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‎.buildinfo‎

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# Sphinx build info version 1
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# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
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config: 3123ef6225f14b74f3288a3e30285e4d
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tags: 645f666f9bcd5a90fca523b33c5a78b7

‎.nojekyll‎

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‎_downloads/34c9cd97c2a90b2d475474c4bc8ee0d9/runmacro_example.zip‎

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‎_sources/getting-started.rst.txt‎

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:tocdepth: -1
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.. index:: getting-started
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.. _getting-started:
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================
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Getting started
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================
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``diffpy.apps`` provides user applications to help with tasks using
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diffpy packages. This page contains the instructions for all applications
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available, including:
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- :ref:`runmacro`
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- :ref:`agentify`
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.. _runmacro:
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Use ``runmacro`` to start refinement with a macro file
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------------------------------------------------------
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The ``runmacro`` application allows users to execute macros written in the
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diffpy macro language.
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.. code-block:: bash
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diffpy.app runmacro <macro_file.dp-in>
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To follow the example,
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1. download the example files from :download:`here <../example/runmacro_example.zip>`
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2. extract the downloaded files and navigate to the extracted directory
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.. code-block:: bash
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mv /path/to/runmacro runmacro_example.zip working_directory
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cd working_directory
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unzip runmacro_example.zip
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3. run the macro using the ``runmacro`` application
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.. code-block:: bash
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diffpy.app runmacro example_macro.dp-in
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How to write macro
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~~~~~~~~~~~~~~~~~~
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Let's still use the Ni example created earlier, but this time we will
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write the macro file from scratch.
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1. Prepare the structure and profile file you want to work with.
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.. note::
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The structure file is a ``.cif`` file representing the atomic arrangement in
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your sample, and the profile file is a ``.gr`` file containing the
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experimental data.
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Start the macro file with the following two lines:
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.. code-block:: text
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load structure G1 from "path/to/structure.cif"
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load profile exp_ni from "path/to/profile.gr"
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``G1`` and ``exp_ni`` are the identifiers used in the macro to refer to the
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structure and profile files, respectively. Quotes ``""`` are must to specify
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the file paths.
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2. (Optional) Declare the space group of the structure.
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.. code-block:: text
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set G1 spacegroup as Fm-3m
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``G1`` is the identifier for the structure file loaded earlier. Space group
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symmetry ``Fm-3m`` is preserved during the refinement. You can also set
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it to be ``auto`` to use the one automatically parsed from the structure file.
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But if space group is not provided, nor can it be determined from the structure
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file, it will be considered as ``P1`` space group.
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3. (Optional) Set the calculation parameters for the refinement.
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.. code-block:: text
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set exp_ni calculation_range as 0.5 20.0 0.01 # r_min, r_max, r_step
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set exp_ni q_range as 0.5 20.0 # q_min, q_max
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``exp_ni`` is the identifier for the profile file loaded earlier.
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``calculation_range`` specifies the range and step size for the calculation,
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while ``q_range`` specifies the range of Q values to be used in the refinement.
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If calculation parameters are not set, it will use the ones
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that are defined in the profile file.
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4. Create the refinement equation.
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.. code-block:: text
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create equation variables s0
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set equation as "G1*s0"
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``G1`` is the identifier for the structure file loaded earlier. In the
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equation, it represents the PDF data generated from the structure `G1`.
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``s0`` is created to count for the scaling factor.
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5. Store the results.
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.. code-block:: text
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save to "output_results.json"
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The results of the refinement will be saved to a file
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named ``output_results.json``.
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6. List variables to be refined.
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.. code-block:: text
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variables:
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---
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- G1.a: 3.52
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- s0: 0.4
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- G1.Uiso_0: 0.005
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- G1.delta2: 2
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- qdamp: 0.04
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- qbroad: 0.02
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---
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Only variables listed in this section will be refined during the
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execution of the macro, and the variables will also be refined in that order.
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Variables with initial values specified here will be used as the
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starting point for the refinement.
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.. note::
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The naming of variables follows the format
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``structure_identifier.parameter``,
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``profile_parameter``, or
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``equation_parameter``.
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For parameters belonging to a specific atom in the parameter,
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the naming follows the format ``structure_identifier.parameter_atomindex``.
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e.g. ``G1.Uiso_0`` here refers to the Uiso parameter of the first atom in
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the structure ``G1``.
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For constrained parameters, it will use the first parameter in the
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constraint. e.g. Here, lattice parameter ``a=b=c``,
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and ``Usio_0=Uiso_i, i=1,2,3``, ``a`` and ``Uiso_0`` are used as the
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reference variables.
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.. _agentify:
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Use ``agentify`` to deploy agent skills ``diffpy.cmi``
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------------------------------------------------------
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The ``agentify`` application allows users to deploy agentic skills in the
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local environment. To use this application, run:
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.. code-block:: bash
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diffpy.app agentify
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``claude`` and ``codex`` agent skills are supported, and ``claude`` is used
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by default. To specify the agent skill, use the ``--agent`` option:
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.. code-block:: bash
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diffpy.app agentify --agent codex
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To deploy the agentic skill to the system directory, use the ``--system`` flag:
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.. code-block:: bash
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diffpy.app agentify --system
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To update the existing ``diffpy.cmi`` agentic skill, use the ``--update`` flag:
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.. code-block:: bash
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diffpy.app agentify --update

‎_sources/index.rst.txt‎

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#######
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|title|
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#######
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.. |title| replace:: diffpy.apps documentation
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``diffpy.apps`` - User applications to help with tasks using diffpy packages
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| Software version |release|
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| Last updated |today|.
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===============
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Getting started
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===============
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Welcome to the ``diffpy.apps`` documentation!
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To get started, please visit the :ref:`Getting started <getting-started>` page.
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=======
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Authors
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=======
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``diffpy.apps`` is developed by Yuchen Xiao, Simon Billinge and members of the Billinge group. This project is maintained by Yuchen Xiao and Simon Billinge. For a detailed list of contributors see
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https://github.com/diffpy/diffpy.apps/graphs/contributors.
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============
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Installation
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============
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See the `README <https://github.com/diffpy/diffpy.apps#installation>`_
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file included with the distribution.
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================
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Acknowledgements
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================
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``diffpy.apps`` is built and maintained with `scikit-package <https://scikit-package.github.io/scikit-package/>`_.
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=================
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Table of contents
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=================
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.. toctree::
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:maxdepth: 2
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getting-started
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release
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license
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=======
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Indices
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=======
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* :ref:`genindex`
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* :ref:`search`

‎_sources/license.rst.txt‎

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:tocdepth: -1
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.. index:: license
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License
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#######
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OPEN SOURCE LICENSE AGREEMENT
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=============================
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BSD 3-Clause License
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Copyright (c) 2026, diffpy.apps contributors.
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All Rights Reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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1. Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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2. Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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3. Neither the name of the copyright holder nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

‎_sources/release.rst.txt‎

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:tocdepth: -1
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.. index:: release notes
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.. include:: ../../CHANGELOG.rst

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