT') + + class display: + @staticmethod + def fit_results(): + calls.append('DISPLAY') + + analysis = _analysis() + + class _summary: + @staticmethod + def show_report(): + calls.append('SUMMARY') + + summary = _summary() + + fake_project = FakeProject() + + # Create a minimal project directory so load doesn't fail on path check + proj_dir = tmp_path / 'proj' + proj_dir.mkdir() + (proj_dir / 'project.cif').write_text('_project.id test\n') + + monkeypatch.setattr(Project, 'load', staticmethod(lambda dir_path: fake_project)) + + result = runner.invoke(main_mod.app, ['fit', str(proj_dir)]) + assert result.exit_code == 0 + assert calls == ['FIT', 'DISPLAY', 'SUMMARY'] + + +def test_cli_fit_dry_clears_path(monkeypatch, tmp_path): + import easydiffraction.__main__ as main_mod + from easydiffraction.project.project import Project + + class FakeInfo: + _path = '/some/path' + + class FakeProject: + info = FakeInfo() + + class _analysis: + @staticmethod + def fit(): + pass + + class display: + @staticmethod + def fit_results(): + pass + + analysis = _analysis() + + class _summary: + @staticmethod + def show_report(): + pass + + summary = _summary() + + fake_project = FakeProject() + + proj_dir = tmp_path / 'proj' + proj_dir.mkdir() + (proj_dir / 'project.cif').write_text('_project.id test\n') + + monkeypatch.setattr(Project, 'load', staticmethod(lambda dir_path: fake_project)) + + result = runner.invoke(main_mod.app, ['fit', '--dry', str(proj_dir)]) + assert result.exit_code == 0 + assert fake_project.info._path is None diff --git a/tmp/cli/lbco_hrpt/analysis/analysis.cif b/tmp/cli/lbco_hrpt/analysis/analysis.cif new file mode 100644 index 00000000..6df5451c --- /dev/null +++ b/tmp/cli/lbco_hrpt/analysis/analysis.cif @@ -0,0 +1,15 @@ +_analysis.fitting_engine lmfit +_analysis.fit_mode single + +loop_ +_alias.label +_alias.param_unique_name +biso_La lbco.atom_site.La.b_iso +biso_Ba lbco.atom_site.Ba.b_iso +occ_La lbco.atom_site.La.occupancy +occ_Ba lbco.atom_site.Ba.occupancy + +loop_ +_constraint.expression +"biso_Ba = biso_La" +"occ_Ba = 1 - occ_La" diff --git a/tmp/cli/lbco_hrpt/experiments/hrpt.cif b/tmp/cli/lbco_hrpt/experiments/hrpt.cif new file mode 100644 index 00000000..9af5e82c --- /dev/null +++ b/tmp/cli/lbco_hrpt/experiments/hrpt.cif @@ -0,0 +1,3156 @@ +data_hrpt + +_expt_type.sample_form powder +_expt_type.beam_mode "constant wavelength" +_expt_type.radiation_probe neutron +_expt_type.scattering_type bragg + +_diffrn.ambient_temperature 300 +_diffrn.ambient_pressure ? +_diffrn.ambient_magnetic_field ? +_diffrn.ambient_electric_field ? + +_peak.broad_gauss_u 0.10(1) +_peak.broad_gauss_v -0.10(1) +_peak.broad_gauss_w 0.10(1) +_peak.broad_lorentz_x 0.0 +_peak.broad_lorentz_y 0.0(1) + +_instr.wavelength 1.494 +_instr.2theta_offset 0.0(1) + +loop_ +_pd_phase_block.id +_pd_phase_block.scale +lbco 10.0(1) + +loop_ +_excluded_region.id +_excluded_region.start +_excluded_region.end +1 0.0 10.2 +2 164.7 180.0 + + +loop_ +_pd_background.id 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0.00000000 0.00000000 excl +164.80000000 3097 0.00000000 168.00000000 30.90000000 0.00000000 0.00000000 excl +164.85000000 3098 0.00000000 109.00000000 41.20000000 0.00000000 0.00000000 excl diff --git a/tmp/cli/lbco_hrpt/project.cif b/tmp/cli/lbco_hrpt/project.cif new file mode 100644 index 00000000..b03ee765 --- /dev/null +++ b/tmp/cli/lbco_hrpt/project.cif @@ -0,0 +1,5 @@ +_project.id lbco@hrpt +_project.title 'Quick Start: LBCO Load Project' +_project.description 'Most minimal example: load a saved project from a directory and run Rietveld refinement of La0.5Ba0.5CoO3' +_project.created '03 Apr 2026 22:22:57' +_project.last_modified '03 Apr 2026 22:22:57' diff --git a/tmp/cli/lbco_hrpt/structures/lbco.cif b/tmp/cli/lbco_hrpt/structures/lbco.cif new file mode 100644 index 00000000..5e11bb81 --- /dev/null +++ b/tmp/cli/lbco_hrpt/structures/lbco.cif @@ -0,0 +1,26 @@ +data_lbco + +_cell.length_a 3.88(1) +_cell.length_b 3.88 +_cell.length_c 3.88 +_cell.angle_alpha 90.0 +_cell.angle_beta 90.0 +_cell.angle_gamma 90.0 + +_space_group.name_H-M_alt "P m -3 m" +_space_group.IT_coordinate_system_code 1 + +loop_ +_atom_site.label +_atom_site.type_symbol +_atom_site.fract_x +_atom_site.fract_y +_atom_site.fract_z +_atom_site.Wyckoff_letter +_atom_site.occupancy +_atom_site.B_iso_or_equiv +_atom_site.adp_type +La La 0.00000000 0.00000000 0.00000000 a 0.5(1) 1.0(1) Biso +Ba Ba 0.00000000 0.00000000 0.00000000 a 0.5 1.0 Biso +Co Co 0.50000000 0.50000000 0.50000000 b 1.0 1.0(1) Biso +O O 0.00000000 0.50000000 0.50000000 c 1.0 1.0(1) Biso diff --git a/tmp/cli/lbco_hrpt/summary.cif b/tmp/cli/lbco_hrpt/summary.cif new file mode 100644 index 00000000..ccc4df03 --- /dev/null +++ b/tmp/cli/lbco_hrpt/summary.cif @@ -0,0 +1 @@ +To be added... \ No newline at end of file