From 697b2b05989578ceb15a32a98119ec5b0740132a Mon Sep 17 00:00:00 2001 From: Sean Kavanagh Date: Thu, 15 Aug 2024 17:04:50 -0400 Subject: [PATCH] Update citation info --- docs/Tips.rst | 9 ++++++ doped/core.py | 15 ++++++--- doped/corrections.py | 6 +++- doped/utils/eigenvalues.py | 6 ++-- examples/advanced_analysis_tutorial.ipynb | 37 +++++++---------------- 5 files changed, 40 insertions(+), 33 deletions(-) diff --git a/docs/Tips.rst b/docs/Tips.rst index cb3b9ff8..c574d5df 100644 --- 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 index 704a9649..4bd75f1a 100644 --- 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 index afdf858c..d3380423 100644 --- 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 index b270e731..7ec762de 100644 --- 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 index aed1084e..7b4b7180 100644 --- 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",