Add function to calculate soap descriptors

.ci_support/condamerge.py

@@ -0,0 +1,57 @@
+import argparse
+import sys
+import yaml
+
+
+def read_file(path):
+    with open(path) as f:
+        return yaml.safe_load(f)
+
+
+def parse_args(argv=None):
+    parser = argparse.ArgumentParser()
+    parser.add_argument('--base', dest='base', help='base environment.yml file')
+    parser.add_argument('--add', dest='add', help='addon environment.yml file')
+    return parser.parse_args(argv)
+
+
+def merge_dependencies(env_base, env_add):
+    base_dict = {f.split()[0]: f for f in env_base}
+    add_dict = {f.split()[0]: f for f in env_add}
+    for k,v in add_dict.items():
+        if k not in base_dict.keys():
+            base_dict[k] = v
+    return list(base_dict.values())
+
+
+def merge_channels(env_base, env_add):
+    for c in env_add:
+        if c not in env_base:
+            env_base.append(c)
+    return env_base
+
+
+def merge_env(env_base, env_add):
+    return {
+        "channels": merge_channels(
+            env_base=env_base['channels'],
+            env_add=env_add['channels']
+        ),
+        'dependencies': merge_dependencies(
+            env_base=env_base['dependencies'],
+            env_add=env_add['dependencies']
+        )
+    }
+
+
+if __name__ == '__main__':
+    arguments = parse_args(argv=None)
+    yaml.dump(
+        merge_env(
+            env_base=read_file(arguments.base),
+            env_add=read_file(arguments.add)
+        ),
+        sys.stdout,
+        indent=2,
+        default_flow_style=False
+    )

.ci_support/environment-dscribe.yml

@@ -0,0 +1,4 @@
+channels:
+  - conda-forge
+dependencies:
+ - dscribe =2.1.0

.github/workflows/unittests.yml

@@ -46,8 +46,6 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Setup environment
-      run: cp .ci_support/environment.yml environment.yml
     - name: Setup Mambaforge
       uses: conda-incubator/setup-miniconda@v2
       with:
@@ -57,6 +55,15 @@ jobs:
         channel-priority: strict
         activate-environment: my-env
         use-mamba: true
+    - name: Setup environment (windows)
+      if: matrix.operating-system == 'windows-latest'
+      run: cp .ci_support/environment.yml environment.yml
+    - name: Setup environment (unix)
+      if: matrix.operating-system != 'windows-latest'
+      shell: bash -l {0}
+      run: |
+        mamba install -y pyyaml
+        python .ci_support/condamerge.py --base .ci_support/environment.yml --add .ci_support/environment-dscribe.yml > environment.yml
     - name: Update environment
       run: mamba env update -n my-env -f environment.yml
     - name: Setup

setup.py

@@ -36,6 +36,7 @@
         'scipy==1.11.2',  # ase already requires scipy
     ],
     extras_require={
+        "dscribe": ["dscribe==2.1.0"],
         "grainboundary": ['aimsgb==1.0.3', 'pymatgen==2023.9.10'],
         "pyscal": ['pyscal2==2.10.18'],
         "nglview": ['nglview==3.0.6'],
@@ -44,7 +45,7 @@
         "symmetry": ['spglib==2.0.2'],
         "surface": ['spglib==2.0.2', 'pymatgen==2023.9.10'],
         "phonopy": ['phonopy==2.20.0', 'spglib==2.0.2'],
-        "pyxtal": ['pyxtal==0.6.0']
+        "pyxtal": ['pyxtal==0.6.0'],
     },
     cmdclass=versioneer.get_cmdclass(),
 )

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 calculate_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 (

structuretoolkit/analyse/dscribe.py

@@ -0,0 +1,44 @@
+def calculate_soap_descriptor_per_atom(
+    structure,
+    r_cut=None,
+    n_max=None,
+    l_max=None,
+    sigma=1.0,
+    rbf="gto",
+    weighting=None,
+    average="off",
+    compression={"mode": "off", "species_weighting": None},
+    species=None,
+    periodic=True,
+    sparse=False,
+    dtype="float64",
+    centers=None,
+    n_jobs=1,
+    only_physical_cores=False,
+    verbose=False,
+):
+    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,
+    )

tests/test_dscribe.py

@@ -0,0 +1,26 @@
+# coding: utf-8
+# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
+# Distributed under the terms of "New BSD License", see the LICENSE file.
+
+import unittest
+from ase.build import bulk
+import numpy as np
+import structuretoolkit as stk
+
+try:
+    import dscribe
+
+    skip_dscribe_test = False
+except ImportError:
+    skip_dscribe_test = True
+
+
+@unittest.skipIf(
+    skip_dscribe_test, "dscribe is not installed, so the dscribe tests are skipped."
+)
+class Testdscribe(unittest.TestCase):
+    def test_calc_soap_descriptor_per_atom(self):
+        structure = bulk('Cu', 'fcc', a=3.6, cubic=True)
+        soap = stk.analyse.calculate_soap_descriptor_per_atom(structure=structure, r_cut=6.0, n_max=8, l_max=6)
+        self.assertEqual(soap.shape, (4, 252))
+        self.assertTrue(np.isclose(soap.sum(), 39450.03009, atol=1.e-5))