Actions Workflow (#154)

.github/workflows/python.yml → .github/workflows/ubuntu.yaml

@@ -14,7 +14,7 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-name: Tests
+name: Tests (Ubuntu)
 
 on:
   push:
@@ -41,33 +41,34 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        os: [ubuntu-latest]
+        # python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        # torch-version: ["1.11.0", "1.12.1", "1.13.1", "2.0.1", "2.1.2", "2.2.2", "2.3.1"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
         torch-version: ["1.11.0", "1.12.1", "1.13.1", "2.0.1", "2.1.2", "2.2.2"]
         exclude:
+          # Check latest versions here: https://download.pytorch.org/whl/torch/
+          #
           # PyTorch now fully supports Python=<3.11
           # see: https://github.com/pytorch/pytorch/issues/86566
           #
-          # PyTorch does not support Python 3.12 (all platforms)
+          # PyTorch does now support Python 3.12 (Linux) for 2.2.0 and newer
           # see: https://github.com/pytorch/pytorch/issues/110436
-          - os: ubuntu-latest
-            python-version: "3.12"
-          - os: macos-latest
-            python-version: "3.12"
-          - os: windows-latest
-            python-version: "3.12"
+          - python-version: "3.12"
+            torch-version: "1.11.0"
+          - python-version: "3.12"
+            torch-version: "1.12.1"
+          - python-version: "3.12"
+            torch-version: "1.13.1"
+          - python-version: "3.12"
+            torch-version: "2.0.1"
+          - python-version: "3.12"
+            torch-version: "2.1.2"
           # PyTorch<1.13.0 does only support Python=<3.10
           - python-version: "3.11"
             torch-version: "1.11.0"
           - python-version: "3.11"
             torch-version: "1.12.1"
-          # On macOS and Windows, 1.13.x is also not supported for Python>=3.10
-          - os: macos-latest
-            python-version: "3.11"
-            torch-version: "1.13.1"
-          - os: windows-latest
-            python-version: "3.11"
-            torch-version: "1.13.1"
 
     runs-on: ${{ matrix.os }}
 
@@ -80,7 +81,7 @@ jobs:
         uses: actions/checkout@v3
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
 
@@ -106,3 +107,5 @@ jobs:
           matrix.os == 'ubuntu-latest'
         with:
           files: ./coverage.xml # optional
+          token: ${{ secrets.CODECOV_TOKEN }} # required
+          verbose: true # optional (default = false)

README.md

@@ -31,9 +31,9 @@
   <a href="https://results.pre-commit.ci/latest/github/grimme-lab/dxtb/main">
     <img src="https://results.pre-commit.ci/badge/github/grimme-lab/dxtb/main.svg" alt="pre-commit.ci Status"/>
   </a>
-  <!-- <a href="https://codecov.io/gh/grimme-lab/dxtb">
-    <img src="https://codecov.io/gh/grimme-lab/dxtb/branch/main/graph/badge.svg?token=" alt="Coverage"/>
-  </a> -->
+  <a href="https://codecov.io/gh/grimme-lab/dxtb">
+    <img src="https://codecov.io/gh/grimme-lab/dxtb/branch/main/graph/badge.svg?token=O18EZ1CNE3" alt="Coverage"/>
+  </a>
   <!---->
   <br>
   <!---->

docs/requirements.txt

@@ -1,3 +1,14 @@
+numpy<2
+pydantic>=2.0.0
+scipy
+tad-dftd3>=0.3.0
+tad-dftd4>=0.2.0
+tad-libcint>=0.1.0
+tad-mctc>=0.2.0
+tad-multicharge
+tomli
+tomli-w
+torch>=1.11.0,<=2.2.2
 sphinx
 sphinx-book-theme
 sphinx-copybutton

pyproject.toml

@@ -44,12 +44,13 @@ plugins = ["covdefaults"]
 source = ["./src"]
 omit = [
   "./src/dxtb/_src/exlibs/xitorch/*",
+  "./src/dxtb/_src/exlibs/scipy/*",
   "./src/dxtb/_src/typing.py",
   "./src/dxtb/components/*",
 ]
 
 [tool.coverage.report]
-fail_under = 80
+fail_under = 75
 
 
 [tool.isort]

src/dxtb/__version__.py

@@ -22,5 +22,5 @@
 
 __all__ = ["__version__", "__tversion__"]
 
-__version__ = "0.0.1"
+__version__ = "0.0.0"
 """Version of ``dxtb`` in semantic versioning."""

src/dxtb/_src/calculators/types/analytical.py

@@ -28,6 +28,7 @@
 
 from dxtb import OutputHandler
 from dxtb import integrals as ints
+from dxtb import labels
 from dxtb._src import ncoord, scf
 from dxtb._src.components.interactions.container import Charges, Potential
 from dxtb._src.components.interactions.field import efield as efield
@@ -326,7 +327,7 @@ def _forces_analytical(
             self.integrals.overlap.to_pt(write_overlap)
 
         # dipole integral
-        if self.opts.ints.level >= ints.levels.INTLEVEL_DIPOLE:
+        if self.opts.ints.level >= labels.INTLEVEL_DIPOLE:
             OutputHandler.write_stdout_nf(" - Dipole            ... ", v=3)
             timer.start("Dipole Integral", parent_uid="Integrals")
             intmats.dipole = self.integrals.build_dipole(positions)
@@ -339,7 +340,7 @@ def _forces_analytical(
                 self.integrals.dipole.to_pt(write_dipole)
 
         # quadrupole integral
-        if self.opts.ints.level >= ints.levels.INTLEVEL_QUADRUPOLE:
+        if self.opts.ints.level >= labels.INTLEVEL_QUADRUPOLE:
             OutputHandler.write_stdout_nf(" - Quadrupole        ... ", v=3)
             timer.start("Quadrupole Integral", parent_uid="Integrals")
             intmats.quadrupole = self.integrals.build_quadrupole(positions)
@@ -358,7 +359,7 @@ def _forces_analytical(
         # To avoid unnecessary data transfer, the core Hamiltonian should
         # be last. Internally, the overlap integral is only transfered back
         # to GPU when all multipole integrals are calculated.
-        if self.opts.ints.level >= ints.levels.INTLEVEL_HCORE:
+        if self.opts.ints.level >= labels.INTLEVEL_HCORE:
             OutputHandler.write_stdout_nf(" - Core Hamiltonian  ... ", v=3)
             timer.start("Core Hamiltonian", parent_uid="Integrals")
             intmats.hcore = self.integrals.build_hcore(positions)

src/dxtb/_src/calculators/types/base.py

@@ -32,6 +32,7 @@ class and implement the :meth:`calculate` method and the corresponding methods
 
 from dxtb import IndexHelper, OutputHandler
 from dxtb import integrals as ints
+from dxtb import labels
 from dxtb._src.calculators.properties.vibration import IRResult, RamanResult, VibResult
 from dxtb._src.components.classicals import (
     Classical,
@@ -565,40 +566,36 @@ def __init__(
 
         # figure out integral level from interactions
         if efield.LABEL_EFIELD in self.interactions.labels:
-            if self.opts.ints.level < ints.levels.INTLEVEL_DIPOLE:
+            if self.opts.ints.level < labels.INTLEVEL_DIPOLE:
                 OutputHandler.warn(
                     "Setting integral level to DIPOLE "
-                    f"({ints.levels.INTLEVEL_DIPOLE}) due to electric field "
+                    f"({labels.INTLEVEL_DIPOLE}) due to electric field "
                     "interaction."
                 )
-            self.opts.ints.level = max(
-                ints.levels.INTLEVEL_DIPOLE, self.opts.ints.level
-            )
+            self.opts.ints.level = max(labels.INTLEVEL_DIPOLE, self.opts.ints.level)
         if efield_grad.LABEL_EFIELD_GRAD in self.interactions.labels:
-            if self.opts.ints.level < ints.levels.INTLEVEL_DIPOLE:
+            if self.opts.ints.level < labels.INTLEVEL_DIPOLE:
                 OutputHandler.warn(
                     "Setting integral level to QUADRUPOLE "
-                    f"{ints.levels.INTLEVEL_DIPOLE} due to electric field "
+                    f"{labels.INTLEVEL_DIPOLE} due to electric field "
                     "gradient interaction."
                 )
-            self.opts.ints.level = max(
-                ints.levels.INTLEVEL_QUADRUPOLE, self.opts.ints.level
-            )
+            self.opts.ints.level = max(labels.INTLEVEL_QUADRUPOLE, self.opts.ints.level)
 
         # setup integral
         driver = self.opts.ints.driver
         self.integrals = ints.Integrals(
             numbers, par, self.ihelp, driver=driver, intlevel=self.opts.ints.level, **dd
         )
 
-        if self.opts.ints.level >= ints.levels.INTLEVEL_OVERLAP:
+        if self.opts.ints.level >= labels.INTLEVEL_OVERLAP:
             self.integrals.hcore = ints.types.HCore(numbers, par, self.ihelp, **dd)
             self.integrals.overlap = ints.types.Overlap(driver=driver, **dd)
 
-        if self.opts.ints.level >= ints.levels.INTLEVEL_DIPOLE:
+        if self.opts.ints.level >= labels.INTLEVEL_DIPOLE:
             self.integrals.dipole = ints.types.Dipole(driver=driver, **dd)
 
-        if self.opts.ints.level >= ints.levels.INTLEVEL_QUADRUPOLE:
+        if self.opts.ints.level >= labels.INTLEVEL_QUADRUPOLE:
             self.integrals.quadrupole = ints.types.Quadrupole(driver=driver, **dd)
 
         OutputHandler.write_stdout("done\n", v=4)

src/dxtb/_src/calculators/types/energy.py

@@ -31,6 +31,7 @@
 
 from dxtb import OutputHandler
 from dxtb import integrals as ints
+from dxtb import labels
 from dxtb._src import scf
 from dxtb._src.constants import defaults
 from dxtb._src.integral.container import IntegralMatrices
@@ -171,7 +172,7 @@ def singlepoint(
             self.integrals.overlap.to_pt(write_overlap)
 
         # dipole integral
-        if self.opts.ints.level >= ints.levels.INTLEVEL_DIPOLE:
+        if self.opts.ints.level >= labels.INTLEVEL_DIPOLE:
             OutputHandler.write_stdout_nf(" - Dipole            ... ", v=3)
             timer.start("Dipole Integral", parent_uid="Integrals")
             intmats.dipole = self.integrals.build_dipole(positions)
@@ -184,7 +185,7 @@ def singlepoint(
                 self.integrals.dipole.to_pt(write_dipole)
 
         # quadrupole integral
-        if self.opts.ints.level >= ints.levels.INTLEVEL_QUADRUPOLE:
+        if self.opts.ints.level >= labels.INTLEVEL_QUADRUPOLE:
             OutputHandler.write_stdout_nf(" - Quadrupole        ... ", v=3)
             timer.start("Quadrupole Integral", parent_uid="Integrals")
             intmats.quadrupole = self.integrals.build_quadrupole(positions)
@@ -203,7 +204,7 @@ def singlepoint(
         # To avoid unnecessary data transfer, the core Hamiltonian should
         # be last. Internally, the overlap integral is only transfered back
         # to GPU when all multipole integrals are calculated.
-        if self.opts.ints.level >= ints.levels.INTLEVEL_HCORE:
+        if self.opts.ints.level >= labels.INTLEVEL_HCORE:
             OutputHandler.write_stdout_nf(" - Core Hamiltonian  ... ", v=3)
             timer.start("Core Hamiltonian", parent_uid="Integrals")
             intmats.hcore = self.integrals.build_hcore(positions)

src/dxtb/_src/constants/labels/integrals.py

@@ -21,7 +21,26 @@
 All labels related to integrals and their computation.
 """
 
-# integral driver
+__all__ = [
+    "INTDRIVER_LIBCINT",
+    "INTDRIVER_LIBCINT_STRS",
+    "INTDRIVER_AUTOGRAD",
+    "INTDRIVER_AUTOGRAD_STRS",
+    "INTDRIVER_ANALYTICAL",
+    "INTDRIVER_ANALYTICAL_STRS",
+    "INTDRIVER_LEGACY",
+    "INTDRIVER_LEGACY_STRS",
+    "INTDRIVER_MAP",
+    #
+    "INTLEVEL_NONE",
+    "INTLEVEL_OVERLAP",
+    "INTLEVEL_HCORE",
+    "INTLEVEL_DIPOLE",
+    "INTLEVEL_QUADRUPOLE",
+]
+
+# integral drivers
+
 INTDRIVER_LIBCINT = 0
 """Integer code for LIBCINT driver."""
 
@@ -57,8 +76,11 @@
 INTLEVEL_OVERLAP = 1
 """Overlap integrals."""
 
-INTLEVEL_DIPOLE = 2
+INTLEVEL_HCORE = 2
+"""Core Hamiltonian integrals."""
+
+INTLEVEL_DIPOLE = 3
 """Dipole integrals."""
 
-INTLEVEL_QUADRUPOLE = 3
+INTLEVEL_QUADRUPOLE = 4
 """Quadrupole integrals."""

src/dxtb/_src/exlibs/libcint/__init__.py

@@ -23,7 +23,7 @@
 
 try:
     from tad_libcint.basis import AtomCGTOBasis, CGTOBasis
-    from tad_libcint.interface.intor import int1e, overlap
+    from tad_libcint.interface.integrals import int1e, overlap
     from tad_libcint.interface.wrapper import LibcintWrapper
 except ImportError as e:
     raise ImportError(

src/dxtb/_src/integral/container.py

@@ -27,12 +27,11 @@
 
 import torch
 
-from dxtb import IndexHelper
+from dxtb import IndexHelper, labels
 from dxtb._src.constants import defaults, labels
 from dxtb._src.param import Param
 from dxtb._src.typing import Any, Tensor
 
-from . import levels
 from .base import IntDriver, IntegralContainer
 from .types import Dipole, HCore, Overlap, Quadrupole
 
@@ -216,7 +215,7 @@ def build_overlap(self, positions: Tensor, **kwargs: Any) -> Tensor:
         # move integral to the correct device...
         if self.force_cpu_for_libcint is True:
             # ... but only if no other multipole integrals are required
-            if self._intlevel <= levels.INTLEVEL_HCORE:
+            if self._intlevel <= labels.INTLEVEL_HCORE:
                 self.overlap.integral = self.overlap.integral.to(device=self.device)
 
                 # FIXME: The matrix has to be moved explicitly, because when
@@ -301,7 +300,7 @@ def build_dipole(self, positions: Tensor, shift: bool = True, **kwargs: Any):
 
         # move integral to the correct device, but only if no other multipole
         # integrals are required
-        if self.force_cpu_for_libcint and self._intlevel <= levels.INTLEVEL_DIPOLE:
+        if self.force_cpu_for_libcint and self._intlevel <= labels.INTLEVEL_DIPOLE:
             self.dipole.integral = self.dipole.integral.to(device=self.device)
             self.dipole.integral.matrix = self.dipole.integral.matrix.to(
                 device=self.device
@@ -389,7 +388,7 @@ def build_quadrupole(
 
         # move integral to the correct device, but only if no other multipole
         # integrals are required
-        if self.force_cpu_for_libcint and self._intlevel <= levels.INTLEVEL_QUADRUPOLE:
+        if self.force_cpu_for_libcint and self._intlevel <= labels.INTLEVEL_QUADRUPOLE:
             self.overlap.integral = self.overlap.integral.to(self.device)
             self.overlap.integral.matrix = self.overlap.integral.matrix.to(self.device)
 
@@ -448,7 +447,7 @@ def checks(self) -> None:
 
             if name != "hcore":
                 family_integral = cls.integral.family  # type: ignore
-                family_driver = self.driver.family
+                family_driver = self.driver.family  # type: ignore
                 if family_integral != family_driver:
                     raise RuntimeError(
                         f"The '{cls.integral.label}' integral implementation "