Merge pull request #166 from pyiron/main

Merge main

Author: jan-janssen

.ci_support/environment-lammps.yml

@@ -0,0 +1,4 @@
+channels:
+- conda-forge
+dependencies:
+- lammps =2023.11.21

.ci_support/environment.yml

@@ -1,19 +1,20 @@
 channels:
 - conda-forge
 dependencies:
-- aimsgb =1.1.0
+- aimsgb =1.1.1
 - ase =3.22.1
 - coverage
-- matplotlib-base =3.8.2
-- nglview =3.1.1
+- dscribe =2.1.0
+- matplotlib-base =3.8.4
+- nglview =3.1.2
 - notebook
-- numpy =1.26.3
-- phonopy =2.21.0
-- plotly =5.18.0
-- pymatgen =2024.1.27
+- numpy =1.26.4
+- phonopy =2.22.1
+- plotly =5.19.0
+- pymatgen =2024.3.1
 - pyscal =2.10.18
 - pyxtal =0.6.2
-- scikit-learn =1.4.0
-- scipy =1.12.0
-- spglib =2.3.0
+- scikit-learn =1.4.2
+- scipy =1.13.0
+- spglib =2.4.0
 - sqsgenerator =0.3

.ci_support/environment_mini.yml

@@ -3,5 +3,5 @@ channels:
 dependencies:
 - ase =3.22.1
 - coverage
-- numpy =1.26.3
-- scipy =1.12.0
+- numpy =1.26.4
+- scipy =1.13.0

.github/dependabot.yml

@@ -3,6 +3,5 @@ updates:
 - package-ecosystem: pip
   directory: "/"
   schedule:
-    interval: weekly
-    day: monday
-  open-pull-requests-limit: 10
+    interval: "daily"
+  open-pull-requests-limit: 10

.github/workflows/unittests.yml

@@ -51,6 +51,9 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+    - name: Merge conda environment
+      if:  matrix.operating-system != 'windows-latest'
+      run: tail --lines=+4 .ci_support/environment-lammps.yml >> .ci_support/environment.yml
     - name: Setup Mambaforge
       uses: conda-incubator/setup-miniconda@v2
       with:
@@ -67,7 +70,7 @@ jobs:
       run: |
         pip install versioneer[toml]==0.29
         pip install . --no-deps --no-build-isolation
-        coverage run --omit structuretoolkit/_version.py -m unittest discover tests
+        coverage run  --omit="structuretoolkit/_version.py,tests/*" -m unittest discover tests
     - name: Coverage
       if:  matrix.label == 'linux-64-py-3-12'
       uses: coverallsapp/github-action@v2

pyproject.toml

@@ -25,8 +25,8 @@ classifiers = [
 ]
 dependencies = [
     "ase==3.22.1",
-    "numpy==1.26.3",
-    "scipy==1.12.0",
+    "numpy==1.26.4",
+    "scipy==1.13.0",
 ]
 dynamic = ["version"]
 
@@ -36,23 +36,24 @@ Documentation = "https://github.com/pyiron/structuretoolkit"
 Repository = "https://github.com/pyiron/structuretoolkit"
 
 [project.optional-dependencies]
+dscribe = ["dscribe==2.1.0"]
 grainboundary = [
-    "aimsgb==1.1.0",
-    "pymatgen==2024.1.27",
+    "aimsgb==1.1.1",
+    "pymatgen==2024.3.1",
 ]
 pyscal = ["pyscal2==2.10.18"]
-nglview = ["nglview==3.1.1"]
-matplotlib = ["matplotlib==3.8.2"]
-plotly = ["plotly==5.18.0"]
-clusters = ["scikit-learn==1.4.0"]
-symmetry = ["spglib==2.3.0"]
+nglview = ["nglview==3.1.2"]
+matplotlib = ["matplotlib==3.8.4"]
+plotly = ["plotly==5.19.0"]
+clusters = ["scikit-learn==1.4.2"]
+symmetry = ["spglib==2.4.0"]
 surface = [
-    "spglib==2.3.0",
-    "pymatgen==2024.1.27",
+    "spglib==2.4.0",
+    "pymatgen==2024.3.1",
 ]
 phonopy = [
-    "phonopy==2.21.0",
-    "spglib==2.3.0",
+    "phonopy==2.22.1",
+    "spglib==2.4.0",
 ]
 pyxtal = ["pyxtal==0.6.2"]
 

structuretoolkit/analyse/__init__.py

@@ -1,6 +1,7 @@
 import numpy as np
 
 from structuretoolkit.analyse.distance import find_mic, get_distances_array
+from structuretoolkit.analyse.dscribe import soap_descriptor_per_atom
 from structuretoolkit.analyse.neighbors import get_neighborhood, get_neighbors
 from structuretoolkit.analyse.phonopy import get_equivalent_atoms
 from structuretoolkit.analyse.pyscal import (
@@ -22,6 +23,11 @@
     get_voronoi_vertices,
 )
 from structuretoolkit.analyse.strain import get_strain
+from structuretoolkit.analyse.snap import (
+    get_snap_descriptor_names,
+    get_snap_descriptors_per_atom,
+    get_snap_descriptor_derivatives,
+)
 
 
 def get_symmetry(

structuretoolkit/analyse/distance.py

@@ -1,7 +1,15 @@
+from typing import Optional
+from ase.atoms import Atoms
 import numpy as np
 
 
-def get_distances_array(structure, p1=None, p2=None, mic=True, vectors=False):
+def get_distances_array(
+    structure: Atoms,
+    p1: Optional[np.ndarray] = None,
+    p2: Optional[np.ndarray] = None,
+    mic: bool = True,
+    vectors: bool = False,
+):
     """
     Return distance matrix of every position in p1 with every position in
     p2. If p2 is not set, it is assumed that distances between all
@@ -39,7 +47,7 @@ def get_distances_array(structure, p1=None, p2=None, mic=True, vectors=False):
     return find_mic(structure=structure, v=diff_relative, vectors=vectors)
 
 
-def find_mic(structure, v, vectors=True):
+def find_mic(structure: Atoms, v: np.ndarray, vectors: bool = True):
     """
     Find vectors following minimum image convention (mic). In principle this
     function does the same as ase.geometry.find_mic

structuretoolkit/analyse/dscribe.py

@@ -0,0 +1,49 @@
+import numpy as np
+from ase.atoms import Atoms
+from typing import Optional
+
+
+def soap_descriptor_per_atom(
+    structure: Atoms,
+    r_cut: Optional[float] = None,
+    n_max: Optional[int] = None,
+    l_max: Optional[int] = None,
+    sigma: Optional[float] = 1.0,
+    rbf: str = "gto",
+    weighting: Optional[np.ndarray] = None,
+    average: str = "off",
+    compression: dict = {"mode": "off", "species_weighting": None},
+    species: Optional[list] = None,
+    periodic: bool = True,
+    sparse: bool = False,
+    dtype: str = "float64",
+    centers: Optional[np.ndarray] = None,
+    n_jobs: int = 1,
+    only_physical_cores: bool = False,
+    verbose: bool = False,
+) -> np.ndarray:
+    from dscribe.descriptors import SOAP
+
+    if species is None:
+        species = list(set(structure.get_chemical_symbols()))
+    periodic_soap = SOAP(
+        r_cut=r_cut,
+        n_max=n_max,
+        l_max=l_max,
+        sigma=sigma,
+        rbf=rbf,
+        weighting=weighting,
+        average=average,
+        compression=compression,
+        species=species,
+        periodic=periodic,
+        sparse=sparse,
+        dtype=dtype,
+    )
+    return periodic_soap.create(
+        system=structure,
+        centers=centers,
+        n_jobs=n_jobs,
+        only_physical_cores=only_physical_cores,
+        verbose=verbose,
+    )