Basic GPAW support

.github/workflows/claude-code-review.yml

@@ -0,0 +1,44 @@
+name: Claude Code Review
+
+on:
+  pull_request:
+    types: [opened, synchronize, ready_for_review, reopened]
+    # Optional: Only run on specific file changes
+    # paths:
+    #   - "src/**/*.ts"
+    #   - "src/**/*.tsx"
+    #   - "src/**/*.js"
+    #   - "src/**/*.jsx"
+
+jobs:
+  claude-review:
+    # Optional: Filter by PR author
+    # if: |
+    #   github.event.pull_request.user.login == 'external-contributor' ||
+    #   github.event.pull_request.user.login == 'new-developer' ||
+    #   github.event.pull_request.author_association == 'FIRST_TIME_CONTRIBUTOR'
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: read
+      issues: read
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Run Claude Code Review
+        id: claude-review
+        uses: anthropics/claude-code-action@v1
+        with:
+          claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+          plugin_marketplaces: 'https://github.com/anthropics/claude-code.git'
+          plugins: 'code-review@claude-code-plugins'
+          prompt: '/code-review:code-review ${{ github.repository }}/pull/${{ github.event.pull_request.number }}'
+          # See https://github.com/anthropics/claude-code-action/blob/main/docs/usage.md
+          # or https://code.claude.com/docs/en/cli-reference for available options
+

.github/workflows/claude.yml

@@ -0,0 +1,50 @@
+name: Claude Code
+
+on:
+  issue_comment:
+    types: [created]
+  pull_request_review_comment:
+    types: [created]
+  issues:
+    types: [opened, assigned]
+  pull_request_review:
+    types: [submitted]
+
+jobs:
+  claude:
+    if: |
+      (github.event_name == 'issue_comment' && contains(github.event.comment.body, '@claude')) ||
+      (github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '@claude')) ||
+      (github.event_name == 'pull_request_review' && contains(github.event.review.body, '@claude')) ||
+      (github.event_name == 'issues' && (contains(github.event.issue.body, '@claude') || contains(github.event.issue.title, '@claude')))
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      pull-requests: read
+      issues: read
+      id-token: write
+      actions: read # Required for Claude to read CI results on PRs
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 1
+
+      - name: Run Claude Code
+        id: claude
+        uses: anthropics/claude-code-action@v1
+        with:
+          claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
+
+          # This is an optional setting that allows Claude to read CI results on PRs
+          additional_permissions: |
+            actions: read
+
+          # Optional: Give a custom prompt to Claude. If this is not specified, Claude will perform the instructions specified in the comment that tagged it.
+          # prompt: 'Update the pull request description to include a summary of changes.'
+
+          # Optional: Add claude_args to customize behavior and configuration
+          # See https://github.com/anthropics/claude-code-action/blob/main/docs/usage.md
+          # or https://code.claude.com/docs/en/cli-reference for available options
+          # claude_args: '--allowed-tools Bash(gh pr *)'
+

.pre-commit-config.yaml

@@ -27,7 +27,8 @@ repos:
     rev: v2.1.0
     hooks:
       - id: mypy
-        <<: *skip_docs
+        # type-check the ``doped`` package + test modules directly under ``tests/``:
+        files: ^(doped/|tests/[^/]+\.py$)
         additional_dependencies:
           - numpy
           - pandas

docs/GPAW_Support.rst

@@ -0,0 +1,109 @@
+GPAW Support
+====================================
+
+``doped`` provides comprehensive support for defect calculations using `GPAW <https://wiki.fysik.dtu.dk/gpaw/>`_, 
+a Density Functional Theory (DFT) Python code based on the projector-augmented wave (PAW) method. 
+This support includes automated input generation, parsing of calculation results, and 
+integration with the full ``doped`` defect analysis workflow.
+
+Installation & Requirements
+---------------------------
+
+To use the GPAW interface, you must have GPAW installed in your Python environment:
+
+.. code-block:: bash
+
+    pip install gpaw
+
+For the Kumagai (eFNV) charge correction, ``pydefect`` is also required:
+
+.. code-block:: bash
+
+    pip install pydefect
+
+Workflow Overview
+-----------------
+
+The workflow for GPAW defect calculations follows the standard ``doped`` logic:
+
+1.  **Generation**: Generate defect structures using ``DefectsGenerator``.
+2.  **Input Preparation**: Write GPAW Python scripts and structure files using ``GPAWDefectRelaxSet``.
+3.  **Execution**: Run the calculations using GPAW (typically via ``mpirun``).
+4.  **Parsing**: Parse the results (``.gpw(.gz)`` files) using ``GPAWDefectsParser``.
+5.  **Analysis**: Perform thermodynamic analysis and plotting.
+
+Input Generation
+----------------
+
+The ``GPAWDefectRelaxSet`` class is used to generate the necessary files for a GPAW relaxation. 
+It produces a ``relax.py`` script and a ``structure.cif`` file.
+
+.. code-block:: python
+
+    from doped.gpaw import GPAWDefectRelaxSet
+    from pymatgen.core.structure import Structure
+
+    # Load your supercell structure
+    structure = Structure.from_file("POSCAR")
+
+    # Define GPAW settings
+    gpaw_settings = {
+        "mode": {"name": "pw", "ecut": 400},
+        "xc": "PBE",
+        "kpts": {"size": (2, 2, 2), "gamma": True},
+    }
+
+    # Initialize the relax set for a +1 charge state
+    relax_set = GPAWDefectRelaxSet(structure, charge_state=1, gpaw_settings=gpaw_settings)
+
+    # Write files to a directory
+    relax_set.write_input("calculation_folder")
+
+Parsing Results
+---------------
+
+Once calculations are complete, ``doped`` can parse the resulting ``relaxed.gpw(.gz)`` files.
+The ``GPAWDefectsParser`` can handle multiple defect folders at once.
+
+.. code-block:: python
+
+    from doped.gpaw import GPAWDefectsParser
+
+    # Initialize the parser
+    # output_path: directory containing defect folders
+    # bulk_path: directory containing the bulk reference calculation
+    parser = GPAWDefectsParser(
+        output_path=".", 
+        bulk_path="calculation_bulk",
+        dielectric=10.0  # Required for charge corrections
+    )
+
+    # Parse all defects
+    defect_dict = parser.parse_all()
+
+Finite-Size Corrections
+-----------------------
+
+GPAW calculations of charged defects require finite-size corrections to account for periodic image interactions. ``doped`` supports both the **Kumagai (eFNV)** correction (highly recommended) and the standard **Freysoldt-Neugebauer-Van de Walle (FNV)** correction for GPAW.
+
+Anisotropic Systems (2D/1D)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+For anisotropic systems like 2D materials (e.g., graphene, MoS2), the default sampling radius 
+calculation in standard tools often fails by setting a radius that encompasses the entire cell. 
+``doped`` implements an improved radius calculation:
+
+- It automatically determines the optimal ``defect_region_radius`` based on the inscribed 
+  sphere of the supercell (half the shortest distance between parallel planes).
+- It includes safety checks to prevent errors when the sampling region is small or empty.
+
+Detailed API
+------------
+
+For more specific information on classes and functions, see the :ref:`doped.gpaw module` documentation.
+
+Example Script
+--------------
+
+An end-to-end example of generating and parsing GPAW defects can be found in the 
+``examples/Graphene_with_GPAW`` directory of the ``doped`` repository.

docs/GPAW_tutorial.ipynb

@@ -0,0 +1 @@
+../examples/GPAW_tutorial.ipynb

docs/Tutorials.rst

@@ -42,3 +42,4 @@ tutorials:
    GGA_workflow_tutorial
    CCD_NEB_tutorial
    stenciling_tutorial
+   GPAW_tutorial

docs/doped.gpaw.rst

@@ -0,0 +1,6 @@
+doped.gpaw module
+=================================================
+.. automodule:: doped.gpaw
+   :members:
+   :undoc-members:
+   :show-inheritance:

docs/doped.rst

@@ -14,6 +14,7 @@ Modules
    doped.core
    doped.corrections
    doped.generation
+   doped.gpaw
    doped.init
    doped.thermodynamics
    doped.utils

docs/index.rst

@@ -266,6 +266,7 @@ Thanks to `Chaoqun Zhang <https://github.com/Warlocat>`__ for uploading the
 
    Installation
    Python API <doped>
+   GPAW_Support
    Tutorials
    Tips
    Code Overview & Workflow Diagrams <https://deepwiki.com/SMTG-Bham/doped>

doped/core.py

@@ -631,7 +631,11 @@ def get_kumagai_correction(
         )
 
         # correction energy error can be estimated from standard error of the mean:
-        correction_error = sem(sampled_pot_diff_array) * abs(self.charge_state)
+        if sampled_pot_diff_array.size > 0:
+            correction_error = sem(sampled_pot_diff_array) * abs(self.charge_state)
+        else:
+            correction_error = np.nan
+
         self.corrections_metadata.update({"kumagai_charge_correction_error": correction_error})
         return self._check_correction_error_and_return_output(
             efnv_correction_output,

doped/corrections.py

@@ -62,7 +62,6 @@
     get_core_potentials_from_outcar,
     get_locpot,
     get_site_mapping_indices,
-    get_wigner_seitz_radius,
 )
 from doped.utils.plotting import doped_plot_style, format_defect_name
 
@@ -464,6 +463,7 @@ def doped_make_efnv_correction(
         dielectric_tensor: np.ndarray,
         defect_coords: np.ndarray | list,
         defect_region_radius: float | None = None,
+        radius_method: str = "min",
         accuracy: float = defaults.ewald_accuracy,
         unit_conversion: float = 180.95128169876497,
         excluded_indices: list | None = None,
@@ -522,7 +522,19 @@ def ewald_rec(self, coord) -> float:
         point_charge_correction = -ewald.lattice_energy * charge**2 if charge else 0.0
 
         if defect_region_radius is None:
-            defect_region_radius = get_wigner_seitz_radius(lattice)
+            # 0.5 * np.pi / norm evaluates to d/4 (half the inscribed sphere radius)
+            distances = [
+                0.5 * np.pi / np.linalg.norm(lattice.reciprocal_lattice.matrix[i]) for i in range(3)
+            ]
+
+            if radius_method.lower() == "min":
+                defect_region_radius = np.min(distances)
+            elif radius_method.lower() == "max":
+                defect_region_radius = np.max(distances)
+            elif radius_method.lower() == "average":
+                defect_region_radius = np.mean(distances)
+            else:
+                raise ValueError("radius_method must be 'min', 'max', or 'average'")
 
         for site, rel_coord in zip(sites, rel_coords, strict=False):
             if site.distance > defect_region_radius:
@@ -609,6 +621,7 @@ def ewald_rec(self, coord) -> float:
             "defect_coords", _get_defect_supercell_frac_coords(defect_entry)
         ),  # _relaxed_ defect coords (except for vacancies)
         defect_region_radius=defect_region_radius,
+        radius_method=kwargs.pop("radius_method", "min"),
         excluded_indices=excluded_indices,
         **kwargs,
     )