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SMTG-Bham · Aug 15, 2024 · 697b2b0 · 697b2b0
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diff --git a/docs/Tips.rst b/docs/Tips.rst
@@ -337,6 +337,15 @@ PHS on the transition level diagram with a clear circle is shown on the right.
  It is recommended to additionally manually check the real-space charge density (i.e. ``PARCHG``) of
  the defect state to confirm the identification of a PHS.
 
+.. note::
+
+ As mentioned above, the eigenvalue analysis functions use code from ``pydefect``, so please cite the
+ ``pydefect`` paper if using these analyses in your work:
+
+ "Insights into oxygen vacancies from high-throughput first-principles calculations"
+ Yu Kumagai, Naoki Tsunoda, Akira Takahashi, and Fumiyasu Oba
+ Phys. Rev. Materials 5, 123803 (2021) -- 10.1103/PhysRevMaterials.5.123803
+
 Spin Polarisation
 -----------------
 Proper accounting of spin polarisation and multiplicity is crucial for accurate defect calculations and

diff --git a/doped/core.py b/doped/core.py
@@ -438,8 +438,6 @@ def get_kumagai_correction(
 
  The correction is added to the ``defect_entry.corrections`` dictionary
  (to be used in following formation energy calculations).
- If this correction is used, please cite the Kumagai & Oba paper:
- 10.1103/PhysRevB.89.195205
 
  Typically for reasonably well-converged supercell sizes, the default
  ``defect_region_radius`` works perfectly well. However, for certain materials
@@ -457,6 +455,13 @@ def get_kumagai_correction(
  This is expected to be a lower bound estimate of the true charge correction
  error.
 
+ If this correction is used, please cite the Kumagai & Oba (eFNV) paper:
+ 10.1103/PhysRevB.89.195205
+ and the ``pydefect`` paper:
+ "Insights into oxygen vacancies from high-throughput first-principles calculations"
+ Yu Kumagai, Naoki Tsunoda, Akira Takahashi, and Fumiyasu Oba
+ Phys. Rev. Materials 5, 123803 (2021) -- 10.1103/PhysRevMaterials.5.123803
+
  Args:
  dielectric (float or int or 3x1 matrix or 3x3 matrix):
  Total dielectric constant of the host compound (including both
@@ -730,8 +735,10 @@ def get_eigenvalue_analysis(
  files (slightly slower but more accurate), or failing that from ``PROCAR(.gz)``
  files if present.
 
- This function uses code from ``pydefect``:
- Citation: https://doi.org/10.1103/PhysRevMaterials.5.123803.
+ This function uses code from ``pydefect``, so please cite the ``pydefect`` paper:
+ "Insights into oxygen vacancies from high-throughput first-principles calculations"
+ Yu Kumagai, Naoki Tsunoda, Akira Takahashi, and Fumiyasu Oba
+ Phys. Rev. Materials 5, 123803 (2021) -- 10.1103/PhysRevMaterials.5.123803
 
  Args:
  plot (bool):

diff --git a/doped/corrections.py b/doped/corrections.py
@@ -329,8 +329,12 @@ def get_kumagai_correction(
 
  This function `does not` add the correction to ``defect_entry.corrections``
  (but the defect_entry.get_kumagai_correction method does).
- If this correction is used, please cite the Kumagai & Oba paper:
+ If this correction is used, please cite the Kumagai & Oba (eFNV) paper:
  10.1103/PhysRevB.89.195205
+ and the ``pydefect`` paper:
+ "Insights into oxygen vacancies from high-throughput first-principles calculations"
+ Yu Kumagai, Naoki Tsunoda, Akira Takahashi, and Fumiyasu Oba
+ Phys. Rev. Materials 5, 123803 (2021) -- 10.1103/PhysRevMaterials.5.123803
 
  Typically for reasonably well-converged supercell sizes, the default
  ``defect_region_radius`` works perfectly well. However, for certain materials

diff --git a/doped/utils/eigenvalues.py b/doped/utils/eigenvalues.py
@@ -416,8 +416,10 @@ def get_eigenvalue_analysis(
  files (slightly slower but more accurate), or failing that from ``PROCAR(.gz)``
  files if present.
 
- This function uses code from ``pydefect``:
- Citation: https://doi.org/10.1103/PhysRevMaterials.5.123803.
+ This function uses code from ``pydefect``, so please cite the ``pydefect`` paper:
+ "Insights into oxygen vacancies from high-throughput first-principles calculations"
+ Yu Kumagai, Naoki Tsunoda, Akira Takahashi, and Fumiyasu Oba
+ Phys. Rev. Materials 5, 123803 (2021) -- 10.1103/PhysRevMaterials.5.123803
 
  Args:
  defect_entry (DefectEntry):

diff --git a/examples/advanced_analysis_tutorial.ipynb b/examples/advanced_analysis_tutorial.ipynb
@@ -943,34 +943,19 @@
  },
  "id": "f94fd9a12ebb6a68"
  },
- {
- "metadata": {
- "ExecuteTime": {
- "end_time": "2024-04-09T21:53:29.799742Z",
- "start_time": "2024-04-09T21:53:29.793037Z"
- }
- },
- "cell_type": "code",
- "source": "print(f\"{0.0001:7.2e}\")",
- "id": "ef0e2298ead2a106",
- "outputs": [
- {
- "name": "stdout",
- "output_type": "stream",
- "text": [
- "1.00e-04\n"
- ]
- }
- ],
- "execution_count": 6
- },
  {
  "metadata": {},
- "cell_type": "code",
- "outputs": [],
- "execution_count": null,
- "source": "",
- "id": "301c9bd96fc5a4ca"
+ "cell_type": "markdown",
+ "source": [
+ "```{note}\n",
+ "The eigenvalue analysis functions use code from `pydefect`, so please cite the `pydefect` paper if using these analyses in your work:\n",
+ "\n",
+ "\"Insights into oxygen vacancies from high-throughput first-principles calculations\"\n",
+ "Yu Kumagai, Naoki Tsunoda, Akira Takahashi, and Fumiyasu Oba\n",
+ "Phys. Rev. Materials 5, 123803 (2021) -- 10.1103/PhysRevMaterials.5.123803\n",
+ "```"
+ ],
+ "id": "c0e69dc52e5a1eee"
  },
  {
  "cell_type": "markdown",