Add support for PseudoDojo v0.5 standard/stringent

.github/workflows/ci.yml

@@ -23,7 +23,7 @@ jobs:
           python-version: "3.11"
 
       - name: Install dependencies
-        run: pip install -e .[pre-commit,tests,analysis]
+        run: pip install -e .[pre-commit,tests,analysis,dev]
 
       - name: Run pre-commit
         run: pre-commit run --all-files || ( git status --short; git diff; exit 1 )

dev/pseudos.py

@@ -0,0 +1,75 @@
+#!/usr/bin/env python
+"""Generate the semicore JSON for a given pseudo family."""
+from collections import OrderedDict
+import hashlib
+from importlib.resources import path
+import json
+
+from aiida_pseudo.data.pseudo.upf import UpfData
+from rich import print  # pylint: disable=redefined-builtin
+from rich.progress import track
+import typer
+from upf_tools import UPFDict
+
+from aiida import load_profile, orm
+
+from aiida_wannier90_workflows.utils.pseudo.data import semicore
+
+load_profile()
+
+
+def generate_semicore_dict(pseudo: UpfData, semicore_threshold=-1.8) -> dict:
+    """Generate the semicore dict for a given pseudo potential."""
+    upf = UPFDict.from_str(pseudo.get_content())
+    filename = pseudo.filename
+    md5_hash = hashlib.md5(pseudo.get_content().encode()).hexdigest()
+
+    label_energy_dict = {
+        wfc["label"]: wfc["pseudo_energy"] for wfc in upf["pswfc"]["chi"]
+    }
+
+    threshold_modifier = {
+        "2S": -1.0,
+        "3P": 0.5,
+        "3D": 0.4,
+        "4P": 0.7,
+        "4D": 0.5,
+        "5P": 0.9,
+        "5D": 0.8,
+    }
+    return {
+        upf["header"]["element"].rstrip(): {
+            "filename": filename,
+            "md5": md5_hash,
+            "pswfcs": list(label_energy_dict.keys()),
+            "semicores": [
+                label
+                for label, energy in label_energy_dict.items()
+                if energy < semicore_threshold + threshold_modifier.get(label, 0)
+            ],
+        }
+    }
+
+
+def cli(pseudo_family: str, semicore_threshold: float = -1.8):
+    """Generate the semicore JSON for a given pseudo family."""
+    pseudo_group = orm.load_group(pseudo_family)
+
+    semicore_dict = {}
+
+    for pseudo in track(
+        pseudo_group.pseudos.values(),
+        description=f"Generating semicore dict for {pseudo_family}",
+    ):
+        semicore_dict.update(generate_semicore_dict(pseudo, semicore_threshold))
+
+    with path(semicore, f"{pseudo_family.replace('/', '_')}.json") as semicore_path:
+        with semicore_path.open("w", encoding="utf8") as handle:
+            json.dump(OrderedDict(sorted(semicore_dict.items())), handle, indent=4)
+
+        print("[bold green]Success:[/] the semicore JSON has been generated at:\n")
+        print(f"  {semicore_path.absolute()}\n")
+
+
+if __name__ == "__main__":
+    typer.run(cli)

dev/test_pseudos.py

@@ -0,0 +1,23 @@
+"""Test that the data provided for the pseudopotentials is complete and correct."""
+
+from aiida import load_profile, orm
+
+from aiida_wannier90_workflows.utils.pseudo import get_pseudo_orbitals
+
+load_profile()
+
+
+for family in (
+    "PseudoDojo/0.4/LDA/SR/standard/upf",
+    "PseudoDojo/0.4/LDA/SR/stringent/upf",
+    "PseudoDojo/0.4/PBE/SR/standard/upf",
+    "PseudoDojo/0.4/PBE/SR/stringent/upf",
+    "PseudoDojo/0.5/PBE/SR/standard/upf",
+    "PseudoDojo/0.5/PBE/SR/stringent/upf",
+):
+    print(f"Testing family {family}")
+    for el, pseudo in orm.load_group(family).pseudos.items():
+        try:
+            get_pseudo_orbitals({el: pseudo})
+        except ValueError as exc:
+            print(exc)

docs/source/developer_guide/index.rst

@@ -0,0 +1,10 @@
+
+Developer guide
+^^^^^^^^^^^^^^^
+
+Below you can find several guides can come in handy for developers/maintainers of the package.
+
+.. toctree::
+   :maxdepth: 2
+
+   pseudos

docs/source/developer_guide/pseudos.rst

@@ -0,0 +1,78 @@
+
+Pseudopotentials
+^^^^^^^^^^^^^^^^
+
+Running the Wannier90 workflows requires specifying which orbitals you will consider as semicore.
+To do this automatically, the pseudo wave functions and which ones are considered semicore are stored in a JSON format for each pseudopotential family in the following directory:
+
+
+.. code-block::
+
+    src/aiida_wannier90_workflows/utils/pseudo/data/semicore
+
+Adding support for more pseudopotentials means adding a new JSON file there where the following is specified for each element in the pseudopotential family:
+
+1. The filename of the pseudopotential.
+2. The ``md5`` hash of the file contents.
+3. The pseudo wave functions (``pswfcs```) and chosen semicore states (``semicores``).
+
+Here's an example:
+
+.. code-block::
+
+    "Ba": {
+        "filename": "Ba.upf",
+        "md5": "ecceda5fc736cf81896add41b7758c6c",
+        "pswfcs": [
+            "5S",
+            "5P",
+            "6S"
+        ],
+        "semicores": [
+            "5S",
+            "5P"
+        ]
+    },
+
+The ``pswfcs`` are all the labels of the wave functions stored in the pseudo.
+These can be found by looking for blocks like this one in the UPF file:
+
+.. code-block::
+
+    <PP_CHI.1
+    type="real"
+    size="1950"
+    columns="4"
+    index="1"
+    occupation=" 2.000"
+    pseudo_energy="   -0.2475035028E+01"
+    label="5S"
+    l="0" >
+
+.. note::
+
+    The above example is only valid for the PseudoDojo pseudopotentials.
+    Other pseudopotentials may have different formats, and you may need to look for the labels and energies in other parts of the file.
+
+Which of the ``pswfcs`` should be treated as semicore is determined somewhat heuristically.
+Simply look at their energy level (``pseudo_energy``), in case it is much lower (an order of magnitude) than other wave functions, they can be considered semicore.
+
+However, which orbitals should be considered semicore is in principle structure-dependent, and can fail in some cases.
+It can only be really tested by using the choice and comparing the wannier-interpolated band structure with one directly calculated using Quantum ESPRESSO.
+
+For the PseudoDojo, you can find the pseudopotentials at:
+
+http://www.pseudo-dojo.org/pseudos/
+
+In the `dev` directory at the root of this repository, you can find a script that can help you generate the JSON files for the PseudoDojo pseudopotentials, called `pseudos.py`.
+Simply run it with the label of the pseudopotential family you want to generate the JSON file for, e.g.:
+
+.. code-block::
+
+    python pseudos.py PseudoDojo/0.4/PBE/SR/standard/upf
+
+This will generate a JSON file in the `src/aiida_wannier90_workflows/utils/pseudo/data/semicore` directory.
+
+.. important::
+
+    The script currently only supports the PseudoDojo pseudopotentials.

docs/source/index.rst

@@ -57,6 +57,7 @@ Contents
    user_guide/index
    module_guide/index
    cli/index
+   developer_guide/index
 
 Indices and tables
 ==================

pyproject.toml

@@ -65,6 +65,10 @@ docs = [
     "furo",
     "markupsafe"
 ]
+dev = [
+    "typer[all]",
+    "upf_tools~=0.1"
+]
 analysis = ["pandas", "tables", "scikit-learn"]
 
 [project.scripts]

src/aiida_wannier90_workflows/utils/pseudo/__init__.py

@@ -49,11 +49,17 @@ def get_pseudo_and_cutoff(
 
 
 def get_pseudo_orbitals(pseudos: ty.Mapping[str, PseudoPotentialData]) -> dict:
-    """Get the pseudo wavefunctions contained in the pseudopotential.
+    """Get the pseudo wave functions contained in the pseudo potential.
 
     Currently only support the following pseudopotentials installed by `aiida-pseudo`:
-        1. SSSP/1.1/PBE/efficiency
-        2. SSSP/1.1/PBEsol/efficiency
+        * SSSP/1.1/PBE/efficiency
+        * SSSP/1.1/PBEsol/efficiency
+        * PseudoDojo/0.4/LDA/SR/standard/upf
+        * PseudoDojo/0.4/LDA/SR/stringent/upf
+        * PseudoDojo/0.4/PBE/SR/standard/upf
+        * PseudoDojo/0.4/PBE/SR/stringent/upf
+        * PseudoDojo/0.5/PBE/SR/standard/upf
+        * PseudoDojo/0.5/PBE/SR/stringent/upf
     """
     from .data import load_pseudo_metadata
 
@@ -63,14 +69,26 @@ def get_pseudo_orbitals(pseudos: ty.Mapping[str, PseudoPotentialData]) -> dict:
     pseudo_data.append(
         load_pseudo_metadata("semicore/PseudoDojo_0.4_PBE_SR_standard_upf.json")
     )
+    pseudo_data.append(
+        load_pseudo_metadata("semicore/PseudoDojo_0.4_PBE_SR_stringent_upf.json")
+    )
+    pseudo_data.append(
+        load_pseudo_metadata("semicore/PseudoDojo_0.5_PBE_SR_standard_upf.json")
+    )
+    pseudo_data.append(
+        load_pseudo_metadata("semicore/PseudoDojo_0.5_PBE_SR_stringent_upf.json")
+    )
     pseudo_data.append(
         load_pseudo_metadata("semicore/PseudoDojo_0.4_LDA_SR_standard_upf.json")
     )
+    pseudo_data.append(
+        load_pseudo_metadata("semicore/PseudoDojo_0.4_LDA_SR_stringent_upf.json")
+    )
 
     pseudo_orbitals = {}
     for element in pseudos:
         for data in pseudo_data:
-            if data[element]["md5"] == pseudos[element].md5:
+            if data.get(element, {}).get("md5", "") == pseudos[element].md5:
                 pseudo_orbitals[element] = data[element]
                 break
         else: