[pull] main from dftd4:main

.github/workflows/fortran-build.yml

@@ -24,7 +24,7 @@ jobs:
           compiler: gnu
           version: 8
 
-        - os: macos-latest
+        - os: macos-13
           build: cmake
           build-type: debug
           compiler: gnu
@@ -36,7 +36,7 @@ jobs:
           compiler: gnu
           version: 9
 
-        - os: macos-latest
+        - os: macos-13
           build: meson
           build-type: debug
           compiler: gnu
@@ -267,6 +267,11 @@ jobs:
         create-args: >-
           python=${{ matrix.python_v }}
 
+    - name: Install ase<3.23 for Python 3.7
+      if: matrix.python_v == '3.7'
+      run: |
+        micromamba install -y -c conda-forge "ase<3.23"
+
     - name: Install GCC (OSX)
       if: ${{ contains(matrix.os, 'macos') }}
       run: |

.github/workflows/wheel.yml

@@ -2,6 +2,10 @@ name: wheel
 
 on: [push, workflow_dispatch]
 
+env:
+  # https://github.com/actions/checkout/issues/1809
+  ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION: true
+
 jobs:
   sdist:
     runs-on: ubuntu-latest
@@ -69,7 +73,7 @@ jobs:
         auditwheel show dftd4-*/dist/*.whl
         auditwheel repair -w . dftd4-*/dist/*.whl --plat ${{ env.plat }}
       env:
-        plat: manylinux${{ matrix.python == '3.6' && '2010' || '_2_12' }}_x86_64
+        plat: manylinux2014_x86_64
     - uses: actions/upload-artifact@v3
       with:
         name: dftd4-python-${{ matrix.python }}

python/dftd4/ase.py

@@ -87,16 +87,17 @@
 
 from typing import List, Optional
 
-from .interface import DispersionModel, DampingParam
+from ase.atoms import Atoms
 from ase.calculators.calculator import (
+    CalculationFailed,
     Calculator,
     InputError,
-    CalculationFailed,
     all_changes,
 )
 from ase.calculators.mixing import SumCalculator
-from ase.atoms import Atoms
-from ase.units import Hartree, Bohr
+from ase.units import Bohr, Hartree
+
+from .interface import DampingParam, DispersionModel
 
 
 class DFTD4(Calculator):

python/dftd4/data.py

@@ -15,10 +15,12 @@
 # along with dftd4.  If not, see <https://www.gnu.org/licenses/>.
 
 from math import sqrt
+
 import numpy as np
 
 try:
-    from os.path import join, dirname
+    from os.path import dirname, join
+
     from ase.collections import Collection
 
     # using a collection will remove the data, but we get at least the structures

python/dftd4/interface.py

@@ -23,8 +23,8 @@
 """
 
 from typing import Optional
-import numpy as np
 
+import numpy as np
 
 from . import library
 

python/dftd4/parameters.py

@@ -14,7 +14,7 @@
 # You should have received a copy of the Lesser GNU General Public License
 # along with dftd4.  If not, see <https://www.gnu.org/licenses/>.
 
-from os.path import join, dirname, exists
+from os.path import dirname, exists, join
 from typing import Optional
 
 # We prefer tomli and tomlkit here, because they are 1.0.0 compliant, while toml is not yet

python/dftd4/pyscf.py

@@ -26,11 +26,11 @@
 except ModuleNotFoundError:
     raise ModuleNotFoundError("This submodule requires pyscf installed")
 
-import numpy as np
 from typing import Tuple
 
-from .interface import DispersionModel, DampingParam
+import numpy as np
 
+from .interface import DampingParam, DispersionModel
 
 GradientsBase = getattr(rhf_grad, "GradientsBase", rhf_grad.Gradients)
 
@@ -101,7 +101,7 @@ def kernel(self) -> Tuple[float, np.ndarray]:
         mol = self.mol
 
         disp = DispersionModel(
-            mol.atom_charges(),
+            np.asarray([gto.charge(sym) for sym in mol.elements]),
             mol.atom_coords(),
             mol.charge,
         )
@@ -177,8 +177,8 @@ def energy(mf):
     -110.917424528592
     """
 
-    from pyscf.scf import hf
     from pyscf.mcscf import casci
+    from pyscf.scf import hf
 
     if not isinstance(mf, (hf.SCF, casci.CASCI)):
         raise TypeError("mf must be an instance of SCF or CASCI")

python/dftd4/qcschema.py

@@ -90,11 +90,12 @@
 """
 
 from typing import Union
-from .interface import DispersionModel, DampingParam
-from .library import get_api_version
+
 import numpy as np
 import qcelemental as qcel
 
+from .interface import DampingParam, DispersionModel
+from .library import get_api_version
 
 _supported_drivers = [
     "energy",

python/dftd4/test_ase.py

@@ -14,14 +14,14 @@
 # You should have received a copy of the Lesser GNU General Public License
 # along with dftd4.  If not, see <https://www.gnu.org/licenses/>.
 
-from dftd4.ase import DFTD4
+import numpy as np
 from ase.build import molecule
 from ase.calculators.emt import EMT
+from dftd4.ase import DFTD4
 from pytest import approx
-import numpy as np
 
 
-def test_ase_scand4():
+def test_ase_scand4() -> None:
     thr = 1.0e-6
 
     forces = np.array(
@@ -47,11 +47,17 @@ def test_ase_scand4():
 
     atoms.calc = DFTD4(method="SCAN").add_calculator(EMT())
     assert approx(atoms.get_potential_energy(), abs=thr) == 3.6624398683434225
-    energies = [calc.get_potential_energy() for calc in atoms.calc.calcs]
+
+    if hasattr(atoms.calc, "calcs"):
+        calcs = atoms.calc.calcs
+    else:
+        calcs = atoms.calc.mixer.calcs
+
+    energies = [calc.get_potential_energy() for calc in calcs]
     assert approx(energies, abs=thr) == [-0.021665446836610563, 3.684105315180033]
 
 
-def test_ase_tpssd4():
+def test_ase_tpssd4() -> None:
     thr = 1.0e-6
 
     forces = np.array(
@@ -79,5 +85,11 @@ def test_ase_tpssd4():
 
     atoms.calc = DFTD4(method="TPSS").add_calculator(EMT())
     assert approx(atoms.get_potential_energy(), abs=thr) == 4.864016486351274
-    energies = [calc.get_potential_energy() for calc in atoms.calc.calcs]
+
+    if hasattr(atoms.calc, 'calcs'):
+        calcs = atoms.calc.calcs
+    else:
+        calcs = atoms.calc.mixer.calcs
+
+    energies = [calc.get_potential_energy() for calc in calcs]
     assert approx(energies, abs=thr) == [-0.24206732765720396, 5.106083814008478]

python/dftd4/test_interface.py

@@ -14,12 +14,12 @@
 # You should have received a copy of the Lesser GNU General Public License
 # along with dftd4.  If not, see <https://www.gnu.org/licenses/>.
 
-from dftd4.interface import Structure, DampingParam, DispersionModel
-from pytest import approx, raises
 import numpy as np
+from dftd4.interface import DampingParam, DispersionModel, Structure
+from pytest import approx, raises
 
 
-def test_rational_damping_noargs():
+def test_rational_damping_noargs() -> None:
     """Check constructor of damping parameters for insufficient arguments"""
 
     with raises(TypeError):
@@ -38,7 +38,7 @@ def test_rational_damping_noargs():
         DampingParam(s8=1.0, a1=0.4, a2=5.0, method="abc")
 
 
-def test_structure():
+def test_structure() -> None:
     """check if the molecular structure data is working as expected."""
 
     numbers = np.array(
@@ -101,7 +101,7 @@ def test_structure():
         mol.update(np.zeros((24, 3)))
 
 
-def test_blypd4():
+def test_blypd4() -> None:
     """Use BLYP-D4 for a mindless molecule"""
     thr = 1.0e-7
 
@@ -157,7 +157,7 @@ def test_blypd4():
     assert approx(res.get("energy"), abs=thr) == -0.06991716314879085
 
 
-def test_pbed4():
+def test_pbed4() -> None:
     """Use PBE-D4 for a mindless molecule"""
     thr = 1.0e-7
 
@@ -213,7 +213,7 @@ def test_pbed4():
     assert approx(res.get("energy"), abs=thr) == -0.028415184156428127
 
 
-def test_r2scan3c():
+def test_r2scan3c() -> None:
     """Use r2SCAN-3c for a mindless molecule"""
     thr = 1.0e-8
 
@@ -273,7 +273,7 @@ def test_r2scan3c():
     assert approx(res.get("energy"), abs=thr) == -0.008016697276824889
 
 
-def test_pair_resolved():
+def test_pair_resolved() -> None:
     """Calculate pairwise resolved dispersion energy for a molecule"""
     thr = 1.0e-8
 
@@ -469,7 +469,7 @@ def test_pair_resolved():
     assert approx(res.get("non-additive pairwise energy"), abs=thr) == pair_disp3
 
 
-def test_properties():
+def test_properties() -> None:
     """Calculate dispersion related properties for a molecule"""
     thr = 1.0e-7
 

python/dftd4/test_library.py

@@ -15,12 +15,13 @@
 # along with dftd4.  If not, see <https://www.gnu.org/licenses/>.
 
 
+from dftd4.library import get_api_version
 from pkg_resources import parse_version
+
 from dftd4 import __version__
-from dftd4.library import get_api_version
 
 
-def test_api_version():
+def test_api_version() -> None:
     """Ensure that the API version is compatible."""
 
     assert parse_version(get_api_version()) == parse_version(__version__)

python/dftd4/test_parameters.py

@@ -15,20 +15,21 @@
 # along with dftd4.  If not, see <https://www.gnu.org/licenses/>.
 
 
+from dftd4.parameters import get_all_damping_params, get_damping_param
 from pytest import approx
-from dftd4.parameters import get_damping_param, get_all_damping_params
 
 
 def get_data_file_name() -> str:
     """Make sure we can still test without installing"""
-    from os.path import join, dirname, exists
+    from os.path import dirname, exists, join
+
     from dftd4.parameters import get_data_file_name as _get_data_file_name
 
     data_file = join(dirname(__file__), "..", "..", "assets", "parameters.toml")
     return data_file if exists(data_file) else _get_data_file_name()
 
 
-def test_get_b3lyp():
+def test_get_b3lyp() -> None:
     expected = {
         "s6": 1.0,
         "s9": 1.0,
@@ -43,7 +44,7 @@ def test_get_b3lyp():
         assert approx(actual[key]) == expected[key]
 
 
-def test_get_b2plyp():
+def test_get_b2plyp() -> None:
     expected = {
         "s6": 0.64,
         "s9": 1.0,
@@ -58,7 +59,7 @@ def test_get_b2plyp():
         assert approx(actual[key]) == expected[key]
 
 
-def test_get_pw6b95():
+def test_get_pw6b95() -> None:
     expected = {
         "s6": 1.0,
         "s9": 1.0,
@@ -75,7 +76,7 @@ def test_get_pw6b95():
         assert approx(actual[key]) == expected[key]
 
 
-def test_all_parameters():
+def test_all_parameters() -> None:
     params = get_all_damping_params()
 
     assert "b3lyp" in params